diff --git a/CHANGELOG b/CHANGELOG
index 822063549d01bf3e67763c25232f558673ce1aa0..e83fc8600d486f04ba3a8f6cd0de7f3468855d4d 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -5,6 +5,11 @@
Changelog
================================================================================
+Release 3.2.1
+--------------------------------------------------------------------------------
+
+* Bugfix release: Updates OpenStructure dependency to 2.3.0
+
Release 3.2.0
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index b58f41d3c278297e6258ca22b316692daf6c1f12..c350a53b11f1e83862a563b3f5a9d6c301d588ca 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,7 +25,7 @@ include(PROMOD3)
# versioning info
set(PROMOD3_VERSION_MAJOR 3)
set(PROMOD3_VERSION_MINOR 2)
-set(PROMOD3_VERSION_PATCH 0)
+set(PROMOD3_VERSION_PATCH 1)
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
@@ -103,7 +103,7 @@ if(NOT DISABLE_DOCUMENTATION)
# this URL should always point to the latest version of OST
set(OST_DOC_URL "https://www.openstructure.org/docs")
endif()
-find_package(OPENSTRUCTURE 2.2.0 REQUIRED
+find_package(OPENSTRUCTURE 2.3.0 REQUIRED
COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)
if(CMAKE_COMPILER_IS_GNUCXX)
diff --git a/NOTICE b/NOTICE
index 4f3f44b0a640bb4bf830d623a3cb3133b6d8e70d..34e65fac4f6c715d5800006dbb5771d5ccf5b221 100644
--- a/NOTICE
+++ b/NOTICE
@@ -7,5 +7,8 @@ The main authors are: Gabriel Studer, Gerardo Tauriello, Stefan Bienert,
Marco Biasini, Niklaus Johner
If you find this software useful, please cite:
-TO BE PUBLISHED
+
+Studer, Gabriel; Tauriello, Gerardo; Bienert, Stefan; Biasini, Marco; Johner,
+Niklaus; Schwede, Torsten (2021). ProMod3 - A versatile homology modelling
+toolbox. PLoS computational biology, 17 (1), e1008667.
diff --git a/container/Dockerfile b/container/Dockerfile
index 20a1c805c7d3b0d6ffbd7bfe929fec6dd7ff2034..d9bb19166ee7b3a49153565200f8326b6ceb999b 100644
--- a/container/Dockerfile
+++ b/container/Dockerfile
@@ -1,9 +1,9 @@
-ARG OPENSTRUCTURE_IMAGE_TAG="2.2.0-focal"
+ARG OPENSTRUCTURE_IMAGE_TAG="2.3.0-focal"
FROM registry.scicore.unibas.ch/schwede/openstructure:${OPENSTRUCTURE_IMAGE_TAG}
# ARGUMENTS
###########
-ARG PROMOD_VERSION="3.2.0"
+ARG PROMOD_VERSION="3.2.1"
ARG SRC_FOLDER="/usr/local/src"
@@ -17,7 +17,7 @@ ENV PROMOD_ROOT="/usr/local"
#################
RUN cd ${SRC_FOLDER} && \
# copy promod release
- wget -O promod-${PROMOD_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/ProMod3/repository/${PROMOD_VERSION}/archive.tar.gz && \
+ wget -O promod-${PROMOD_VERSION}.tar.gz -nc https://git.scicore.unibas.ch/schwede/ProMod3/-/archive/${PROMOD_VERSION}/promod-${PROMOD_VERSION}.tar.gz && \
mkdir promod-${PROMOD_VERSION} && \
tar xf promod-${PROMOD_VERSION}.tar.gz -C ${SRC_FOLDER}/promod-${PROMOD_VERSION} --strip-components=1 && \
mkdir -p ${SRC_FOLDER}/promod-${PROMOD_VERSION}/build && \
diff --git a/container/Singularity b/container/Singularity
index ccb464c7d6ce0fcbc58a7ef5db54a1eb4a068e79..11a920f192d13f3040e35f879ae7bead5719cdf0 100644
--- a/container/Singularity
+++ b/container/Singularity
@@ -1,5 +1,5 @@
BootStrap: docker
-From: registry.scicore.unibas.ch/schwede/promod3:3.2.0-OST2.2.0-focal
+From: registry.scicore.unibas.ch/schwede/promod3:3.2.1-OST2.3.0-focal
%post
##############################################################################
# POST
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 4840eb328a28a1201185757fcb089242d1f322c6..d00634a2a04492443ec1044a9803a8892225649a 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -58,7 +58,7 @@ master_doc = 'index'
# General information about the project.
project = u'ProMod3'
-copyright = u'2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# pylint: disable=redefined-builtin
+copyright = u'2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# pylint: disable=redefined-builtin
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -286,7 +286,7 @@ rst_epilog = """
.. |cmake| replace:: CMake
.. |ost_l| replace:: OpenStructure
.. |ost_s| replace:: OST
-.. |ost_version| replace:: 2.2.0
+.. |ost_version| replace:: 2.3.0
.. |python| replace:: Python
.. |sphinx| replace:: Sphinx
.. _sphinx: http://sphinx-doc.org/
diff --git a/doc/html/_sources/changelog.rst.txt b/doc/html/_sources/changelog.rst.txt
index 822063549d01bf3e67763c25232f558673ce1aa0..e83fc8600d486f04ba3a8f6cd0de7f3468855d4d 100644
--- a/doc/html/_sources/changelog.rst.txt
+++ b/doc/html/_sources/changelog.rst.txt
@@ -5,6 +5,11 @@
Changelog
================================================================================
+Release 3.2.1
+--------------------------------------------------------------------------------
+
+* Bugfix release: Updates OpenStructure dependency to 2.3.0
+
Release 3.2.0
--------------------------------------------------------------------------------
diff --git a/doc/html/_static/ajax-loader.gif b/doc/html/_static/ajax-loader.gif
new file mode 100644
index 0000000000000000000000000000000000000000..61faf8cab23993bd3e1560bff0668bd628642330
Binary files /dev/null and b/doc/html/_static/ajax-loader.gif differ
diff --git a/doc/html/_static/alabaster.css b/doc/html/_static/alabaster.css
index 0eddaeb07d19bffb50884d7bd7996418b6461a09..517cb43e58b2e57a766cbed1ca59eddbe7f4515c 100644
--- a/doc/html/_static/alabaster.css
+++ b/doc/html/_static/alabaster.css
@@ -1,11 +1,28 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
@import url("basic.css");
/* -- page layout ----------------------------------------------------------- */
body {
- font-family: Georgia, serif;
+ font-family: 'goudy old style', 'minion pro', 'bell mt', Georgia, 'Hiragino Mincho Pro', serif;
font-size: 17px;
- background-color: #fff;
+ background-color: white;
color: #000;
margin: 0;
padding: 0;
@@ -37,7 +54,7 @@ hr {
}
div.body {
- background-color: #fff;
+ background-color: #ffffff;
color: #3E4349;
padding: 0 30px 0 30px;
}
@@ -59,7 +76,7 @@ div.footer a {
}
p.caption {
- font-family: inherit;
+ font-family: ;
font-size: inherit;
}
@@ -107,7 +124,7 @@ div.sphinxsidebarwrapper p.blurb {
div.sphinxsidebar h3,
div.sphinxsidebar h4 {
- font-family: Georgia, serif;
+ font-family: 'Garamond', 'Georgia', serif;
color: #444;
font-size: 24px;
font-weight: normal;
@@ -151,7 +168,7 @@ div.sphinxsidebar ul li.toctree-l2 > a {
div.sphinxsidebar input {
border: 1px solid #CCC;
- font-family: Georgia, serif;
+ font-family: 'goudy old style', 'minion pro', 'bell mt', Georgia, 'Hiragino Mincho Pro', serif;
font-size: 1em;
}
@@ -166,19 +183,6 @@ div.sphinxsidebar hr {
width: 50%;
}
-div.sphinxsidebar .badge {
- border-bottom: none;
-}
-
-div.sphinxsidebar .badge:hover {
- border-bottom: none;
-}
-
-/* To address an issue with donation coming after search */
-div.sphinxsidebar h3.donation {
- margin-top: 10px;
-}
-
/* -- body styles ----------------------------------------------------------- */
a {
@@ -197,7 +201,7 @@ div.body h3,
div.body h4,
div.body h5,
div.body h6 {
- font-family: Georgia, serif;
+ font-family: 'Garamond', 'Georgia', serif;
font-weight: normal;
margin: 30px 0px 10px 0px;
padding: 0;
@@ -228,17 +232,21 @@ div.body p, div.body dd, div.body li {
div.admonition {
margin: 20px 0px;
padding: 10px 30px;
- background-color: #EEE;
- border: 1px solid #CCC;
+ background-color: #FCC;
+ border: 1px solid #FAA;
}
-div.admonition tt.xref, div.admonition code.xref, div.admonition a tt {
- background-color: #FBFBFB;
+div.admonition tt.xref, div.admonition a tt {
border-bottom: 1px solid #fafafa;
}
+dd div.admonition {
+ margin-left: -60px;
+ padding-left: 60px;
+}
+
div.admonition p.admonition-title {
- font-family: Georgia, serif;
+ font-family: 'Garamond', 'Georgia', serif;
font-weight: normal;
font-size: 24px;
margin: 0 0 10px 0;
@@ -251,71 +259,25 @@ div.admonition p.last {
}
div.highlight {
- background-color: #fff;
+ background-color: white;
}
dt:target, .highlight {
background: #FAF3E8;
}
-div.warning {
- background-color: #FCC;
- border: 1px solid #FAA;
-}
-
-div.danger {
- background-color: #FCC;
- border: 1px solid #FAA;
- -moz-box-shadow: 2px 2px 4px #D52C2C;
- -webkit-box-shadow: 2px 2px 4px #D52C2C;
- box-shadow: 2px 2px 4px #D52C2C;
-}
-
-div.error {
- background-color: #FCC;
- border: 1px solid #FAA;
- -moz-box-shadow: 2px 2px 4px #D52C2C;
- -webkit-box-shadow: 2px 2px 4px #D52C2C;
- box-shadow: 2px 2px 4px #D52C2C;
-}
-
-div.caution {
- background-color: #FCC;
- border: 1px solid #FAA;
-}
-
-div.attention {
- background-color: #FCC;
- border: 1px solid #FAA;
-}
-
-div.important {
- background-color: #EEE;
- border: 1px solid #CCC;
-}
-
div.note {
background-color: #EEE;
border: 1px solid #CCC;
}
-div.tip {
- background-color: #EEE;
- border: 1px solid #CCC;
-}
-
-div.hint {
- background-color: #EEE;
- border: 1px solid #CCC;
-}
-
div.seealso {
background-color: #EEE;
border: 1px solid #CCC;
}
div.topic {
- background-color: #EEE;
+ background-color: #eee;
}
p.admonition-title {
@@ -327,7 +289,7 @@ p.admonition-title:after {
}
pre, tt, code {
- font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
+ font-family: 'Consolas', 'Menlo', 'Deja Vu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
font-size: 0.9em;
}
@@ -350,16 +312,16 @@ tt.descname, code.descname {
}
img.screenshot {
- -moz-box-shadow: 2px 2px 4px #EEE;
- -webkit-box-shadow: 2px 2px 4px #EEE;
- box-shadow: 2px 2px 4px #EEE;
+ -moz-box-shadow: 2px 2px 4px #eee;
+ -webkit-box-shadow: 2px 2px 4px #eee;
+ box-shadow: 2px 2px 4px #eee;
}
table.docutils {
border: 1px solid #888;
- -moz-box-shadow: 2px 2px 4px #EEE;
- -webkit-box-shadow: 2px 2px 4px #EEE;
- box-shadow: 2px 2px 4px #EEE;
+ -moz-box-shadow: 2px 2px 4px #eee;
+ -webkit-box-shadow: 2px 2px 4px #eee;
+ box-shadow: 2px 2px 4px #eee;
}
table.docutils td, table.docutils th {
@@ -399,16 +361,6 @@ table.field-list p {
margin-bottom: 0.8em;
}
-/* Cloned from
- * https://github.com/sphinx-doc/sphinx/commit/ef60dbfce09286b20b7385333d63a60321784e68
- */
-.field-name {
- -moz-hyphens: manual;
- -ms-hyphens: manual;
- -webkit-hyphens: manual;
- hyphens: manual;
-}
-
table.footnote td.label {
width: .1px;
padding: 0.3em 0 0.3em 0.5em;
@@ -445,15 +397,16 @@ pre {
line-height: 1.3em;
}
-div.viewcode-block:target {
- background: #ffd;
-}
-
dl pre, blockquote pre, li pre {
margin-left: 0;
padding-left: 30px;
}
+dl dl pre {
+ margin-left: -90px;
+ padding-left: 90px;
+}
+
tt, code {
background-color: #ecf0f3;
color: #222;
@@ -462,7 +415,7 @@ tt, code {
tt.xref, code.xref, a tt {
background-color: #FBFBFB;
- border-bottom: 1px solid #fff;
+ border-bottom: 1px solid white;
}
a.reference {
@@ -564,7 +517,7 @@ a:hover tt, a:hover code {
div.documentwrapper {
float: none;
- background: #fff;
+ background: white;
}
div.sphinxsidebar {
@@ -579,7 +532,7 @@ a:hover tt, a:hover code {
div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p,
div.sphinxsidebar h3 a {
- color: #fff;
+ color: white;
}
div.sphinxsidebar a {
@@ -651,51 +604,4 @@ table.docutils.citation, table.docutils.citation td, table.docutils.citation th
-moz-box-shadow: none;
-webkit-box-shadow: none;
box-shadow: none;
-}
-
-
-/* relbar */
-
-.related {
- line-height: 30px;
- width: 100%;
- font-size: 0.9rem;
-}
-
-.related.top {
- border-bottom: 1px solid #EEE;
- margin-bottom: 20px;
-}
-
-.related.bottom {
- border-top: 1px solid #EEE;
-}
-
-.related ul {
- padding: 0;
- margin: 0;
- list-style: none;
-}
-
-.related li {
- display: inline;
-}
-
-nav#rellinks {
- float: right;
-}
-
-nav#rellinks li+li:before {
- content: "|";
-}
-
-nav#breadcrumbs li+li:before {
- content: "\00BB";
-}
-
-/* Hide certain items when printing */
-@media print {
- div.related {
- display: none;
- }
}
\ No newline at end of file
diff --git a/doc/html/_static/basic.css b/doc/html/_static/basic.css
index c41d718e429affb53084be2e5d2a2fe26aea164b..0807176ec0cb13c1214ddacecadfbfde5ecd7514 100644
--- a/doc/html/_static/basic.css
+++ b/doc/html/_static/basic.css
@@ -231,16 +231,6 @@ a.headerlink {
visibility: hidden;
}
-a.brackets:before,
-span.brackets > a:before{
- content: "[";
-}
-
-a.brackets:after,
-span.brackets > a:after {
- content: "]";
-}
-
h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
@@ -289,12 +279,6 @@ img.align-center, .figure.align-center, object.align-center {
margin-right: auto;
}
-img.align-default, .figure.align-default {
- display: block;
- margin-left: auto;
- margin-right: auto;
-}
-
.align-left {
text-align: left;
}
@@ -303,10 +287,6 @@ img.align-default, .figure.align-default {
text-align: center;
}
-.align-default {
- text-align: center;
-}
-
.align-right {
text-align: right;
}
@@ -378,11 +358,6 @@ table.align-center {
margin-right: auto;
}
-table.align-default {
- margin-left: auto;
- margin-right: auto;
-}
-
table caption span.caption-number {
font-style: italic;
}
@@ -416,16 +391,6 @@ table.citation td {
border-bottom: none;
}
-th > p:first-child,
-td > p:first-child {
- margin-top: 0px;
-}
-
-th > p:last-child,
-td > p:last-child {
- margin-bottom: 0px;
-}
-
/* -- figures --------------------------------------------------------------- */
div.figure {
@@ -495,57 +460,11 @@ ol.upperroman {
list-style: upper-roman;
}
-li > p:first-child {
- margin-top: 0px;
-}
-
-li > p:last-child {
- margin-bottom: 0px;
-}
-
-dl.footnote > dt,
-dl.citation > dt {
- float: left;
-}
-
-dl.footnote > dd,
-dl.citation > dd {
- margin-bottom: 0em;
-}
-
-dl.footnote > dd:after,
-dl.citation > dd:after {
- content: "";
- clear: both;
-}
-
-dl.field-list {
- display: flex;
- flex-wrap: wrap;
-}
-
-dl.field-list > dt {
- flex-basis: 20%;
- font-weight: bold;
- word-break: break-word;
-}
-
-dl.field-list > dt:after {
- content: ":";
-}
-
-dl.field-list > dd {
- flex-basis: 70%;
- padding-left: 1em;
- margin-left: 0em;
- margin-bottom: 0em;
-}
-
dl {
margin-bottom: 15px;
}
-dd > p:first-child {
+dd p {
margin-top: 0px;
}
@@ -618,12 +537,6 @@ dl.glossary dt {
font-style: oblique;
}
-.classifier:before {
- font-style: normal;
- margin: 0.5em;
- content: ":";
-}
-
abbr, acronym {
border-bottom: dotted 1px;
cursor: help;
diff --git a/doc/html/_static/comment-bright.png b/doc/html/_static/comment-bright.png
new file mode 100644
index 0000000000000000000000000000000000000000..15e27edb12ac25701ac0ac21b97b52bb4e45415e
Binary files /dev/null and b/doc/html/_static/comment-bright.png differ
diff --git a/doc/html/_static/comment-close.png b/doc/html/_static/comment-close.png
new file mode 100644
index 0000000000000000000000000000000000000000..4d91bcf57de866a901a89a2a68c0f36af1114841
Binary files /dev/null and b/doc/html/_static/comment-close.png differ
diff --git a/doc/html/_static/comment.png b/doc/html/_static/comment.png
new file mode 100644
index 0000000000000000000000000000000000000000..dfbc0cbd512bdeefcb1984c99d8e577efb77f006
Binary files /dev/null and b/doc/html/_static/comment.png differ
diff --git a/doc/html/_static/doctools.js b/doc/html/_static/doctools.js
index b33f87fcb249ea9b0e0a07fa9c5f2595ea925709..344db17ddbb7aea09b227835a7cd1c3265aeb172 100644
--- a/doc/html/_static/doctools.js
+++ b/doc/html/_static/doctools.js
@@ -87,13 +87,14 @@ jQuery.fn.highlightText = function(text, className) {
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
+ var bbox = span.getBBox();
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
- var bbox = node.parentElement.getBBox();
- rect.x.baseVal.value = bbox.x;
+ rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute('class', className);
+ var parentOfText = node.parentNode.parentNode;
addItems.push({
"parent": node.parentNode,
"target": rect});
diff --git a/doc/html/_static/documentation_options.js b/doc/html/_static/documentation_options.js
index 42c91446bcb95d168a9e3f067debdc598e518dc9..22999c300b2e17707358b76492cab207c4d44548 100644
--- a/doc/html/_static/documentation_options.js
+++ b/doc/html/_static/documentation_options.js
@@ -1,10 +1,10 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: '3.2.0',
+ VERSION: '3.2.1',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt',
- NAVIGATION_WITH_KEYS: false
+ NAVIGATION_WITH_KEYS: false,
};
\ No newline at end of file
diff --git a/doc/html/_static/down-pressed.png b/doc/html/_static/down-pressed.png
new file mode 100644
index 0000000000000000000000000000000000000000..5756c8cad8854722893dc70b9eb4bb0400343a39
Binary files /dev/null and b/doc/html/_static/down-pressed.png differ
diff --git a/doc/html/_static/down.png b/doc/html/_static/down.png
new file mode 100644
index 0000000000000000000000000000000000000000..1b3bdad2ceffae91cee61b32f3295f9bbe646e48
Binary files /dev/null and b/doc/html/_static/down.png differ
diff --git a/doc/html/_static/jquery-3.2.1.js b/doc/html/_static/jquery-3.2.1.js
deleted file mode 100644
index d2d8ca4790e52b0537f3cbb7dcd766099b789583..0000000000000000000000000000000000000000
--- a/doc/html/_static/jquery-3.2.1.js
+++ /dev/null
@@ -1,10253 +0,0 @@
-/*!
- * jQuery JavaScript Library v3.2.1
- * https://jquery.com/
- *
- * Includes Sizzle.js
- * https://sizzlejs.com/
- *
- * Copyright JS Foundation and other contributors
- * Released under the MIT license
- * https://jquery.org/license
- *
- * Date: 2017-03-20T18:59Z
- */
-( function( global, factory ) {
-
- "use strict";
-
- if ( typeof module === "object" && typeof module.exports === "object" ) {
-
- // For CommonJS and CommonJS-like environments where a proper `window`
- // is present, execute the factory and get jQuery.
- // For environments that do not have a `window` with a `document`
- // (such as Node.js), expose a factory as module.exports.
- // This accentuates the need for the creation of a real `window`.
- // e.g. var jQuery = require("jquery")(window);
- // See ticket #14549 for more info.
- module.exports = global.document ?
- factory( global, true ) :
- function( w ) {
- if ( !w.document ) {
- throw new Error( "jQuery requires a window with a document" );
- }
- return factory( w );
- };
- } else {
- factory( global );
- }
-
-// Pass this if window is not defined yet
-} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
-
-// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1
-// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode
-// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common
-// enough that all such attempts are guarded in a try block.
-"use strict";
-
-var arr = [];
-
-var document = window.document;
-
-var getProto = Object.getPrototypeOf;
-
-var slice = arr.slice;
-
-var concat = arr.concat;
-
-var push = arr.push;
-
-var indexOf = arr.indexOf;
-
-var class2type = {};
-
-var toString = class2type.toString;
-
-var hasOwn = class2type.hasOwnProperty;
-
-var fnToString = hasOwn.toString;
-
-var ObjectFunctionString = fnToString.call( Object );
-
-var support = {};
-
-
-
- function DOMEval( code, doc ) {
- doc = doc || document;
-
- var script = doc.createElement( "script" );
-
- script.text = code;
- doc.head.appendChild( script ).parentNode.removeChild( script );
- }
-/* global Symbol */
-// Defining this global in .eslintrc.json would create a danger of using the global
-// unguarded in another place, it seems safer to define global only for this module
-
-
-
-var
- version = "3.2.1",
-
- // Define a local copy of jQuery
- jQuery = function( selector, context ) {
-
- // The jQuery object is actually just the init constructor 'enhanced'
- // Need init if jQuery is called (just allow error to be thrown if not included)
- return new jQuery.fn.init( selector, context );
- },
-
- // Support: Android <=4.0 only
- // Make sure we trim BOM and NBSP
- rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,
-
- // Matches dashed string for camelizing
- rmsPrefix = /^-ms-/,
- rdashAlpha = /-([a-z])/g,
-
- // Used by jQuery.camelCase as callback to replace()
- fcamelCase = function( all, letter ) {
- return letter.toUpperCase();
- };
-
-jQuery.fn = jQuery.prototype = {
-
- // The current version of jQuery being used
- jquery: version,
-
- constructor: jQuery,
-
- // The default length of a jQuery object is 0
- length: 0,
-
- toArray: function() {
- return slice.call( this );
- },
-
- // Get the Nth element in the matched element set OR
- // Get the whole matched element set as a clean array
- get: function( num ) {
-
- // Return all the elements in a clean array
- if ( num == null ) {
- return slice.call( this );
- }
-
- // Return just the one element from the set
- return num < 0 ? this[ num + this.length ] : this[ num ];
- },
-
- // Take an array of elements and push it onto the stack
- // (returning the new matched element set)
- pushStack: function( elems ) {
-
- // Build a new jQuery matched element set
- var ret = jQuery.merge( this.constructor(), elems );
-
- // Add the old object onto the stack (as a reference)
- ret.prevObject = this;
-
- // Return the newly-formed element set
- return ret;
- },
-
- // Execute a callback for every element in the matched set.
- each: function( callback ) {
- return jQuery.each( this, callback );
- },
-
- map: function( callback ) {
- return this.pushStack( jQuery.map( this, function( elem, i ) {
- return callback.call( elem, i, elem );
- } ) );
- },
-
- slice: function() {
- return this.pushStack( slice.apply( this, arguments ) );
- },
-
- first: function() {
- return this.eq( 0 );
- },
-
- last: function() {
- return this.eq( -1 );
- },
-
- eq: function( i ) {
- var len = this.length,
- j = +i + ( i < 0 ? len : 0 );
- return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] );
- },
-
- end: function() {
- return this.prevObject || this.constructor();
- },
-
- // For internal use only.
- // Behaves like an Array's method, not like a jQuery method.
- push: push,
- sort: arr.sort,
- splice: arr.splice
-};
-
-jQuery.extend = jQuery.fn.extend = function() {
- var options, name, src, copy, copyIsArray, clone,
- target = arguments[ 0 ] || {},
- i = 1,
- length = arguments.length,
- deep = false;
-
- // Handle a deep copy situation
- if ( typeof target === "boolean" ) {
- deep = target;
-
- // Skip the boolean and the target
- target = arguments[ i ] || {};
- i++;
- }
-
- // Handle case when target is a string or something (possible in deep copy)
- if ( typeof target !== "object" && !jQuery.isFunction( target ) ) {
- target = {};
- }
-
- // Extend jQuery itself if only one argument is passed
- if ( i === length ) {
- target = this;
- i--;
- }
-
- for ( ; i < length; i++ ) {
-
- // Only deal with non-null/undefined values
- if ( ( options = arguments[ i ] ) != null ) {
-
- // Extend the base object
- for ( name in options ) {
- src = target[ name ];
- copy = options[ name ];
-
- // Prevent never-ending loop
- if ( target === copy ) {
- continue;
- }
-
- // Recurse if we're merging plain objects or arrays
- if ( deep && copy && ( jQuery.isPlainObject( copy ) ||
- ( copyIsArray = Array.isArray( copy ) ) ) ) {
-
- if ( copyIsArray ) {
- copyIsArray = false;
- clone = src && Array.isArray( src ) ? src : [];
-
- } else {
- clone = src && jQuery.isPlainObject( src ) ? src : {};
- }
-
- // Never move original objects, clone them
- target[ name ] = jQuery.extend( deep, clone, copy );
-
- // Don't bring in undefined values
- } else if ( copy !== undefined ) {
- target[ name ] = copy;
- }
- }
- }
- }
-
- // Return the modified object
- return target;
-};
-
-jQuery.extend( {
-
- // Unique for each copy of jQuery on the page
- expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ),
-
- // Assume jQuery is ready without the ready module
- isReady: true,
-
- error: function( msg ) {
- throw new Error( msg );
- },
-
- noop: function() {},
-
- isFunction: function( obj ) {
- return jQuery.type( obj ) === "function";
- },
-
- isWindow: function( obj ) {
- return obj != null && obj === obj.window;
- },
-
- isNumeric: function( obj ) {
-
- // As of jQuery 3.0, isNumeric is limited to
- // strings and numbers (primitives or objects)
- // that can be coerced to finite numbers (gh-2662)
- var type = jQuery.type( obj );
- return ( type === "number" || type === "string" ) &&
-
- // parseFloat NaNs numeric-cast false positives ("")
- // ...but misinterprets leading-number strings, particularly hex literals ("0x...")
- // subtraction forces infinities to NaN
- !isNaN( obj - parseFloat( obj ) );
- },
-
- isPlainObject: function( obj ) {
- var proto, Ctor;
-
- // Detect obvious negatives
- // Use toString instead of jQuery.type to catch host objects
- if ( !obj || toString.call( obj ) !== "[object Object]" ) {
- return false;
- }
-
- proto = getProto( obj );
-
- // Objects with no prototype (e.g., `Object.create( null )`) are plain
- if ( !proto ) {
- return true;
- }
-
- // Objects with prototype are plain iff they were constructed by a global Object function
- Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor;
- return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString;
- },
-
- isEmptyObject: function( obj ) {
-
- /* eslint-disable no-unused-vars */
- // See https://github.com/eslint/eslint/issues/6125
- var name;
-
- for ( name in obj ) {
- return false;
- }
- return true;
- },
-
- type: function( obj ) {
- if ( obj == null ) {
- return obj + "";
- }
-
- // Support: Android <=2.3 only (functionish RegExp)
- return typeof obj === "object" || typeof obj === "function" ?
- class2type[ toString.call( obj ) ] || "object" :
- typeof obj;
- },
-
- // Evaluates a script in a global context
- globalEval: function( code ) {
- DOMEval( code );
- },
-
- // Convert dashed to camelCase; used by the css and data modules
- // Support: IE <=9 - 11, Edge 12 - 13
- // Microsoft forgot to hump their vendor prefix (#9572)
- camelCase: function( string ) {
- return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
- },
-
- each: function( obj, callback ) {
- var length, i = 0;
-
- if ( isArrayLike( obj ) ) {
- length = obj.length;
- for ( ; i < length; i++ ) {
- if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
- break;
- }
- }
- } else {
- for ( i in obj ) {
- if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
- break;
- }
- }
- }
-
- return obj;
- },
-
- // Support: Android <=4.0 only
- trim: function( text ) {
- return text == null ?
- "" :
- ( text + "" ).replace( rtrim, "" );
- },
-
- // results is for internal usage only
- makeArray: function( arr, results ) {
- var ret = results || [];
-
- if ( arr != null ) {
- if ( isArrayLike( Object( arr ) ) ) {
- jQuery.merge( ret,
- typeof arr === "string" ?
- [ arr ] : arr
- );
- } else {
- push.call( ret, arr );
- }
- }
-
- return ret;
- },
-
- inArray: function( elem, arr, i ) {
- return arr == null ? -1 : indexOf.call( arr, elem, i );
- },
-
- // Support: Android <=4.0 only, PhantomJS 1 only
- // push.apply(_, arraylike) throws on ancient WebKit
- merge: function( first, second ) {
- var len = +second.length,
- j = 0,
- i = first.length;
-
- for ( ; j < len; j++ ) {
- first[ i++ ] = second[ j ];
- }
-
- first.length = i;
-
- return first;
- },
-
- grep: function( elems, callback, invert ) {
- var callbackInverse,
- matches = [],
- i = 0,
- length = elems.length,
- callbackExpect = !invert;
-
- // Go through the array, only saving the items
- // that pass the validator function
- for ( ; i < length; i++ ) {
- callbackInverse = !callback( elems[ i ], i );
- if ( callbackInverse !== callbackExpect ) {
- matches.push( elems[ i ] );
- }
- }
-
- return matches;
- },
-
- // arg is for internal usage only
- map: function( elems, callback, arg ) {
- var length, value,
- i = 0,
- ret = [];
-
- // Go through the array, translating each of the items to their new values
- if ( isArrayLike( elems ) ) {
- length = elems.length;
- for ( ; i < length; i++ ) {
- value = callback( elems[ i ], i, arg );
-
- if ( value != null ) {
- ret.push( value );
- }
- }
-
- // Go through every key on the object,
- } else {
- for ( i in elems ) {
- value = callback( elems[ i ], i, arg );
-
- if ( value != null ) {
- ret.push( value );
- }
- }
- }
-
- // Flatten any nested arrays
- return concat.apply( [], ret );
- },
-
- // A global GUID counter for objects
- guid: 1,
-
- // Bind a function to a context, optionally partially applying any
- // arguments.
- proxy: function( fn, context ) {
- var tmp, args, proxy;
-
- if ( typeof context === "string" ) {
- tmp = fn[ context ];
- context = fn;
- fn = tmp;
- }
-
- // Quick check to determine if target is callable, in the spec
- // this throws a TypeError, but we will just return undefined.
- if ( !jQuery.isFunction( fn ) ) {
- return undefined;
- }
-
- // Simulated bind
- args = slice.call( arguments, 2 );
- proxy = function() {
- return fn.apply( context || this, args.concat( slice.call( arguments ) ) );
- };
-
- // Set the guid of unique handler to the same of original handler, so it can be removed
- proxy.guid = fn.guid = fn.guid || jQuery.guid++;
-
- return proxy;
- },
-
- now: Date.now,
-
- // jQuery.support is not used in Core but other projects attach their
- // properties to it so it needs to exist.
- support: support
-} );
-
-if ( typeof Symbol === "function" ) {
- jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ];
-}
-
-// Populate the class2type map
-jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ),
-function( i, name ) {
- class2type[ "[object " + name + "]" ] = name.toLowerCase();
-} );
-
-function isArrayLike( obj ) {
-
- // Support: real iOS 8.2 only (not reproducible in simulator)
- // `in` check used to prevent JIT error (gh-2145)
- // hasOwn isn't used here due to false negatives
- // regarding Nodelist length in IE
- var length = !!obj && "length" in obj && obj.length,
- type = jQuery.type( obj );
-
- if ( type === "function" || jQuery.isWindow( obj ) ) {
- return false;
- }
-
- return type === "array" || length === 0 ||
- typeof length === "number" && length > 0 && ( length - 1 ) in obj;
-}
-var Sizzle =
-/*!
- * Sizzle CSS Selector Engine v2.3.3
- * https://sizzlejs.com/
- *
- * Copyright jQuery Foundation and other contributors
- * Released under the MIT license
- * http://jquery.org/license
- *
- * Date: 2016-08-08
- */
-(function( window ) {
-
-var i,
- support,
- Expr,
- getText,
- isXML,
- tokenize,
- compile,
- select,
- outermostContext,
- sortInput,
- hasDuplicate,
-
- // Local document vars
- setDocument,
- document,
- docElem,
- documentIsHTML,
- rbuggyQSA,
- rbuggyMatches,
- matches,
- contains,
-
- // Instance-specific data
- expando = "sizzle" + 1 * new Date(),
- preferredDoc = window.document,
- dirruns = 0,
- done = 0,
- classCache = createCache(),
- tokenCache = createCache(),
- compilerCache = createCache(),
- sortOrder = function( a, b ) {
- if ( a === b ) {
- hasDuplicate = true;
- }
- return 0;
- },
-
- // Instance methods
- hasOwn = ({}).hasOwnProperty,
- arr = [],
- pop = arr.pop,
- push_native = arr.push,
- push = arr.push,
- slice = arr.slice,
- // Use a stripped-down indexOf as it's faster than native
- // https://jsperf.com/thor-indexof-vs-for/5
- indexOf = function( list, elem ) {
- var i = 0,
- len = list.length;
- for ( ; i < len; i++ ) {
- if ( list[i] === elem ) {
- return i;
- }
- }
- return -1;
- },
-
- booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped",
-
- // Regular expressions
-
- // http://www.w3.org/TR/css3-selectors/#whitespace
- whitespace = "[\\x20\\t\\r\\n\\f]",
-
- // http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
- identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+",
-
- // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors
- attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace +
- // Operator (capture 2)
- "*([*^$|!~]?=)" + whitespace +
- // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]"
- "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace +
- "*\\]",
-
- pseudos = ":(" + identifier + ")(?:\\((" +
- // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:
- // 1. quoted (capture 3; capture 4 or capture 5)
- "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" +
- // 2. simple (capture 6)
- "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" +
- // 3. anything else (capture 2)
- ".*" +
- ")\\)|)",
-
- // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
- rwhitespace = new RegExp( whitespace + "+", "g" ),
- rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
-
- rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
- rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ),
-
- rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ),
-
- rpseudo = new RegExp( pseudos ),
- ridentifier = new RegExp( "^" + identifier + "$" ),
-
- matchExpr = {
- "ID": new RegExp( "^#(" + identifier + ")" ),
- "CLASS": new RegExp( "^\\.(" + identifier + ")" ),
- "TAG": new RegExp( "^(" + identifier + "|[*])" ),
- "ATTR": new RegExp( "^" + attributes ),
- "PSEUDO": new RegExp( "^" + pseudos ),
- "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace +
- "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace +
- "*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
- "bool": new RegExp( "^(?:" + booleans + ")$", "i" ),
- // For use in libraries implementing .is()
- // We use this for POS matching in `select`
- "needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" +
- whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" )
- },
-
- rinputs = /^(?:input|select|textarea|button)$/i,
- rheader = /^h\d$/i,
-
- rnative = /^[^{]+\{\s*\[native \w/,
-
- // Easily-parseable/retrievable ID or TAG or CLASS selectors
- rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
-
- rsibling = /[+~]/,
-
- // CSS escapes
- // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
- runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ),
- funescape = function( _, escaped, escapedWhitespace ) {
- var high = "0x" + escaped - 0x10000;
- // NaN means non-codepoint
- // Support: Firefox<24
- // Workaround erroneous numeric interpretation of +"0x"
- return high !== high || escapedWhitespace ?
- escaped :
- high < 0 ?
- // BMP codepoint
- String.fromCharCode( high + 0x10000 ) :
- // Supplemental Plane codepoint (surrogate pair)
- String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
- },
-
- // CSS string/identifier serialization
- // https://drafts.csswg.org/cssom/#common-serializing-idioms
- rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g,
- fcssescape = function( ch, asCodePoint ) {
- if ( asCodePoint ) {
-
- // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER
- if ( ch === "\0" ) {
- return "\uFFFD";
- }
-
- // Control characters and (dependent upon position) numbers get escaped as code points
- return ch.slice( 0, -1 ) + "\\" + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " ";
- }
-
- // Other potentially-special ASCII characters get backslash-escaped
- return "\\" + ch;
- },
-
- // Used for iframes
- // See setDocument()
- // Removing the function wrapper causes a "Permission Denied"
- // error in IE
- unloadHandler = function() {
- setDocument();
- },
-
- disabledAncestor = addCombinator(
- function( elem ) {
- return elem.disabled === true && ("form" in elem || "label" in elem);
- },
- { dir: "parentNode", next: "legend" }
- );
-
-// Optimize for push.apply( _, NodeList )
-try {
- push.apply(
- (arr = slice.call( preferredDoc.childNodes )),
- preferredDoc.childNodes
- );
- // Support: Android<4.0
- // Detect silently failing push.apply
- arr[ preferredDoc.childNodes.length ].nodeType;
-} catch ( e ) {
- push = { apply: arr.length ?
-
- // Leverage slice if possible
- function( target, els ) {
- push_native.apply( target, slice.call(els) );
- } :
-
- // Support: IE<9
- // Otherwise append directly
- function( target, els ) {
- var j = target.length,
- i = 0;
- // Can't trust NodeList.length
- while ( (target[j++] = els[i++]) ) {}
- target.length = j - 1;
- }
- };
-}
-
-function Sizzle( selector, context, results, seed ) {
- var m, i, elem, nid, match, groups, newSelector,
- newContext = context && context.ownerDocument,
-
- // nodeType defaults to 9, since context defaults to document
- nodeType = context ? context.nodeType : 9;
-
- results = results || [];
-
- // Return early from calls with invalid selector or context
- if ( typeof selector !== "string" || !selector ||
- nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) {
-
- return results;
- }
-
- // Try to shortcut find operations (as opposed to filters) in HTML documents
- if ( !seed ) {
-
- if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
- setDocument( context );
- }
- context = context || document;
-
- if ( documentIsHTML ) {
-
- // If the selector is sufficiently simple, try using a "get*By*" DOM method
- // (excepting DocumentFragment context, where the methods don't exist)
- if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) {
-
- // ID selector
- if ( (m = match[1]) ) {
-
- // Document context
- if ( nodeType === 9 ) {
- if ( (elem = context.getElementById( m )) ) {
-
- // Support: IE, Opera, Webkit
- // TODO: identify versions
- // getElementById can match elements by name instead of ID
- if ( elem.id === m ) {
- results.push( elem );
- return results;
- }
- } else {
- return results;
- }
-
- // Element context
- } else {
-
- // Support: IE, Opera, Webkit
- // TODO: identify versions
- // getElementById can match elements by name instead of ID
- if ( newContext && (elem = newContext.getElementById( m )) &&
- contains( context, elem ) &&
- elem.id === m ) {
-
- results.push( elem );
- return results;
- }
- }
-
- // Type selector
- } else if ( match[2] ) {
- push.apply( results, context.getElementsByTagName( selector ) );
- return results;
-
- // Class selector
- } else if ( (m = match[3]) && support.getElementsByClassName &&
- context.getElementsByClassName ) {
-
- push.apply( results, context.getElementsByClassName( m ) );
- return results;
- }
- }
-
- // Take advantage of querySelectorAll
- if ( support.qsa &&
- !compilerCache[ selector + " " ] &&
- (!rbuggyQSA || !rbuggyQSA.test( selector )) ) {
-
- if ( nodeType !== 1 ) {
- newContext = context;
- newSelector = selector;
-
- // qSA looks outside Element context, which is not what we want
- // Thanks to Andrew Dupont for this workaround technique
- // Support: IE <=8
- // Exclude object elements
- } else if ( context.nodeName.toLowerCase() !== "object" ) {
-
- // Capture the context ID, setting it first if necessary
- if ( (nid = context.getAttribute( "id" )) ) {
- nid = nid.replace( rcssescape, fcssescape );
- } else {
- context.setAttribute( "id", (nid = expando) );
- }
-
- // Prefix every selector in the list
- groups = tokenize( selector );
- i = groups.length;
- while ( i-- ) {
- groups[i] = "#" + nid + " " + toSelector( groups[i] );
- }
- newSelector = groups.join( "," );
-
- // Expand context for sibling selectors
- newContext = rsibling.test( selector ) && testContext( context.parentNode ) ||
- context;
- }
-
- if ( newSelector ) {
- try {
- push.apply( results,
- newContext.querySelectorAll( newSelector )
- );
- return results;
- } catch ( qsaError ) {
- } finally {
- if ( nid === expando ) {
- context.removeAttribute( "id" );
- }
- }
- }
- }
- }
- }
-
- // All others
- return select( selector.replace( rtrim, "$1" ), context, results, seed );
-}
-
-/**
- * Create key-value caches of limited size
- * @returns {function(string, object)} Returns the Object data after storing it on itself with
- * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
- * deleting the oldest entry
- */
-function createCache() {
- var keys = [];
-
- function cache( key, value ) {
- // Use (key + " ") to avoid collision with native prototype properties (see Issue #157)
- if ( keys.push( key + " " ) > Expr.cacheLength ) {
- // Only keep the most recent entries
- delete cache[ keys.shift() ];
- }
- return (cache[ key + " " ] = value);
- }
- return cache;
-}
-
-/**
- * Mark a function for special use by Sizzle
- * @param {Function} fn The function to mark
- */
-function markFunction( fn ) {
- fn[ expando ] = true;
- return fn;
-}
-
-/**
- * Support testing using an element
- * @param {Function} fn Passed the created element and returns a boolean result
- */
-function assert( fn ) {
- var el = document.createElement("fieldset");
-
- try {
- return !!fn( el );
- } catch (e) {
- return false;
- } finally {
- // Remove from its parent by default
- if ( el.parentNode ) {
- el.parentNode.removeChild( el );
- }
- // release memory in IE
- el = null;
- }
-}
-
-/**
- * Adds the same handler for all of the specified attrs
- * @param {String} attrs Pipe-separated list of attributes
- * @param {Function} handler The method that will be applied
- */
-function addHandle( attrs, handler ) {
- var arr = attrs.split("|"),
- i = arr.length;
-
- while ( i-- ) {
- Expr.attrHandle[ arr[i] ] = handler;
- }
-}
-
-/**
- * Checks document order of two siblings
- * @param {Element} a
- * @param {Element} b
- * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b
- */
-function siblingCheck( a, b ) {
- var cur = b && a,
- diff = cur && a.nodeType === 1 && b.nodeType === 1 &&
- a.sourceIndex - b.sourceIndex;
-
- // Use IE sourceIndex if available on both nodes
- if ( diff ) {
- return diff;
- }
-
- // Check if b follows a
- if ( cur ) {
- while ( (cur = cur.nextSibling) ) {
- if ( cur === b ) {
- return -1;
- }
- }
- }
-
- return a ? 1 : -1;
-}
-
-/**
- * Returns a function to use in pseudos for input types
- * @param {String} type
- */
-function createInputPseudo( type ) {
- return function( elem ) {
- var name = elem.nodeName.toLowerCase();
- return name === "input" && elem.type === type;
- };
-}
-
-/**
- * Returns a function to use in pseudos for buttons
- * @param {String} type
- */
-function createButtonPseudo( type ) {
- return function( elem ) {
- var name = elem.nodeName.toLowerCase();
- return (name === "input" || name === "button") && elem.type === type;
- };
-}
-
-/**
- * Returns a function to use in pseudos for :enabled/:disabled
- * @param {Boolean} disabled true for :disabled; false for :enabled
- */
-function createDisabledPseudo( disabled ) {
-
- // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable
- return function( elem ) {
-
- // Only certain elements can match :enabled or :disabled
- // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled
- // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled
- if ( "form" in elem ) {
-
- // Check for inherited disabledness on relevant non-disabled elements:
- // * listed form-associated elements in a disabled fieldset
- // https://html.spec.whatwg.org/multipage/forms.html#category-listed
- // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled
- // * option elements in a disabled optgroup
- // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled
- // All such elements have a "form" property.
- if ( elem.parentNode && elem.disabled === false ) {
-
- // Option elements defer to a parent optgroup if present
- if ( "label" in elem ) {
- if ( "label" in elem.parentNode ) {
- return elem.parentNode.disabled === disabled;
- } else {
- return elem.disabled === disabled;
- }
- }
-
- // Support: IE 6 - 11
- // Use the isDisabled shortcut property to check for disabled fieldset ancestors
- return elem.isDisabled === disabled ||
-
- // Where there is no isDisabled, check manually
- /* jshint -W018 */
- elem.isDisabled !== !disabled &&
- disabledAncestor( elem ) === disabled;
- }
-
- return elem.disabled === disabled;
-
- // Try to winnow out elements that can't be disabled before trusting the disabled property.
- // Some victims get caught in our net (label, legend, menu, track), but it shouldn't
- // even exist on them, let alone have a boolean value.
- } else if ( "label" in elem ) {
- return elem.disabled === disabled;
- }
-
- // Remaining elements are neither :enabled nor :disabled
- return false;
- };
-}
-
-/**
- * Returns a function to use in pseudos for positionals
- * @param {Function} fn
- */
-function createPositionalPseudo( fn ) {
- return markFunction(function( argument ) {
- argument = +argument;
- return markFunction(function( seed, matches ) {
- var j,
- matchIndexes = fn( [], seed.length, argument ),
- i = matchIndexes.length;
-
- // Match elements found at the specified indexes
- while ( i-- ) {
- if ( seed[ (j = matchIndexes[i]) ] ) {
- seed[j] = !(matches[j] = seed[j]);
- }
- }
- });
- });
-}
-
-/**
- * Checks a node for validity as a Sizzle context
- * @param {Element|Object=} context
- * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value
- */
-function testContext( context ) {
- return context && typeof context.getElementsByTagName !== "undefined" && context;
-}
-
-// Expose support vars for convenience
-support = Sizzle.support = {};
-
-/**
- * Detects XML nodes
- * @param {Element|Object} elem An element or a document
- * @returns {Boolean} True iff elem is a non-HTML XML node
- */
-isXML = Sizzle.isXML = function( elem ) {
- // documentElement is verified for cases where it doesn't yet exist
- // (such as loading iframes in IE - #4833)
- var documentElement = elem && (elem.ownerDocument || elem).documentElement;
- return documentElement ? documentElement.nodeName !== "HTML" : false;
-};
-
-/**
- * Sets document-related variables once based on the current document
- * @param {Element|Object} [doc] An element or document object to use to set the document
- * @returns {Object} Returns the current document
- */
-setDocument = Sizzle.setDocument = function( node ) {
- var hasCompare, subWindow,
- doc = node ? node.ownerDocument || node : preferredDoc;
-
- // Return early if doc is invalid or already selected
- if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {
- return document;
- }
-
- // Update global variables
- document = doc;
- docElem = document.documentElement;
- documentIsHTML = !isXML( document );
-
- // Support: IE 9-11, Edge
- // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936)
- if ( preferredDoc !== document &&
- (subWindow = document.defaultView) && subWindow.top !== subWindow ) {
-
- // Support: IE 11, Edge
- if ( subWindow.addEventListener ) {
- subWindow.addEventListener( "unload", unloadHandler, false );
-
- // Support: IE 9 - 10 only
- } else if ( subWindow.attachEvent ) {
- subWindow.attachEvent( "onunload", unloadHandler );
- }
- }
-
- /* Attributes
- ---------------------------------------------------------------------- */
-
- // Support: IE<8
- // Verify that getAttribute really returns attributes and not properties
- // (excepting IE8 booleans)
- support.attributes = assert(function( el ) {
- el.className = "i";
- return !el.getAttribute("className");
- });
-
- /* getElement(s)By*
- ---------------------------------------------------------------------- */
-
- // Check if getElementsByTagName("*") returns only elements
- support.getElementsByTagName = assert(function( el ) {
- el.appendChild( document.createComment("") );
- return !el.getElementsByTagName("*").length;
- });
-
- // Support: IE<9
- support.getElementsByClassName = rnative.test( document.getElementsByClassName );
-
- // Support: IE<10
- // Check if getElementById returns elements by name
- // The broken getElementById methods don't pick up programmatically-set names,
- // so use a roundabout getElementsByName test
- support.getById = assert(function( el ) {
- docElem.appendChild( el ).id = expando;
- return !document.getElementsByName || !document.getElementsByName( expando ).length;
- });
-
- // ID filter and find
- if ( support.getById ) {
- Expr.filter["ID"] = function( id ) {
- var attrId = id.replace( runescape, funescape );
- return function( elem ) {
- return elem.getAttribute("id") === attrId;
- };
- };
- Expr.find["ID"] = function( id, context ) {
- if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
- var elem = context.getElementById( id );
- return elem ? [ elem ] : [];
- }
- };
- } else {
- Expr.filter["ID"] = function( id ) {
- var attrId = id.replace( runescape, funescape );
- return function( elem ) {
- var node = typeof elem.getAttributeNode !== "undefined" &&
- elem.getAttributeNode("id");
- return node && node.value === attrId;
- };
- };
-
- // Support: IE 6 - 7 only
- // getElementById is not reliable as a find shortcut
- Expr.find["ID"] = function( id, context ) {
- if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
- var node, i, elems,
- elem = context.getElementById( id );
-
- if ( elem ) {
-
- // Verify the id attribute
- node = elem.getAttributeNode("id");
- if ( node && node.value === id ) {
- return [ elem ];
- }
-
- // Fall back on getElementsByName
- elems = context.getElementsByName( id );
- i = 0;
- while ( (elem = elems[i++]) ) {
- node = elem.getAttributeNode("id");
- if ( node && node.value === id ) {
- return [ elem ];
- }
- }
- }
-
- return [];
- }
- };
- }
-
- // Tag
- Expr.find["TAG"] = support.getElementsByTagName ?
- function( tag, context ) {
- if ( typeof context.getElementsByTagName !== "undefined" ) {
- return context.getElementsByTagName( tag );
-
- // DocumentFragment nodes don't have gEBTN
- } else if ( support.qsa ) {
- return context.querySelectorAll( tag );
- }
- } :
-
- function( tag, context ) {
- var elem,
- tmp = [],
- i = 0,
- // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too
- results = context.getElementsByTagName( tag );
-
- // Filter out possible comments
- if ( tag === "*" ) {
- while ( (elem = results[i++]) ) {
- if ( elem.nodeType === 1 ) {
- tmp.push( elem );
- }
- }
-
- return tmp;
- }
- return results;
- };
-
- // Class
- Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) {
- if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) {
- return context.getElementsByClassName( className );
- }
- };
-
- /* QSA/matchesSelector
- ---------------------------------------------------------------------- */
-
- // QSA and matchesSelector support
-
- // matchesSelector(:active) reports false when true (IE9/Opera 11.5)
- rbuggyMatches = [];
-
- // qSa(:focus) reports false when true (Chrome 21)
- // We allow this because of a bug in IE8/9 that throws an error
- // whenever `document.activeElement` is accessed on an iframe
- // So, we allow :focus to pass through QSA all the time to avoid the IE error
- // See https://bugs.jquery.com/ticket/13378
- rbuggyQSA = [];
-
- if ( (support.qsa = rnative.test( document.querySelectorAll )) ) {
- // Build QSA regex
- // Regex strategy adopted from Diego Perini
- assert(function( el ) {
- // Select is set to empty string on purpose
- // This is to test IE's treatment of not explicitly
- // setting a boolean content attribute,
- // since its presence should be enough
- // https://bugs.jquery.com/ticket/12359
- docElem.appendChild( el ).innerHTML = "<a id='" + expando + "'></a>" +
- "<select id='" + expando + "-\r\\' msallowcapture=''>" +
- "<option selected=''></option></select>";
-
- // Support: IE8, Opera 11-12.16
- // Nothing should be selected when empty strings follow ^= or $= or *=
- // The test attribute must be unknown in Opera but "safe" for WinRT
- // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
- if ( el.querySelectorAll("[msallowcapture^='']").length ) {
- rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
- }
-
- // Support: IE8
- // Boolean attributes and "value" are not treated correctly
- if ( !el.querySelectorAll("[selected]").length ) {
- rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" );
- }
-
- // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+
- if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) {
- rbuggyQSA.push("~=");
- }
-
- // Webkit/Opera - :checked should return selected option elements
- // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
- // IE8 throws error here and will not see later tests
- if ( !el.querySelectorAll(":checked").length ) {
- rbuggyQSA.push(":checked");
- }
-
- // Support: Safari 8+, iOS 8+
- // https://bugs.webkit.org/show_bug.cgi?id=136851
- // In-page `selector#id sibling-combinator selector` fails
- if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) {
- rbuggyQSA.push(".#.+[+~]");
- }
- });
-
- assert(function( el ) {
- el.innerHTML = "<a href='' disabled='disabled'></a>" +
- "<select disabled='disabled'><option/></select>";
-
- // Support: Windows 8 Native Apps
- // The type and name attributes are restricted during .innerHTML assignment
- var input = document.createElement("input");
- input.setAttribute( "type", "hidden" );
- el.appendChild( input ).setAttribute( "name", "D" );
-
- // Support: IE8
- // Enforce case-sensitivity of name attribute
- if ( el.querySelectorAll("[name=d]").length ) {
- rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" );
- }
-
- // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
- // IE8 throws error here and will not see later tests
- if ( el.querySelectorAll(":enabled").length !== 2 ) {
- rbuggyQSA.push( ":enabled", ":disabled" );
- }
-
- // Support: IE9-11+
- // IE's :disabled selector does not pick up the children of disabled fieldsets
- docElem.appendChild( el ).disabled = true;
- if ( el.querySelectorAll(":disabled").length !== 2 ) {
- rbuggyQSA.push( ":enabled", ":disabled" );
- }
-
- // Opera 10-11 does not throw on post-comma invalid pseudos
- el.querySelectorAll("*,:x");
- rbuggyQSA.push(",.*:");
- });
- }
-
- if ( (support.matchesSelector = rnative.test( (matches = docElem.matches ||
- docElem.webkitMatchesSelector ||
- docElem.mozMatchesSelector ||
- docElem.oMatchesSelector ||
- docElem.msMatchesSelector) )) ) {
-
- assert(function( el ) {
- // Check to see if it's possible to do matchesSelector
- // on a disconnected node (IE 9)
- support.disconnectedMatch = matches.call( el, "*" );
-
- // This should fail with an exception
- // Gecko does not error, returns false instead
- matches.call( el, "[s!='']:x" );
- rbuggyMatches.push( "!=", pseudos );
- });
- }
-
- rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") );
- rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") );
-
- /* Contains
- ---------------------------------------------------------------------- */
- hasCompare = rnative.test( docElem.compareDocumentPosition );
-
- // Element contains another
- // Purposefully self-exclusive
- // As in, an element does not contain itself
- contains = hasCompare || rnative.test( docElem.contains ) ?
- function( a, b ) {
- var adown = a.nodeType === 9 ? a.documentElement : a,
- bup = b && b.parentNode;
- return a === bup || !!( bup && bup.nodeType === 1 && (
- adown.contains ?
- adown.contains( bup ) :
- a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16
- ));
- } :
- function( a, b ) {
- if ( b ) {
- while ( (b = b.parentNode) ) {
- if ( b === a ) {
- return true;
- }
- }
- }
- return false;
- };
-
- /* Sorting
- ---------------------------------------------------------------------- */
-
- // Document order sorting
- sortOrder = hasCompare ?
- function( a, b ) {
-
- // Flag for duplicate removal
- if ( a === b ) {
- hasDuplicate = true;
- return 0;
- }
-
- // Sort on method existence if only one input has compareDocumentPosition
- var compare = !a.compareDocumentPosition - !b.compareDocumentPosition;
- if ( compare ) {
- return compare;
- }
-
- // Calculate position if both inputs belong to the same document
- compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ?
- a.compareDocumentPosition( b ) :
-
- // Otherwise we know they are disconnected
- 1;
-
- // Disconnected nodes
- if ( compare & 1 ||
- (!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) {
-
- // Choose the first element that is related to our preferred document
- if ( a === document || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) {
- return -1;
- }
- if ( b === document || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) {
- return 1;
- }
-
- // Maintain original order
- return sortInput ?
- ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
- 0;
- }
-
- return compare & 4 ? -1 : 1;
- } :
- function( a, b ) {
- // Exit early if the nodes are identical
- if ( a === b ) {
- hasDuplicate = true;
- return 0;
- }
-
- var cur,
- i = 0,
- aup = a.parentNode,
- bup = b.parentNode,
- ap = [ a ],
- bp = [ b ];
-
- // Parentless nodes are either documents or disconnected
- if ( !aup || !bup ) {
- return a === document ? -1 :
- b === document ? 1 :
- aup ? -1 :
- bup ? 1 :
- sortInput ?
- ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
- 0;
-
- // If the nodes are siblings, we can do a quick check
- } else if ( aup === bup ) {
- return siblingCheck( a, b );
- }
-
- // Otherwise we need full lists of their ancestors for comparison
- cur = a;
- while ( (cur = cur.parentNode) ) {
- ap.unshift( cur );
- }
- cur = b;
- while ( (cur = cur.parentNode) ) {
- bp.unshift( cur );
- }
-
- // Walk down the tree looking for a discrepancy
- while ( ap[i] === bp[i] ) {
- i++;
- }
-
- return i ?
- // Do a sibling check if the nodes have a common ancestor
- siblingCheck( ap[i], bp[i] ) :
-
- // Otherwise nodes in our document sort first
- ap[i] === preferredDoc ? -1 :
- bp[i] === preferredDoc ? 1 :
- 0;
- };
-
- return document;
-};
-
-Sizzle.matches = function( expr, elements ) {
- return Sizzle( expr, null, null, elements );
-};
-
-Sizzle.matchesSelector = function( elem, expr ) {
- // Set document vars if needed
- if ( ( elem.ownerDocument || elem ) !== document ) {
- setDocument( elem );
- }
-
- // Make sure that attribute selectors are quoted
- expr = expr.replace( rattributeQuotes, "='$1']" );
-
- if ( support.matchesSelector && documentIsHTML &&
- !compilerCache[ expr + " " ] &&
- ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) &&
- ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) {
-
- try {
- var ret = matches.call( elem, expr );
-
- // IE 9's matchesSelector returns false on disconnected nodes
- if ( ret || support.disconnectedMatch ||
- // As well, disconnected nodes are said to be in a document
- // fragment in IE 9
- elem.document && elem.document.nodeType !== 11 ) {
- return ret;
- }
- } catch (e) {}
- }
-
- return Sizzle( expr, document, null, [ elem ] ).length > 0;
-};
-
-Sizzle.contains = function( context, elem ) {
- // Set document vars if needed
- if ( ( context.ownerDocument || context ) !== document ) {
- setDocument( context );
- }
- return contains( context, elem );
-};
-
-Sizzle.attr = function( elem, name ) {
- // Set document vars if needed
- if ( ( elem.ownerDocument || elem ) !== document ) {
- setDocument( elem );
- }
-
- var fn = Expr.attrHandle[ name.toLowerCase() ],
- // Don't get fooled by Object.prototype properties (jQuery #13807)
- val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ?
- fn( elem, name, !documentIsHTML ) :
- undefined;
-
- return val !== undefined ?
- val :
- support.attributes || !documentIsHTML ?
- elem.getAttribute( name ) :
- (val = elem.getAttributeNode(name)) && val.specified ?
- val.value :
- null;
-};
-
-Sizzle.escape = function( sel ) {
- return (sel + "").replace( rcssescape, fcssescape );
-};
-
-Sizzle.error = function( msg ) {
- throw new Error( "Syntax error, unrecognized expression: " + msg );
-};
-
-/**
- * Document sorting and removing duplicates
- * @param {ArrayLike} results
- */
-Sizzle.uniqueSort = function( results ) {
- var elem,
- duplicates = [],
- j = 0,
- i = 0;
-
- // Unless we *know* we can detect duplicates, assume their presence
- hasDuplicate = !support.detectDuplicates;
- sortInput = !support.sortStable && results.slice( 0 );
- results.sort( sortOrder );
-
- if ( hasDuplicate ) {
- while ( (elem = results[i++]) ) {
- if ( elem === results[ i ] ) {
- j = duplicates.push( i );
- }
- }
- while ( j-- ) {
- results.splice( duplicates[ j ], 1 );
- }
- }
-
- // Clear input after sorting to release objects
- // See https://github.com/jquery/sizzle/pull/225
- sortInput = null;
-
- return results;
-};
-
-/**
- * Utility function for retrieving the text value of an array of DOM nodes
- * @param {Array|Element} elem
- */
-getText = Sizzle.getText = function( elem ) {
- var node,
- ret = "",
- i = 0,
- nodeType = elem.nodeType;
-
- if ( !nodeType ) {
- // If no nodeType, this is expected to be an array
- while ( (node = elem[i++]) ) {
- // Do not traverse comment nodes
- ret += getText( node );
- }
- } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
- // Use textContent for elements
- // innerText usage removed for consistency of new lines (jQuery #11153)
- if ( typeof elem.textContent === "string" ) {
- return elem.textContent;
- } else {
- // Traverse its children
- for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
- ret += getText( elem );
- }
- }
- } else if ( nodeType === 3 || nodeType === 4 ) {
- return elem.nodeValue;
- }
- // Do not include comment or processing instruction nodes
-
- return ret;
-};
-
-Expr = Sizzle.selectors = {
-
- // Can be adjusted by the user
- cacheLength: 50,
-
- createPseudo: markFunction,
-
- match: matchExpr,
-
- attrHandle: {},
-
- find: {},
-
- relative: {
- ">": { dir: "parentNode", first: true },
- " ": { dir: "parentNode" },
- "+": { dir: "previousSibling", first: true },
- "~": { dir: "previousSibling" }
- },
-
- preFilter: {
- "ATTR": function( match ) {
- match[1] = match[1].replace( runescape, funescape );
-
- // Move the given value to match[3] whether quoted or unquoted
- match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape );
-
- if ( match[2] === "~=" ) {
- match[3] = " " + match[3] + " ";
- }
-
- return match.slice( 0, 4 );
- },
-
- "CHILD": function( match ) {
- /* matches from matchExpr["CHILD"]
- 1 type (only|nth|...)
- 2 what (child|of-type)
- 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...)
- 4 xn-component of xn+y argument ([+-]?\d*n|)
- 5 sign of xn-component
- 6 x of xn-component
- 7 sign of y-component
- 8 y of y-component
- */
- match[1] = match[1].toLowerCase();
-
- if ( match[1].slice( 0, 3 ) === "nth" ) {
- // nth-* requires argument
- if ( !match[3] ) {
- Sizzle.error( match[0] );
- }
-
- // numeric x and y parameters for Expr.filter.CHILD
- // remember that false/true cast respectively to 0/1
- match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) );
- match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" );
-
- // other types prohibit arguments
- } else if ( match[3] ) {
- Sizzle.error( match[0] );
- }
-
- return match;
- },
-
- "PSEUDO": function( match ) {
- var excess,
- unquoted = !match[6] && match[2];
-
- if ( matchExpr["CHILD"].test( match[0] ) ) {
- return null;
- }
-
- // Accept quoted arguments as-is
- if ( match[3] ) {
- match[2] = match[4] || match[5] || "";
-
- // Strip excess characters from unquoted arguments
- } else if ( unquoted && rpseudo.test( unquoted ) &&
- // Get excess from tokenize (recursively)
- (excess = tokenize( unquoted, true )) &&
- // advance to the next closing parenthesis
- (excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) {
-
- // excess is a negative index
- match[0] = match[0].slice( 0, excess );
- match[2] = unquoted.slice( 0, excess );
- }
-
- // Return only captures needed by the pseudo filter method (type and argument)
- return match.slice( 0, 3 );
- }
- },
-
- filter: {
-
- "TAG": function( nodeNameSelector ) {
- var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase();
- return nodeNameSelector === "*" ?
- function() { return true; } :
- function( elem ) {
- return elem.nodeName && elem.nodeName.toLowerCase() === nodeName;
- };
- },
-
- "CLASS": function( className ) {
- var pattern = classCache[ className + " " ];
-
- return pattern ||
- (pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) &&
- classCache( className, function( elem ) {
- return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || "" );
- });
- },
-
- "ATTR": function( name, operator, check ) {
- return function( elem ) {
- var result = Sizzle.attr( elem, name );
-
- if ( result == null ) {
- return operator === "!=";
- }
- if ( !operator ) {
- return true;
- }
-
- result += "";
-
- return operator === "=" ? result === check :
- operator === "!=" ? result !== check :
- operator === "^=" ? check && result.indexOf( check ) === 0 :
- operator === "*=" ? check && result.indexOf( check ) > -1 :
- operator === "$=" ? check && result.slice( -check.length ) === check :
- operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 :
- operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" :
- false;
- };
- },
-
- "CHILD": function( type, what, argument, first, last ) {
- var simple = type.slice( 0, 3 ) !== "nth",
- forward = type.slice( -4 ) !== "last",
- ofType = what === "of-type";
-
- return first === 1 && last === 0 ?
-
- // Shortcut for :nth-*(n)
- function( elem ) {
- return !!elem.parentNode;
- } :
-
- function( elem, context, xml ) {
- var cache, uniqueCache, outerCache, node, nodeIndex, start,
- dir = simple !== forward ? "nextSibling" : "previousSibling",
- parent = elem.parentNode,
- name = ofType && elem.nodeName.toLowerCase(),
- useCache = !xml && !ofType,
- diff = false;
-
- if ( parent ) {
-
- // :(first|last|only)-(child|of-type)
- if ( simple ) {
- while ( dir ) {
- node = elem;
- while ( (node = node[ dir ]) ) {
- if ( ofType ?
- node.nodeName.toLowerCase() === name :
- node.nodeType === 1 ) {
-
- return false;
- }
- }
- // Reverse direction for :only-* (if we haven't yet done so)
- start = dir = type === "only" && !start && "nextSibling";
- }
- return true;
- }
-
- start = [ forward ? parent.firstChild : parent.lastChild ];
-
- // non-xml :nth-child(...) stores cache data on `parent`
- if ( forward && useCache ) {
-
- // Seek `elem` from a previously-cached index
-
- // ...in a gzip-friendly way
- node = parent;
- outerCache = node[ expando ] || (node[ expando ] = {});
-
- // Support: IE <9 only
- // Defend against cloned attroperties (jQuery gh-1709)
- uniqueCache = outerCache[ node.uniqueID ] ||
- (outerCache[ node.uniqueID ] = {});
-
- cache = uniqueCache[ type ] || [];
- nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];
- diff = nodeIndex && cache[ 2 ];
- node = nodeIndex && parent.childNodes[ nodeIndex ];
-
- while ( (node = ++nodeIndex && node && node[ dir ] ||
-
- // Fallback to seeking `elem` from the start
- (diff = nodeIndex = 0) || start.pop()) ) {
-
- // When found, cache indexes on `parent` and break
- if ( node.nodeType === 1 && ++diff && node === elem ) {
- uniqueCache[ type ] = [ dirruns, nodeIndex, diff ];
- break;
- }
- }
-
- } else {
- // Use previously-cached element index if available
- if ( useCache ) {
- // ...in a gzip-friendly way
- node = elem;
- outerCache = node[ expando ] || (node[ expando ] = {});
-
- // Support: IE <9 only
- // Defend against cloned attroperties (jQuery gh-1709)
- uniqueCache = outerCache[ node.uniqueID ] ||
- (outerCache[ node.uniqueID ] = {});
-
- cache = uniqueCache[ type ] || [];
- nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];
- diff = nodeIndex;
- }
-
- // xml :nth-child(...)
- // or :nth-last-child(...) or :nth(-last)?-of-type(...)
- if ( diff === false ) {
- // Use the same loop as above to seek `elem` from the start
- while ( (node = ++nodeIndex && node && node[ dir ] ||
- (diff = nodeIndex = 0) || start.pop()) ) {
-
- if ( ( ofType ?
- node.nodeName.toLowerCase() === name :
- node.nodeType === 1 ) &&
- ++diff ) {
-
- // Cache the index of each encountered element
- if ( useCache ) {
- outerCache = node[ expando ] || (node[ expando ] = {});
-
- // Support: IE <9 only
- // Defend against cloned attroperties (jQuery gh-1709)
- uniqueCache = outerCache[ node.uniqueID ] ||
- (outerCache[ node.uniqueID ] = {});
-
- uniqueCache[ type ] = [ dirruns, diff ];
- }
-
- if ( node === elem ) {
- break;
- }
- }
- }
- }
- }
-
- // Incorporate the offset, then check against cycle size
- diff -= last;
- return diff === first || ( diff % first === 0 && diff / first >= 0 );
- }
- };
- },
-
- "PSEUDO": function( pseudo, argument ) {
- // pseudo-class names are case-insensitive
- // http://www.w3.org/TR/selectors/#pseudo-classes
- // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters
- // Remember that setFilters inherits from pseudos
- var args,
- fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||
- Sizzle.error( "unsupported pseudo: " + pseudo );
-
- // The user may use createPseudo to indicate that
- // arguments are needed to create the filter function
- // just as Sizzle does
- if ( fn[ expando ] ) {
- return fn( argument );
- }
-
- // But maintain support for old signatures
- if ( fn.length > 1 ) {
- args = [ pseudo, pseudo, "", argument ];
- return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?
- markFunction(function( seed, matches ) {
- var idx,
- matched = fn( seed, argument ),
- i = matched.length;
- while ( i-- ) {
- idx = indexOf( seed, matched[i] );
- seed[ idx ] = !( matches[ idx ] = matched[i] );
- }
- }) :
- function( elem ) {
- return fn( elem, 0, args );
- };
- }
-
- return fn;
- }
- },
-
- pseudos: {
- // Potentially complex pseudos
- "not": markFunction(function( selector ) {
- // Trim the selector passed to compile
- // to avoid treating leading and trailing
- // spaces as combinators
- var input = [],
- results = [],
- matcher = compile( selector.replace( rtrim, "$1" ) );
-
- return matcher[ expando ] ?
- markFunction(function( seed, matches, context, xml ) {
- var elem,
- unmatched = matcher( seed, null, xml, [] ),
- i = seed.length;
-
- // Match elements unmatched by `matcher`
- while ( i-- ) {
- if ( (elem = unmatched[i]) ) {
- seed[i] = !(matches[i] = elem);
- }
- }
- }) :
- function( elem, context, xml ) {
- input[0] = elem;
- matcher( input, null, xml, results );
- // Don't keep the element (issue #299)
- input[0] = null;
- return !results.pop();
- };
- }),
-
- "has": markFunction(function( selector ) {
- return function( elem ) {
- return Sizzle( selector, elem ).length > 0;
- };
- }),
-
- "contains": markFunction(function( text ) {
- text = text.replace( runescape, funescape );
- return function( elem ) {
- return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1;
- };
- }),
-
- // "Whether an element is represented by a :lang() selector
- // is based solely on the element's language value
- // being equal to the identifier C,
- // or beginning with the identifier C immediately followed by "-".
- // The matching of C against the element's language value is performed case-insensitively.
- // The identifier C does not have to be a valid language name."
- // http://www.w3.org/TR/selectors/#lang-pseudo
- "lang": markFunction( function( lang ) {
- // lang value must be a valid identifier
- if ( !ridentifier.test(lang || "") ) {
- Sizzle.error( "unsupported lang: " + lang );
- }
- lang = lang.replace( runescape, funescape ).toLowerCase();
- return function( elem ) {
- var elemLang;
- do {
- if ( (elemLang = documentIsHTML ?
- elem.lang :
- elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) {
-
- elemLang = elemLang.toLowerCase();
- return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0;
- }
- } while ( (elem = elem.parentNode) && elem.nodeType === 1 );
- return false;
- };
- }),
-
- // Miscellaneous
- "target": function( elem ) {
- var hash = window.location && window.location.hash;
- return hash && hash.slice( 1 ) === elem.id;
- },
-
- "root": function( elem ) {
- return elem === docElem;
- },
-
- "focus": function( elem ) {
- return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex);
- },
-
- // Boolean properties
- "enabled": createDisabledPseudo( false ),
- "disabled": createDisabledPseudo( true ),
-
- "checked": function( elem ) {
- // In CSS3, :checked should return both checked and selected elements
- // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
- var nodeName = elem.nodeName.toLowerCase();
- return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected);
- },
-
- "selected": function( elem ) {
- // Accessing this property makes selected-by-default
- // options in Safari work properly
- if ( elem.parentNode ) {
- elem.parentNode.selectedIndex;
- }
-
- return elem.selected === true;
- },
-
- // Contents
- "empty": function( elem ) {
- // http://www.w3.org/TR/selectors/#empty-pseudo
- // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5),
- // but not by others (comment: 8; processing instruction: 7; etc.)
- // nodeType < 6 works because attributes (2) do not appear as children
- for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
- if ( elem.nodeType < 6 ) {
- return false;
- }
- }
- return true;
- },
-
- "parent": function( elem ) {
- return !Expr.pseudos["empty"]( elem );
- },
-
- // Element/input types
- "header": function( elem ) {
- return rheader.test( elem.nodeName );
- },
-
- "input": function( elem ) {
- return rinputs.test( elem.nodeName );
- },
-
- "button": function( elem ) {
- var name = elem.nodeName.toLowerCase();
- return name === "input" && elem.type === "button" || name === "button";
- },
-
- "text": function( elem ) {
- var attr;
- return elem.nodeName.toLowerCase() === "input" &&
- elem.type === "text" &&
-
- // Support: IE<8
- // New HTML5 attribute values (e.g., "search") appear with elem.type === "text"
- ( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" );
- },
-
- // Position-in-collection
- "first": createPositionalPseudo(function() {
- return [ 0 ];
- }),
-
- "last": createPositionalPseudo(function( matchIndexes, length ) {
- return [ length - 1 ];
- }),
-
- "eq": createPositionalPseudo(function( matchIndexes, length, argument ) {
- return [ argument < 0 ? argument + length : argument ];
- }),
-
- "even": createPositionalPseudo(function( matchIndexes, length ) {
- var i = 0;
- for ( ; i < length; i += 2 ) {
- matchIndexes.push( i );
- }
- return matchIndexes;
- }),
-
- "odd": createPositionalPseudo(function( matchIndexes, length ) {
- var i = 1;
- for ( ; i < length; i += 2 ) {
- matchIndexes.push( i );
- }
- return matchIndexes;
- }),
-
- "lt": createPositionalPseudo(function( matchIndexes, length, argument ) {
- var i = argument < 0 ? argument + length : argument;
- for ( ; --i >= 0; ) {
- matchIndexes.push( i );
- }
- return matchIndexes;
- }),
-
- "gt": createPositionalPseudo(function( matchIndexes, length, argument ) {
- var i = argument < 0 ? argument + length : argument;
- for ( ; ++i < length; ) {
- matchIndexes.push( i );
- }
- return matchIndexes;
- })
- }
-};
-
-Expr.pseudos["nth"] = Expr.pseudos["eq"];
-
-// Add button/input type pseudos
-for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) {
- Expr.pseudos[ i ] = createInputPseudo( i );
-}
-for ( i in { submit: true, reset: true } ) {
- Expr.pseudos[ i ] = createButtonPseudo( i );
-}
-
-// Easy API for creating new setFilters
-function setFilters() {}
-setFilters.prototype = Expr.filters = Expr.pseudos;
-Expr.setFilters = new setFilters();
-
-tokenize = Sizzle.tokenize = function( selector, parseOnly ) {
- var matched, match, tokens, type,
- soFar, groups, preFilters,
- cached = tokenCache[ selector + " " ];
-
- if ( cached ) {
- return parseOnly ? 0 : cached.slice( 0 );
- }
-
- soFar = selector;
- groups = [];
- preFilters = Expr.preFilter;
-
- while ( soFar ) {
-
- // Comma and first run
- if ( !matched || (match = rcomma.exec( soFar )) ) {
- if ( match ) {
- // Don't consume trailing commas as valid
- soFar = soFar.slice( match[0].length ) || soFar;
- }
- groups.push( (tokens = []) );
- }
-
- matched = false;
-
- // Combinators
- if ( (match = rcombinators.exec( soFar )) ) {
- matched = match.shift();
- tokens.push({
- value: matched,
- // Cast descendant combinators to space
- type: match[0].replace( rtrim, " " )
- });
- soFar = soFar.slice( matched.length );
- }
-
- // Filters
- for ( type in Expr.filter ) {
- if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] ||
- (match = preFilters[ type ]( match ))) ) {
- matched = match.shift();
- tokens.push({
- value: matched,
- type: type,
- matches: match
- });
- soFar = soFar.slice( matched.length );
- }
- }
-
- if ( !matched ) {
- break;
- }
- }
-
- // Return the length of the invalid excess
- // if we're just parsing
- // Otherwise, throw an error or return tokens
- return parseOnly ?
- soFar.length :
- soFar ?
- Sizzle.error( selector ) :
- // Cache the tokens
- tokenCache( selector, groups ).slice( 0 );
-};
-
-function toSelector( tokens ) {
- var i = 0,
- len = tokens.length,
- selector = "";
- for ( ; i < len; i++ ) {
- selector += tokens[i].value;
- }
- return selector;
-}
-
-function addCombinator( matcher, combinator, base ) {
- var dir = combinator.dir,
- skip = combinator.next,
- key = skip || dir,
- checkNonElements = base && key === "parentNode",
- doneName = done++;
-
- return combinator.first ?
- // Check against closest ancestor/preceding element
- function( elem, context, xml ) {
- while ( (elem = elem[ dir ]) ) {
- if ( elem.nodeType === 1 || checkNonElements ) {
- return matcher( elem, context, xml );
- }
- }
- return false;
- } :
-
- // Check against all ancestor/preceding elements
- function( elem, context, xml ) {
- var oldCache, uniqueCache, outerCache,
- newCache = [ dirruns, doneName ];
-
- // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching
- if ( xml ) {
- while ( (elem = elem[ dir ]) ) {
- if ( elem.nodeType === 1 || checkNonElements ) {
- if ( matcher( elem, context, xml ) ) {
- return true;
- }
- }
- }
- } else {
- while ( (elem = elem[ dir ]) ) {
- if ( elem.nodeType === 1 || checkNonElements ) {
- outerCache = elem[ expando ] || (elem[ expando ] = {});
-
- // Support: IE <9 only
- // Defend against cloned attroperties (jQuery gh-1709)
- uniqueCache = outerCache[ elem.uniqueID ] || (outerCache[ elem.uniqueID ] = {});
-
- if ( skip && skip === elem.nodeName.toLowerCase() ) {
- elem = elem[ dir ] || elem;
- } else if ( (oldCache = uniqueCache[ key ]) &&
- oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) {
-
- // Assign to newCache so results back-propagate to previous elements
- return (newCache[ 2 ] = oldCache[ 2 ]);
- } else {
- // Reuse newcache so results back-propagate to previous elements
- uniqueCache[ key ] = newCache;
-
- // A match means we're done; a fail means we have to keep checking
- if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) {
- return true;
- }
- }
- }
- }
- }
- return false;
- };
-}
-
-function elementMatcher( matchers ) {
- return matchers.length > 1 ?
- function( elem, context, xml ) {
- var i = matchers.length;
- while ( i-- ) {
- if ( !matchers[i]( elem, context, xml ) ) {
- return false;
- }
- }
- return true;
- } :
- matchers[0];
-}
-
-function multipleContexts( selector, contexts, results ) {
- var i = 0,
- len = contexts.length;
- for ( ; i < len; i++ ) {
- Sizzle( selector, contexts[i], results );
- }
- return results;
-}
-
-function condense( unmatched, map, filter, context, xml ) {
- var elem,
- newUnmatched = [],
- i = 0,
- len = unmatched.length,
- mapped = map != null;
-
- for ( ; i < len; i++ ) {
- if ( (elem = unmatched[i]) ) {
- if ( !filter || filter( elem, context, xml ) ) {
- newUnmatched.push( elem );
- if ( mapped ) {
- map.push( i );
- }
- }
- }
- }
-
- return newUnmatched;
-}
-
-function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
- if ( postFilter && !postFilter[ expando ] ) {
- postFilter = setMatcher( postFilter );
- }
- if ( postFinder && !postFinder[ expando ] ) {
- postFinder = setMatcher( postFinder, postSelector );
- }
- return markFunction(function( seed, results, context, xml ) {
- var temp, i, elem,
- preMap = [],
- postMap = [],
- preexisting = results.length,
-
- // Get initial elements from seed or context
- elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ),
-
- // Prefilter to get matcher input, preserving a map for seed-results synchronization
- matcherIn = preFilter && ( seed || !selector ) ?
- condense( elems, preMap, preFilter, context, xml ) :
- elems,
-
- matcherOut = matcher ?
- // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,
- postFinder || ( seed ? preFilter : preexisting || postFilter ) ?
-
- // ...intermediate processing is necessary
- [] :
-
- // ...otherwise use results directly
- results :
- matcherIn;
-
- // Find primary matches
- if ( matcher ) {
- matcher( matcherIn, matcherOut, context, xml );
- }
-
- // Apply postFilter
- if ( postFilter ) {
- temp = condense( matcherOut, postMap );
- postFilter( temp, [], context, xml );
-
- // Un-match failing elements by moving them back to matcherIn
- i = temp.length;
- while ( i-- ) {
- if ( (elem = temp[i]) ) {
- matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem);
- }
- }
- }
-
- if ( seed ) {
- if ( postFinder || preFilter ) {
- if ( postFinder ) {
- // Get the final matcherOut by condensing this intermediate into postFinder contexts
- temp = [];
- i = matcherOut.length;
- while ( i-- ) {
- if ( (elem = matcherOut[i]) ) {
- // Restore matcherIn since elem is not yet a final match
- temp.push( (matcherIn[i] = elem) );
- }
- }
- postFinder( null, (matcherOut = []), temp, xml );
- }
-
- // Move matched elements from seed to results to keep them synchronized
- i = matcherOut.length;
- while ( i-- ) {
- if ( (elem = matcherOut[i]) &&
- (temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) {
-
- seed[temp] = !(results[temp] = elem);
- }
- }
- }
-
- // Add elements to results, through postFinder if defined
- } else {
- matcherOut = condense(
- matcherOut === results ?
- matcherOut.splice( preexisting, matcherOut.length ) :
- matcherOut
- );
- if ( postFinder ) {
- postFinder( null, results, matcherOut, xml );
- } else {
- push.apply( results, matcherOut );
- }
- }
- });
-}
-
-function matcherFromTokens( tokens ) {
- var checkContext, matcher, j,
- len = tokens.length,
- leadingRelative = Expr.relative[ tokens[0].type ],
- implicitRelative = leadingRelative || Expr.relative[" "],
- i = leadingRelative ? 1 : 0,
-
- // The foundational matcher ensures that elements are reachable from top-level context(s)
- matchContext = addCombinator( function( elem ) {
- return elem === checkContext;
- }, implicitRelative, true ),
- matchAnyContext = addCombinator( function( elem ) {
- return indexOf( checkContext, elem ) > -1;
- }, implicitRelative, true ),
- matchers = [ function( elem, context, xml ) {
- var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
- (checkContext = context).nodeType ?
- matchContext( elem, context, xml ) :
- matchAnyContext( elem, context, xml ) );
- // Avoid hanging onto element (issue #299)
- checkContext = null;
- return ret;
- } ];
-
- for ( ; i < len; i++ ) {
- if ( (matcher = Expr.relative[ tokens[i].type ]) ) {
- matchers = [ addCombinator(elementMatcher( matchers ), matcher) ];
- } else {
- matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches );
-
- // Return special upon seeing a positional matcher
- if ( matcher[ expando ] ) {
- // Find the next relative operator (if any) for proper handling
- j = ++i;
- for ( ; j < len; j++ ) {
- if ( Expr.relative[ tokens[j].type ] ) {
- break;
- }
- }
- return setMatcher(
- i > 1 && elementMatcher( matchers ),
- i > 1 && toSelector(
- // If the preceding token was a descendant combinator, insert an implicit any-element `*`
- tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" })
- ).replace( rtrim, "$1" ),
- matcher,
- i < j && matcherFromTokens( tokens.slice( i, j ) ),
- j < len && matcherFromTokens( (tokens = tokens.slice( j )) ),
- j < len && toSelector( tokens )
- );
- }
- matchers.push( matcher );
- }
- }
-
- return elementMatcher( matchers );
-}
-
-function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
- var bySet = setMatchers.length > 0,
- byElement = elementMatchers.length > 0,
- superMatcher = function( seed, context, xml, results, outermost ) {
- var elem, j, matcher,
- matchedCount = 0,
- i = "0",
- unmatched = seed && [],
- setMatched = [],
- contextBackup = outermostContext,
- // We must always have either seed elements or outermost context
- elems = seed || byElement && Expr.find["TAG"]( "*", outermost ),
- // Use integer dirruns iff this is the outermost matcher
- dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1),
- len = elems.length;
-
- if ( outermost ) {
- outermostContext = context === document || context || outermost;
- }
-
- // Add elements passing elementMatchers directly to results
- // Support: IE<9, Safari
- // Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id
- for ( ; i !== len && (elem = elems[i]) != null; i++ ) {
- if ( byElement && elem ) {
- j = 0;
- if ( !context && elem.ownerDocument !== document ) {
- setDocument( elem );
- xml = !documentIsHTML;
- }
- while ( (matcher = elementMatchers[j++]) ) {
- if ( matcher( elem, context || document, xml) ) {
- results.push( elem );
- break;
- }
- }
- if ( outermost ) {
- dirruns = dirrunsUnique;
- }
- }
-
- // Track unmatched elements for set filters
- if ( bySet ) {
- // They will have gone through all possible matchers
- if ( (elem = !matcher && elem) ) {
- matchedCount--;
- }
-
- // Lengthen the array for every element, matched or not
- if ( seed ) {
- unmatched.push( elem );
- }
- }
- }
-
- // `i` is now the count of elements visited above, and adding it to `matchedCount`
- // makes the latter nonnegative.
- matchedCount += i;
-
- // Apply set filters to unmatched elements
- // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount`
- // equals `i`), unless we didn't visit _any_ elements in the above loop because we have
- // no element matchers and no seed.
- // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that
- // case, which will result in a "00" `matchedCount` that differs from `i` but is also
- // numerically zero.
- if ( bySet && i !== matchedCount ) {
- j = 0;
- while ( (matcher = setMatchers[j++]) ) {
- matcher( unmatched, setMatched, context, xml );
- }
-
- if ( seed ) {
- // Reintegrate element matches to eliminate the need for sorting
- if ( matchedCount > 0 ) {
- while ( i-- ) {
- if ( !(unmatched[i] || setMatched[i]) ) {
- setMatched[i] = pop.call( results );
- }
- }
- }
-
- // Discard index placeholder values to get only actual matches
- setMatched = condense( setMatched );
- }
-
- // Add matches to results
- push.apply( results, setMatched );
-
- // Seedless set matches succeeding multiple successful matchers stipulate sorting
- if ( outermost && !seed && setMatched.length > 0 &&
- ( matchedCount + setMatchers.length ) > 1 ) {
-
- Sizzle.uniqueSort( results );
- }
- }
-
- // Override manipulation of globals by nested matchers
- if ( outermost ) {
- dirruns = dirrunsUnique;
- outermostContext = contextBackup;
- }
-
- return unmatched;
- };
-
- return bySet ?
- markFunction( superMatcher ) :
- superMatcher;
-}
-
-compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) {
- var i,
- setMatchers = [],
- elementMatchers = [],
- cached = compilerCache[ selector + " " ];
-
- if ( !cached ) {
- // Generate a function of recursive functions that can be used to check each element
- if ( !match ) {
- match = tokenize( selector );
- }
- i = match.length;
- while ( i-- ) {
- cached = matcherFromTokens( match[i] );
- if ( cached[ expando ] ) {
- setMatchers.push( cached );
- } else {
- elementMatchers.push( cached );
- }
- }
-
- // Cache the compiled function
- cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );
-
- // Save selector and tokenization
- cached.selector = selector;
- }
- return cached;
-};
-
-/**
- * A low-level selection function that works with Sizzle's compiled
- * selector functions
- * @param {String|Function} selector A selector or a pre-compiled
- * selector function built with Sizzle.compile
- * @param {Element} context
- * @param {Array} [results]
- * @param {Array} [seed] A set of elements to match against
- */
-select = Sizzle.select = function( selector, context, results, seed ) {
- var i, tokens, token, type, find,
- compiled = typeof selector === "function" && selector,
- match = !seed && tokenize( (selector = compiled.selector || selector) );
-
- results = results || [];
-
- // Try to minimize operations if there is only one selector in the list and no seed
- // (the latter of which guarantees us context)
- if ( match.length === 1 ) {
-
- // Reduce context if the leading compound selector is an ID
- tokens = match[0] = match[0].slice( 0 );
- if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
- context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[1].type ] ) {
-
- context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0];
- if ( !context ) {
- return results;
-
- // Precompiled matchers will still verify ancestry, so step up a level
- } else if ( compiled ) {
- context = context.parentNode;
- }
-
- selector = selector.slice( tokens.shift().value.length );
- }
-
- // Fetch a seed set for right-to-left matching
- i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length;
- while ( i-- ) {
- token = tokens[i];
-
- // Abort if we hit a combinator
- if ( Expr.relative[ (type = token.type) ] ) {
- break;
- }
- if ( (find = Expr.find[ type ]) ) {
- // Search, expanding context for leading sibling combinators
- if ( (seed = find(
- token.matches[0].replace( runescape, funescape ),
- rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context
- )) ) {
-
- // If seed is empty or no tokens remain, we can return early
- tokens.splice( i, 1 );
- selector = seed.length && toSelector( tokens );
- if ( !selector ) {
- push.apply( results, seed );
- return results;
- }
-
- break;
- }
- }
- }
- }
-
- // Compile and execute a filtering function if one is not provided
- // Provide `match` to avoid retokenization if we modified the selector above
- ( compiled || compile( selector, match ) )(
- seed,
- context,
- !documentIsHTML,
- results,
- !context || rsibling.test( selector ) && testContext( context.parentNode ) || context
- );
- return results;
-};
-
-// One-time assignments
-
-// Sort stability
-support.sortStable = expando.split("").sort( sortOrder ).join("") === expando;
-
-// Support: Chrome 14-35+
-// Always assume duplicates if they aren't passed to the comparison function
-support.detectDuplicates = !!hasDuplicate;
-
-// Initialize against the default document
-setDocument();
-
-// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)
-// Detached nodes confoundingly follow *each other*
-support.sortDetached = assert(function( el ) {
- // Should return 1, but returns 4 (following)
- return el.compareDocumentPosition( document.createElement("fieldset") ) & 1;
-});
-
-// Support: IE<8
-// Prevent attribute/property "interpolation"
-// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
-if ( !assert(function( el ) {
- el.innerHTML = "<a href='#'></a>";
- return el.firstChild.getAttribute("href") === "#" ;
-}) ) {
- addHandle( "type|href|height|width", function( elem, name, isXML ) {
- if ( !isXML ) {
- return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 );
- }
- });
-}
-
-// Support: IE<9
-// Use defaultValue in place of getAttribute("value")
-if ( !support.attributes || !assert(function( el ) {
- el.innerHTML = "<input/>";
- el.firstChild.setAttribute( "value", "" );
- return el.firstChild.getAttribute( "value" ) === "";
-}) ) {
- addHandle( "value", function( elem, name, isXML ) {
- if ( !isXML && elem.nodeName.toLowerCase() === "input" ) {
- return elem.defaultValue;
- }
- });
-}
-
-// Support: IE<9
-// Use getAttributeNode to fetch booleans when getAttribute lies
-if ( !assert(function( el ) {
- return el.getAttribute("disabled") == null;
-}) ) {
- addHandle( booleans, function( elem, name, isXML ) {
- var val;
- if ( !isXML ) {
- return elem[ name ] === true ? name.toLowerCase() :
- (val = elem.getAttributeNode( name )) && val.specified ?
- val.value :
- null;
- }
- });
-}
-
-return Sizzle;
-
-})( window );
-
-
-
-jQuery.find = Sizzle;
-jQuery.expr = Sizzle.selectors;
-
-// Deprecated
-jQuery.expr[ ":" ] = jQuery.expr.pseudos;
-jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort;
-jQuery.text = Sizzle.getText;
-jQuery.isXMLDoc = Sizzle.isXML;
-jQuery.contains = Sizzle.contains;
-jQuery.escapeSelector = Sizzle.escape;
-
-
-
-
-var dir = function( elem, dir, until ) {
- var matched = [],
- truncate = until !== undefined;
-
- while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) {
- if ( elem.nodeType === 1 ) {
- if ( truncate && jQuery( elem ).is( until ) ) {
- break;
- }
- matched.push( elem );
- }
- }
- return matched;
-};
-
-
-var siblings = function( n, elem ) {
- var matched = [];
-
- for ( ; n; n = n.nextSibling ) {
- if ( n.nodeType === 1 && n !== elem ) {
- matched.push( n );
- }
- }
-
- return matched;
-};
-
-
-var rneedsContext = jQuery.expr.match.needsContext;
-
-
-
-function nodeName( elem, name ) {
-
- return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
-
-};
-var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i );
-
-
-
-var risSimple = /^.[^:#\[\.,]*$/;
-
-// Implement the identical functionality for filter and not
-function winnow( elements, qualifier, not ) {
- if ( jQuery.isFunction( qualifier ) ) {
- return jQuery.grep( elements, function( elem, i ) {
- return !!qualifier.call( elem, i, elem ) !== not;
- } );
- }
-
- // Single element
- if ( qualifier.nodeType ) {
- return jQuery.grep( elements, function( elem ) {
- return ( elem === qualifier ) !== not;
- } );
- }
-
- // Arraylike of elements (jQuery, arguments, Array)
- if ( typeof qualifier !== "string" ) {
- return jQuery.grep( elements, function( elem ) {
- return ( indexOf.call( qualifier, elem ) > -1 ) !== not;
- } );
- }
-
- // Simple selector that can be filtered directly, removing non-Elements
- if ( risSimple.test( qualifier ) ) {
- return jQuery.filter( qualifier, elements, not );
- }
-
- // Complex selector, compare the two sets, removing non-Elements
- qualifier = jQuery.filter( qualifier, elements );
- return jQuery.grep( elements, function( elem ) {
- return ( indexOf.call( qualifier, elem ) > -1 ) !== not && elem.nodeType === 1;
- } );
-}
-
-jQuery.filter = function( expr, elems, not ) {
- var elem = elems[ 0 ];
-
- if ( not ) {
- expr = ":not(" + expr + ")";
- }
-
- if ( elems.length === 1 && elem.nodeType === 1 ) {
- return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [];
- }
-
- return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {
- return elem.nodeType === 1;
- } ) );
-};
-
-jQuery.fn.extend( {
- find: function( selector ) {
- var i, ret,
- len = this.length,
- self = this;
-
- if ( typeof selector !== "string" ) {
- return this.pushStack( jQuery( selector ).filter( function() {
- for ( i = 0; i < len; i++ ) {
- if ( jQuery.contains( self[ i ], this ) ) {
- return true;
- }
- }
- } ) );
- }
-
- ret = this.pushStack( [] );
-
- for ( i = 0; i < len; i++ ) {
- jQuery.find( selector, self[ i ], ret );
- }
-
- return len > 1 ? jQuery.uniqueSort( ret ) : ret;
- },
- filter: function( selector ) {
- return this.pushStack( winnow( this, selector || [], false ) );
- },
- not: function( selector ) {
- return this.pushStack( winnow( this, selector || [], true ) );
- },
- is: function( selector ) {
- return !!winnow(
- this,
-
- // If this is a positional/relative selector, check membership in the returned set
- // so $("p:first").is("p:last") won't return true for a doc with two "p".
- typeof selector === "string" && rneedsContext.test( selector ) ?
- jQuery( selector ) :
- selector || [],
- false
- ).length;
- }
-} );
-
-
-// Initialize a jQuery object
-
-
-// A central reference to the root jQuery(document)
-var rootjQuery,
-
- // A simple way to check for HTML strings
- // Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
- // Strict HTML recognition (#11290: must start with <)
- // Shortcut simple #id case for speed
- rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/,
-
- init = jQuery.fn.init = function( selector, context, root ) {
- var match, elem;
-
- // HANDLE: $(""), $(null), $(undefined), $(false)
- if ( !selector ) {
- return this;
- }
-
- // Method init() accepts an alternate rootjQuery
- // so migrate can support jQuery.sub (gh-2101)
- root = root || rootjQuery;
-
- // Handle HTML strings
- if ( typeof selector === "string" ) {
- if ( selector[ 0 ] === "<" &&
- selector[ selector.length - 1 ] === ">" &&
- selector.length >= 3 ) {
-
- // Assume that strings that start and end with <> are HTML and skip the regex check
- match = [ null, selector, null ];
-
- } else {
- match = rquickExpr.exec( selector );
- }
-
- // Match html or make sure no context is specified for #id
- if ( match && ( match[ 1 ] || !context ) ) {
-
- // HANDLE: $(html) -> $(array)
- if ( match[ 1 ] ) {
- context = context instanceof jQuery ? context[ 0 ] : context;
-
- // Option to run scripts is true for back-compat
- // Intentionally let the error be thrown if parseHTML is not present
- jQuery.merge( this, jQuery.parseHTML(
- match[ 1 ],
- context && context.nodeType ? context.ownerDocument || context : document,
- true
- ) );
-
- // HANDLE: $(html, props)
- if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) {
- for ( match in context ) {
-
- // Properties of context are called as methods if possible
- if ( jQuery.isFunction( this[ match ] ) ) {
- this[ match ]( context[ match ] );
-
- // ...and otherwise set as attributes
- } else {
- this.attr( match, context[ match ] );
- }
- }
- }
-
- return this;
-
- // HANDLE: $(#id)
- } else {
- elem = document.getElementById( match[ 2 ] );
-
- if ( elem ) {
-
- // Inject the element directly into the jQuery object
- this[ 0 ] = elem;
- this.length = 1;
- }
- return this;
- }
-
- // HANDLE: $(expr, $(...))
- } else if ( !context || context.jquery ) {
- return ( context || root ).find( selector );
-
- // HANDLE: $(expr, context)
- // (which is just equivalent to: $(context).find(expr)
- } else {
- return this.constructor( context ).find( selector );
- }
-
- // HANDLE: $(DOMElement)
- } else if ( selector.nodeType ) {
- this[ 0 ] = selector;
- this.length = 1;
- return this;
-
- // HANDLE: $(function)
- // Shortcut for document ready
- } else if ( jQuery.isFunction( selector ) ) {
- return root.ready !== undefined ?
- root.ready( selector ) :
-
- // Execute immediately if ready is not present
- selector( jQuery );
- }
-
- return jQuery.makeArray( selector, this );
- };
-
-// Give the init function the jQuery prototype for later instantiation
-init.prototype = jQuery.fn;
-
-// Initialize central reference
-rootjQuery = jQuery( document );
-
-
-var rparentsprev = /^(?:parents|prev(?:Until|All))/,
-
- // Methods guaranteed to produce a unique set when starting from a unique set
- guaranteedUnique = {
- children: true,
- contents: true,
- next: true,
- prev: true
- };
-
-jQuery.fn.extend( {
- has: function( target ) {
- var targets = jQuery( target, this ),
- l = targets.length;
-
- return this.filter( function() {
- var i = 0;
- for ( ; i < l; i++ ) {
- if ( jQuery.contains( this, targets[ i ] ) ) {
- return true;
- }
- }
- } );
- },
-
- closest: function( selectors, context ) {
- var cur,
- i = 0,
- l = this.length,
- matched = [],
- targets = typeof selectors !== "string" && jQuery( selectors );
-
- // Positional selectors never match, since there's no _selection_ context
- if ( !rneedsContext.test( selectors ) ) {
- for ( ; i < l; i++ ) {
- for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) {
-
- // Always skip document fragments
- if ( cur.nodeType < 11 && ( targets ?
- targets.index( cur ) > -1 :
-
- // Don't pass non-elements to Sizzle
- cur.nodeType === 1 &&
- jQuery.find.matchesSelector( cur, selectors ) ) ) {
-
- matched.push( cur );
- break;
- }
- }
- }
- }
-
- return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched );
- },
-
- // Determine the position of an element within the set
- index: function( elem ) {
-
- // No argument, return index in parent
- if ( !elem ) {
- return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1;
- }
-
- // Index in selector
- if ( typeof elem === "string" ) {
- return indexOf.call( jQuery( elem ), this[ 0 ] );
- }
-
- // Locate the position of the desired element
- return indexOf.call( this,
-
- // If it receives a jQuery object, the first element is used
- elem.jquery ? elem[ 0 ] : elem
- );
- },
-
- add: function( selector, context ) {
- return this.pushStack(
- jQuery.uniqueSort(
- jQuery.merge( this.get(), jQuery( selector, context ) )
- )
- );
- },
-
- addBack: function( selector ) {
- return this.add( selector == null ?
- this.prevObject : this.prevObject.filter( selector )
- );
- }
-} );
-
-function sibling( cur, dir ) {
- while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {}
- return cur;
-}
-
-jQuery.each( {
- parent: function( elem ) {
- var parent = elem.parentNode;
- return parent && parent.nodeType !== 11 ? parent : null;
- },
- parents: function( elem ) {
- return dir( elem, "parentNode" );
- },
- parentsUntil: function( elem, i, until ) {
- return dir( elem, "parentNode", until );
- },
- next: function( elem ) {
- return sibling( elem, "nextSibling" );
- },
- prev: function( elem ) {
- return sibling( elem, "previousSibling" );
- },
- nextAll: function( elem ) {
- return dir( elem, "nextSibling" );
- },
- prevAll: function( elem ) {
- return dir( elem, "previousSibling" );
- },
- nextUntil: function( elem, i, until ) {
- return dir( elem, "nextSibling", until );
- },
- prevUntil: function( elem, i, until ) {
- return dir( elem, "previousSibling", until );
- },
- siblings: function( elem ) {
- return siblings( ( elem.parentNode || {} ).firstChild, elem );
- },
- children: function( elem ) {
- return siblings( elem.firstChild );
- },
- contents: function( elem ) {
- if ( nodeName( elem, "iframe" ) ) {
- return elem.contentDocument;
- }
-
- // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only
- // Treat the template element as a regular one in browsers that
- // don't support it.
- if ( nodeName( elem, "template" ) ) {
- elem = elem.content || elem;
- }
-
- return jQuery.merge( [], elem.childNodes );
- }
-}, function( name, fn ) {
- jQuery.fn[ name ] = function( until, selector ) {
- var matched = jQuery.map( this, fn, until );
-
- if ( name.slice( -5 ) !== "Until" ) {
- selector = until;
- }
-
- if ( selector && typeof selector === "string" ) {
- matched = jQuery.filter( selector, matched );
- }
-
- if ( this.length > 1 ) {
-
- // Remove duplicates
- if ( !guaranteedUnique[ name ] ) {
- jQuery.uniqueSort( matched );
- }
-
- // Reverse order for parents* and prev-derivatives
- if ( rparentsprev.test( name ) ) {
- matched.reverse();
- }
- }
-
- return this.pushStack( matched );
- };
-} );
-var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g );
-
-
-
-// Convert String-formatted options into Object-formatted ones
-function createOptions( options ) {
- var object = {};
- jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) {
- object[ flag ] = true;
- } );
- return object;
-}
-
-/*
- * Create a callback list using the following parameters:
- *
- * options: an optional list of space-separated options that will change how
- * the callback list behaves or a more traditional option object
- *
- * By default a callback list will act like an event callback list and can be
- * "fired" multiple times.
- *
- * Possible options:
- *
- * once: will ensure the callback list can only be fired once (like a Deferred)
- *
- * memory: will keep track of previous values and will call any callback added
- * after the list has been fired right away with the latest "memorized"
- * values (like a Deferred)
- *
- * unique: will ensure a callback can only be added once (no duplicate in the list)
- *
- * stopOnFalse: interrupt callings when a callback returns false
- *
- */
-jQuery.Callbacks = function( options ) {
-
- // Convert options from String-formatted to Object-formatted if needed
- // (we check in cache first)
- options = typeof options === "string" ?
- createOptions( options ) :
- jQuery.extend( {}, options );
-
- var // Flag to know if list is currently firing
- firing,
-
- // Last fire value for non-forgettable lists
- memory,
-
- // Flag to know if list was already fired
- fired,
-
- // Flag to prevent firing
- locked,
-
- // Actual callback list
- list = [],
-
- // Queue of execution data for repeatable lists
- queue = [],
-
- // Index of currently firing callback (modified by add/remove as needed)
- firingIndex = -1,
-
- // Fire callbacks
- fire = function() {
-
- // Enforce single-firing
- locked = locked || options.once;
-
- // Execute callbacks for all pending executions,
- // respecting firingIndex overrides and runtime changes
- fired = firing = true;
- for ( ; queue.length; firingIndex = -1 ) {
- memory = queue.shift();
- while ( ++firingIndex < list.length ) {
-
- // Run callback and check for early termination
- if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false &&
- options.stopOnFalse ) {
-
- // Jump to end and forget the data so .add doesn't re-fire
- firingIndex = list.length;
- memory = false;
- }
- }
- }
-
- // Forget the data if we're done with it
- if ( !options.memory ) {
- memory = false;
- }
-
- firing = false;
-
- // Clean up if we're done firing for good
- if ( locked ) {
-
- // Keep an empty list if we have data for future add calls
- if ( memory ) {
- list = [];
-
- // Otherwise, this object is spent
- } else {
- list = "";
- }
- }
- },
-
- // Actual Callbacks object
- self = {
-
- // Add a callback or a collection of callbacks to the list
- add: function() {
- if ( list ) {
-
- // If we have memory from a past run, we should fire after adding
- if ( memory && !firing ) {
- firingIndex = list.length - 1;
- queue.push( memory );
- }
-
- ( function add( args ) {
- jQuery.each( args, function( _, arg ) {
- if ( jQuery.isFunction( arg ) ) {
- if ( !options.unique || !self.has( arg ) ) {
- list.push( arg );
- }
- } else if ( arg && arg.length && jQuery.type( arg ) !== "string" ) {
-
- // Inspect recursively
- add( arg );
- }
- } );
- } )( arguments );
-
- if ( memory && !firing ) {
- fire();
- }
- }
- return this;
- },
-
- // Remove a callback from the list
- remove: function() {
- jQuery.each( arguments, function( _, arg ) {
- var index;
- while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
- list.splice( index, 1 );
-
- // Handle firing indexes
- if ( index <= firingIndex ) {
- firingIndex--;
- }
- }
- } );
- return this;
- },
-
- // Check if a given callback is in the list.
- // If no argument is given, return whether or not list has callbacks attached.
- has: function( fn ) {
- return fn ?
- jQuery.inArray( fn, list ) > -1 :
- list.length > 0;
- },
-
- // Remove all callbacks from the list
- empty: function() {
- if ( list ) {
- list = [];
- }
- return this;
- },
-
- // Disable .fire and .add
- // Abort any current/pending executions
- // Clear all callbacks and values
- disable: function() {
- locked = queue = [];
- list = memory = "";
- return this;
- },
- disabled: function() {
- return !list;
- },
-
- // Disable .fire
- // Also disable .add unless we have memory (since it would have no effect)
- // Abort any pending executions
- lock: function() {
- locked = queue = [];
- if ( !memory && !firing ) {
- list = memory = "";
- }
- return this;
- },
- locked: function() {
- return !!locked;
- },
-
- // Call all callbacks with the given context and arguments
- fireWith: function( context, args ) {
- if ( !locked ) {
- args = args || [];
- args = [ context, args.slice ? args.slice() : args ];
- queue.push( args );
- if ( !firing ) {
- fire();
- }
- }
- return this;
- },
-
- // Call all the callbacks with the given arguments
- fire: function() {
- self.fireWith( this, arguments );
- return this;
- },
-
- // To know if the callbacks have already been called at least once
- fired: function() {
- return !!fired;
- }
- };
-
- return self;
-};
-
-
-function Identity( v ) {
- return v;
-}
-function Thrower( ex ) {
- throw ex;
-}
-
-function adoptValue( value, resolve, reject, noValue ) {
- var method;
-
- try {
-
- // Check for promise aspect first to privilege synchronous behavior
- if ( value && jQuery.isFunction( ( method = value.promise ) ) ) {
- method.call( value ).done( resolve ).fail( reject );
-
- // Other thenables
- } else if ( value && jQuery.isFunction( ( method = value.then ) ) ) {
- method.call( value, resolve, reject );
-
- // Other non-thenables
- } else {
-
- // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer:
- // * false: [ value ].slice( 0 ) => resolve( value )
- // * true: [ value ].slice( 1 ) => resolve()
- resolve.apply( undefined, [ value ].slice( noValue ) );
- }
-
- // For Promises/A+, convert exceptions into rejections
- // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in
- // Deferred#then to conditionally suppress rejection.
- } catch ( value ) {
-
- // Support: Android 4.0 only
- // Strict mode functions invoked without .call/.apply get global-object context
- reject.apply( undefined, [ value ] );
- }
-}
-
-jQuery.extend( {
-
- Deferred: function( func ) {
- var tuples = [
-
- // action, add listener, callbacks,
- // ... .then handlers, argument index, [final state]
- [ "notify", "progress", jQuery.Callbacks( "memory" ),
- jQuery.Callbacks( "memory" ), 2 ],
- [ "resolve", "done", jQuery.Callbacks( "once memory" ),
- jQuery.Callbacks( "once memory" ), 0, "resolved" ],
- [ "reject", "fail", jQuery.Callbacks( "once memory" ),
- jQuery.Callbacks( "once memory" ), 1, "rejected" ]
- ],
- state = "pending",
- promise = {
- state: function() {
- return state;
- },
- always: function() {
- deferred.done( arguments ).fail( arguments );
- return this;
- },
- "catch": function( fn ) {
- return promise.then( null, fn );
- },
-
- // Keep pipe for back-compat
- pipe: function( /* fnDone, fnFail, fnProgress */ ) {
- var fns = arguments;
-
- return jQuery.Deferred( function( newDefer ) {
- jQuery.each( tuples, function( i, tuple ) {
-
- // Map tuples (progress, done, fail) to arguments (done, fail, progress)
- var fn = jQuery.isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ];
-
- // deferred.progress(function() { bind to newDefer or newDefer.notify })
- // deferred.done(function() { bind to newDefer or newDefer.resolve })
- // deferred.fail(function() { bind to newDefer or newDefer.reject })
- deferred[ tuple[ 1 ] ]( function() {
- var returned = fn && fn.apply( this, arguments );
- if ( returned && jQuery.isFunction( returned.promise ) ) {
- returned.promise()
- .progress( newDefer.notify )
- .done( newDefer.resolve )
- .fail( newDefer.reject );
- } else {
- newDefer[ tuple[ 0 ] + "With" ](
- this,
- fn ? [ returned ] : arguments
- );
- }
- } );
- } );
- fns = null;
- } ).promise();
- },
- then: function( onFulfilled, onRejected, onProgress ) {
- var maxDepth = 0;
- function resolve( depth, deferred, handler, special ) {
- return function() {
- var that = this,
- args = arguments,
- mightThrow = function() {
- var returned, then;
-
- // Support: Promises/A+ section 2.3.3.3.3
- // https://promisesaplus.com/#point-59
- // Ignore double-resolution attempts
- if ( depth < maxDepth ) {
- return;
- }
-
- returned = handler.apply( that, args );
-
- // Support: Promises/A+ section 2.3.1
- // https://promisesaplus.com/#point-48
- if ( returned === deferred.promise() ) {
- throw new TypeError( "Thenable self-resolution" );
- }
-
- // Support: Promises/A+ sections 2.3.3.1, 3.5
- // https://promisesaplus.com/#point-54
- // https://promisesaplus.com/#point-75
- // Retrieve `then` only once
- then = returned &&
-
- // Support: Promises/A+ section 2.3.4
- // https://promisesaplus.com/#point-64
- // Only check objects and functions for thenability
- ( typeof returned === "object" ||
- typeof returned === "function" ) &&
- returned.then;
-
- // Handle a returned thenable
- if ( jQuery.isFunction( then ) ) {
-
- // Special processors (notify) just wait for resolution
- if ( special ) {
- then.call(
- returned,
- resolve( maxDepth, deferred, Identity, special ),
- resolve( maxDepth, deferred, Thrower, special )
- );
-
- // Normal processors (resolve) also hook into progress
- } else {
-
- // ...and disregard older resolution values
- maxDepth++;
-
- then.call(
- returned,
- resolve( maxDepth, deferred, Identity, special ),
- resolve( maxDepth, deferred, Thrower, special ),
- resolve( maxDepth, deferred, Identity,
- deferred.notifyWith )
- );
- }
-
- // Handle all other returned values
- } else {
-
- // Only substitute handlers pass on context
- // and multiple values (non-spec behavior)
- if ( handler !== Identity ) {
- that = undefined;
- args = [ returned ];
- }
-
- // Process the value(s)
- // Default process is resolve
- ( special || deferred.resolveWith )( that, args );
- }
- },
-
- // Only normal processors (resolve) catch and reject exceptions
- process = special ?
- mightThrow :
- function() {
- try {
- mightThrow();
- } catch ( e ) {
-
- if ( jQuery.Deferred.exceptionHook ) {
- jQuery.Deferred.exceptionHook( e,
- process.stackTrace );
- }
-
- // Support: Promises/A+ section 2.3.3.3.4.1
- // https://promisesaplus.com/#point-61
- // Ignore post-resolution exceptions
- if ( depth + 1 >= maxDepth ) {
-
- // Only substitute handlers pass on context
- // and multiple values (non-spec behavior)
- if ( handler !== Thrower ) {
- that = undefined;
- args = [ e ];
- }
-
- deferred.rejectWith( that, args );
- }
- }
- };
-
- // Support: Promises/A+ section 2.3.3.3.1
- // https://promisesaplus.com/#point-57
- // Re-resolve promises immediately to dodge false rejection from
- // subsequent errors
- if ( depth ) {
- process();
- } else {
-
- // Call an optional hook to record the stack, in case of exception
- // since it's otherwise lost when execution goes async
- if ( jQuery.Deferred.getStackHook ) {
- process.stackTrace = jQuery.Deferred.getStackHook();
- }
- window.setTimeout( process );
- }
- };
- }
-
- return jQuery.Deferred( function( newDefer ) {
-
- // progress_handlers.add( ... )
- tuples[ 0 ][ 3 ].add(
- resolve(
- 0,
- newDefer,
- jQuery.isFunction( onProgress ) ?
- onProgress :
- Identity,
- newDefer.notifyWith
- )
- );
-
- // fulfilled_handlers.add( ... )
- tuples[ 1 ][ 3 ].add(
- resolve(
- 0,
- newDefer,
- jQuery.isFunction( onFulfilled ) ?
- onFulfilled :
- Identity
- )
- );
-
- // rejected_handlers.add( ... )
- tuples[ 2 ][ 3 ].add(
- resolve(
- 0,
- newDefer,
- jQuery.isFunction( onRejected ) ?
- onRejected :
- Thrower
- )
- );
- } ).promise();
- },
-
- // Get a promise for this deferred
- // If obj is provided, the promise aspect is added to the object
- promise: function( obj ) {
- return obj != null ? jQuery.extend( obj, promise ) : promise;
- }
- },
- deferred = {};
-
- // Add list-specific methods
- jQuery.each( tuples, function( i, tuple ) {
- var list = tuple[ 2 ],
- stateString = tuple[ 5 ];
-
- // promise.progress = list.add
- // promise.done = list.add
- // promise.fail = list.add
- promise[ tuple[ 1 ] ] = list.add;
-
- // Handle state
- if ( stateString ) {
- list.add(
- function() {
-
- // state = "resolved" (i.e., fulfilled)
- // state = "rejected"
- state = stateString;
- },
-
- // rejected_callbacks.disable
- // fulfilled_callbacks.disable
- tuples[ 3 - i ][ 2 ].disable,
-
- // progress_callbacks.lock
- tuples[ 0 ][ 2 ].lock
- );
- }
-
- // progress_handlers.fire
- // fulfilled_handlers.fire
- // rejected_handlers.fire
- list.add( tuple[ 3 ].fire );
-
- // deferred.notify = function() { deferred.notifyWith(...) }
- // deferred.resolve = function() { deferred.resolveWith(...) }
- // deferred.reject = function() { deferred.rejectWith(...) }
- deferred[ tuple[ 0 ] ] = function() {
- deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments );
- return this;
- };
-
- // deferred.notifyWith = list.fireWith
- // deferred.resolveWith = list.fireWith
- // deferred.rejectWith = list.fireWith
- deferred[ tuple[ 0 ] + "With" ] = list.fireWith;
- } );
-
- // Make the deferred a promise
- promise.promise( deferred );
-
- // Call given func if any
- if ( func ) {
- func.call( deferred, deferred );
- }
-
- // All done!
- return deferred;
- },
-
- // Deferred helper
- when: function( singleValue ) {
- var
-
- // count of uncompleted subordinates
- remaining = arguments.length,
-
- // count of unprocessed arguments
- i = remaining,
-
- // subordinate fulfillment data
- resolveContexts = Array( i ),
- resolveValues = slice.call( arguments ),
-
- // the master Deferred
- master = jQuery.Deferred(),
-
- // subordinate callback factory
- updateFunc = function( i ) {
- return function( value ) {
- resolveContexts[ i ] = this;
- resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
- if ( !( --remaining ) ) {
- master.resolveWith( resolveContexts, resolveValues );
- }
- };
- };
-
- // Single- and empty arguments are adopted like Promise.resolve
- if ( remaining <= 1 ) {
- adoptValue( singleValue, master.done( updateFunc( i ) ).resolve, master.reject,
- !remaining );
-
- // Use .then() to unwrap secondary thenables (cf. gh-3000)
- if ( master.state() === "pending" ||
- jQuery.isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) {
-
- return master.then();
- }
- }
-
- // Multiple arguments are aggregated like Promise.all array elements
- while ( i-- ) {
- adoptValue( resolveValues[ i ], updateFunc( i ), master.reject );
- }
-
- return master.promise();
- }
-} );
-
-
-// These usually indicate a programmer mistake during development,
-// warn about them ASAP rather than swallowing them by default.
-var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/;
-
-jQuery.Deferred.exceptionHook = function( error, stack ) {
-
- // Support: IE 8 - 9 only
- // Console exists when dev tools are open, which can happen at any time
- if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) {
- window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack );
- }
-};
-
-
-
-
-jQuery.readyException = function( error ) {
- window.setTimeout( function() {
- throw error;
- } );
-};
-
-
-
-
-// The deferred used on DOM ready
-var readyList = jQuery.Deferred();
-
-jQuery.fn.ready = function( fn ) {
-
- readyList
- .then( fn )
-
- // Wrap jQuery.readyException in a function so that the lookup
- // happens at the time of error handling instead of callback
- // registration.
- .catch( function( error ) {
- jQuery.readyException( error );
- } );
-
- return this;
-};
-
-jQuery.extend( {
-
- // Is the DOM ready to be used? Set to true once it occurs.
- isReady: false,
-
- // A counter to track how many items to wait for before
- // the ready event fires. See #6781
- readyWait: 1,
-
- // Handle when the DOM is ready
- ready: function( wait ) {
-
- // Abort if there are pending holds or we're already ready
- if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
- return;
- }
-
- // Remember that the DOM is ready
- jQuery.isReady = true;
-
- // If a normal DOM Ready event fired, decrement, and wait if need be
- if ( wait !== true && --jQuery.readyWait > 0 ) {
- return;
- }
-
- // If there are functions bound, to execute
- readyList.resolveWith( document, [ jQuery ] );
- }
-} );
-
-jQuery.ready.then = readyList.then;
-
-// The ready event handler and self cleanup method
-function completed() {
- document.removeEventListener( "DOMContentLoaded", completed );
- window.removeEventListener( "load", completed );
- jQuery.ready();
-}
-
-// Catch cases where $(document).ready() is called
-// after the browser event has already occurred.
-// Support: IE <=9 - 10 only
-// Older IE sometimes signals "interactive" too soon
-if ( document.readyState === "complete" ||
- ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) {
-
- // Handle it asynchronously to allow scripts the opportunity to delay ready
- window.setTimeout( jQuery.ready );
-
-} else {
-
- // Use the handy event callback
- document.addEventListener( "DOMContentLoaded", completed );
-
- // A fallback to window.onload, that will always work
- window.addEventListener( "load", completed );
-}
-
-
-
-
-// Multifunctional method to get and set values of a collection
-// The value/s can optionally be executed if it's a function
-var access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
- var i = 0,
- len = elems.length,
- bulk = key == null;
-
- // Sets many values
- if ( jQuery.type( key ) === "object" ) {
- chainable = true;
- for ( i in key ) {
- access( elems, fn, i, key[ i ], true, emptyGet, raw );
- }
-
- // Sets one value
- } else if ( value !== undefined ) {
- chainable = true;
-
- if ( !jQuery.isFunction( value ) ) {
- raw = true;
- }
-
- if ( bulk ) {
-
- // Bulk operations run against the entire set
- if ( raw ) {
- fn.call( elems, value );
- fn = null;
-
- // ...except when executing function values
- } else {
- bulk = fn;
- fn = function( elem, key, value ) {
- return bulk.call( jQuery( elem ), value );
- };
- }
- }
-
- if ( fn ) {
- for ( ; i < len; i++ ) {
- fn(
- elems[ i ], key, raw ?
- value :
- value.call( elems[ i ], i, fn( elems[ i ], key ) )
- );
- }
- }
- }
-
- if ( chainable ) {
- return elems;
- }
-
- // Gets
- if ( bulk ) {
- return fn.call( elems );
- }
-
- return len ? fn( elems[ 0 ], key ) : emptyGet;
-};
-var acceptData = function( owner ) {
-
- // Accepts only:
- // - Node
- // - Node.ELEMENT_NODE
- // - Node.DOCUMENT_NODE
- // - Object
- // - Any
- return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType );
-};
-
-
-
-
-function Data() {
- this.expando = jQuery.expando + Data.uid++;
-}
-
-Data.uid = 1;
-
-Data.prototype = {
-
- cache: function( owner ) {
-
- // Check if the owner object already has a cache
- var value = owner[ this.expando ];
-
- // If not, create one
- if ( !value ) {
- value = {};
-
- // We can accept data for non-element nodes in modern browsers,
- // but we should not, see #8335.
- // Always return an empty object.
- if ( acceptData( owner ) ) {
-
- // If it is a node unlikely to be stringify-ed or looped over
- // use plain assignment
- if ( owner.nodeType ) {
- owner[ this.expando ] = value;
-
- // Otherwise secure it in a non-enumerable property
- // configurable must be true to allow the property to be
- // deleted when data is removed
- } else {
- Object.defineProperty( owner, this.expando, {
- value: value,
- configurable: true
- } );
- }
- }
- }
-
- return value;
- },
- set: function( owner, data, value ) {
- var prop,
- cache = this.cache( owner );
-
- // Handle: [ owner, key, value ] args
- // Always use camelCase key (gh-2257)
- if ( typeof data === "string" ) {
- cache[ jQuery.camelCase( data ) ] = value;
-
- // Handle: [ owner, { properties } ] args
- } else {
-
- // Copy the properties one-by-one to the cache object
- for ( prop in data ) {
- cache[ jQuery.camelCase( prop ) ] = data[ prop ];
- }
- }
- return cache;
- },
- get: function( owner, key ) {
- return key === undefined ?
- this.cache( owner ) :
-
- // Always use camelCase key (gh-2257)
- owner[ this.expando ] && owner[ this.expando ][ jQuery.camelCase( key ) ];
- },
- access: function( owner, key, value ) {
-
- // In cases where either:
- //
- // 1. No key was specified
- // 2. A string key was specified, but no value provided
- //
- // Take the "read" path and allow the get method to determine
- // which value to return, respectively either:
- //
- // 1. The entire cache object
- // 2. The data stored at the key
- //
- if ( key === undefined ||
- ( ( key && typeof key === "string" ) && value === undefined ) ) {
-
- return this.get( owner, key );
- }
-
- // When the key is not a string, or both a key and value
- // are specified, set or extend (existing objects) with either:
- //
- // 1. An object of properties
- // 2. A key and value
- //
- this.set( owner, key, value );
-
- // Since the "set" path can have two possible entry points
- // return the expected data based on which path was taken[*]
- return value !== undefined ? value : key;
- },
- remove: function( owner, key ) {
- var i,
- cache = owner[ this.expando ];
-
- if ( cache === undefined ) {
- return;
- }
-
- if ( key !== undefined ) {
-
- // Support array or space separated string of keys
- if ( Array.isArray( key ) ) {
-
- // If key is an array of keys...
- // We always set camelCase keys, so remove that.
- key = key.map( jQuery.camelCase );
- } else {
- key = jQuery.camelCase( key );
-
- // If a key with the spaces exists, use it.
- // Otherwise, create an array by matching non-whitespace
- key = key in cache ?
- [ key ] :
- ( key.match( rnothtmlwhite ) || [] );
- }
-
- i = key.length;
-
- while ( i-- ) {
- delete cache[ key[ i ] ];
- }
- }
-
- // Remove the expando if there's no more data
- if ( key === undefined || jQuery.isEmptyObject( cache ) ) {
-
- // Support: Chrome <=35 - 45
- // Webkit & Blink performance suffers when deleting properties
- // from DOM nodes, so set to undefined instead
- // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted)
- if ( owner.nodeType ) {
- owner[ this.expando ] = undefined;
- } else {
- delete owner[ this.expando ];
- }
- }
- },
- hasData: function( owner ) {
- var cache = owner[ this.expando ];
- return cache !== undefined && !jQuery.isEmptyObject( cache );
- }
-};
-var dataPriv = new Data();
-
-var dataUser = new Data();
-
-
-
-// Implementation Summary
-//
-// 1. Enforce API surface and semantic compatibility with 1.9.x branch
-// 2. Improve the module's maintainability by reducing the storage
-// paths to a single mechanism.
-// 3. Use the same single mechanism to support "private" and "user" data.
-// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData)
-// 5. Avoid exposing implementation details on user objects (eg. expando properties)
-// 6. Provide a clear path for implementation upgrade to WeakMap in 2014
-
-var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
- rmultiDash = /[A-Z]/g;
-
-function getData( data ) {
- if ( data === "true" ) {
- return true;
- }
-
- if ( data === "false" ) {
- return false;
- }
-
- if ( data === "null" ) {
- return null;
- }
-
- // Only convert to a number if it doesn't change the string
- if ( data === +data + "" ) {
- return +data;
- }
-
- if ( rbrace.test( data ) ) {
- return JSON.parse( data );
- }
-
- return data;
-}
-
-function dataAttr( elem, key, data ) {
- var name;
-
- // If nothing was found internally, try to fetch any
- // data from the HTML5 data-* attribute
- if ( data === undefined && elem.nodeType === 1 ) {
- name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase();
- data = elem.getAttribute( name );
-
- if ( typeof data === "string" ) {
- try {
- data = getData( data );
- } catch ( e ) {}
-
- // Make sure we set the data so it isn't changed later
- dataUser.set( elem, key, data );
- } else {
- data = undefined;
- }
- }
- return data;
-}
-
-jQuery.extend( {
- hasData: function( elem ) {
- return dataUser.hasData( elem ) || dataPriv.hasData( elem );
- },
-
- data: function( elem, name, data ) {
- return dataUser.access( elem, name, data );
- },
-
- removeData: function( elem, name ) {
- dataUser.remove( elem, name );
- },
-
- // TODO: Now that all calls to _data and _removeData have been replaced
- // with direct calls to dataPriv methods, these can be deprecated.
- _data: function( elem, name, data ) {
- return dataPriv.access( elem, name, data );
- },
-
- _removeData: function( elem, name ) {
- dataPriv.remove( elem, name );
- }
-} );
-
-jQuery.fn.extend( {
- data: function( key, value ) {
- var i, name, data,
- elem = this[ 0 ],
- attrs = elem && elem.attributes;
-
- // Gets all values
- if ( key === undefined ) {
- if ( this.length ) {
- data = dataUser.get( elem );
-
- if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) {
- i = attrs.length;
- while ( i-- ) {
-
- // Support: IE 11 only
- // The attrs elements can be null (#14894)
- if ( attrs[ i ] ) {
- name = attrs[ i ].name;
- if ( name.indexOf( "data-" ) === 0 ) {
- name = jQuery.camelCase( name.slice( 5 ) );
- dataAttr( elem, name, data[ name ] );
- }
- }
- }
- dataPriv.set( elem, "hasDataAttrs", true );
- }
- }
-
- return data;
- }
-
- // Sets multiple values
- if ( typeof key === "object" ) {
- return this.each( function() {
- dataUser.set( this, key );
- } );
- }
-
- return access( this, function( value ) {
- var data;
-
- // The calling jQuery object (element matches) is not empty
- // (and therefore has an element appears at this[ 0 ]) and the
- // `value` parameter was not undefined. An empty jQuery object
- // will result in `undefined` for elem = this[ 0 ] which will
- // throw an exception if an attempt to read a data cache is made.
- if ( elem && value === undefined ) {
-
- // Attempt to get data from the cache
- // The key will always be camelCased in Data
- data = dataUser.get( elem, key );
- if ( data !== undefined ) {
- return data;
- }
-
- // Attempt to "discover" the data in
- // HTML5 custom data-* attrs
- data = dataAttr( elem, key );
- if ( data !== undefined ) {
- return data;
- }
-
- // We tried really hard, but the data doesn't exist.
- return;
- }
-
- // Set the data...
- this.each( function() {
-
- // We always store the camelCased key
- dataUser.set( this, key, value );
- } );
- }, null, value, arguments.length > 1, null, true );
- },
-
- removeData: function( key ) {
- return this.each( function() {
- dataUser.remove( this, key );
- } );
- }
-} );
-
-
-jQuery.extend( {
- queue: function( elem, type, data ) {
- var queue;
-
- if ( elem ) {
- type = ( type || "fx" ) + "queue";
- queue = dataPriv.get( elem, type );
-
- // Speed up dequeue by getting out quickly if this is just a lookup
- if ( data ) {
- if ( !queue || Array.isArray( data ) ) {
- queue = dataPriv.access( elem, type, jQuery.makeArray( data ) );
- } else {
- queue.push( data );
- }
- }
- return queue || [];
- }
- },
-
- dequeue: function( elem, type ) {
- type = type || "fx";
-
- var queue = jQuery.queue( elem, type ),
- startLength = queue.length,
- fn = queue.shift(),
- hooks = jQuery._queueHooks( elem, type ),
- next = function() {
- jQuery.dequeue( elem, type );
- };
-
- // If the fx queue is dequeued, always remove the progress sentinel
- if ( fn === "inprogress" ) {
- fn = queue.shift();
- startLength--;
- }
-
- if ( fn ) {
-
- // Add a progress sentinel to prevent the fx queue from being
- // automatically dequeued
- if ( type === "fx" ) {
- queue.unshift( "inprogress" );
- }
-
- // Clear up the last queue stop function
- delete hooks.stop;
- fn.call( elem, next, hooks );
- }
-
- if ( !startLength && hooks ) {
- hooks.empty.fire();
- }
- },
-
- // Not public - generate a queueHooks object, or return the current one
- _queueHooks: function( elem, type ) {
- var key = type + "queueHooks";
- return dataPriv.get( elem, key ) || dataPriv.access( elem, key, {
- empty: jQuery.Callbacks( "once memory" ).add( function() {
- dataPriv.remove( elem, [ type + "queue", key ] );
- } )
- } );
- }
-} );
-
-jQuery.fn.extend( {
- queue: function( type, data ) {
- var setter = 2;
-
- if ( typeof type !== "string" ) {
- data = type;
- type = "fx";
- setter--;
- }
-
- if ( arguments.length < setter ) {
- return jQuery.queue( this[ 0 ], type );
- }
-
- return data === undefined ?
- this :
- this.each( function() {
- var queue = jQuery.queue( this, type, data );
-
- // Ensure a hooks for this queue
- jQuery._queueHooks( this, type );
-
- if ( type === "fx" && queue[ 0 ] !== "inprogress" ) {
- jQuery.dequeue( this, type );
- }
- } );
- },
- dequeue: function( type ) {
- return this.each( function() {
- jQuery.dequeue( this, type );
- } );
- },
- clearQueue: function( type ) {
- return this.queue( type || "fx", [] );
- },
-
- // Get a promise resolved when queues of a certain type
- // are emptied (fx is the type by default)
- promise: function( type, obj ) {
- var tmp,
- count = 1,
- defer = jQuery.Deferred(),
- elements = this,
- i = this.length,
- resolve = function() {
- if ( !( --count ) ) {
- defer.resolveWith( elements, [ elements ] );
- }
- };
-
- if ( typeof type !== "string" ) {
- obj = type;
- type = undefined;
- }
- type = type || "fx";
-
- while ( i-- ) {
- tmp = dataPriv.get( elements[ i ], type + "queueHooks" );
- if ( tmp && tmp.empty ) {
- count++;
- tmp.empty.add( resolve );
- }
- }
- resolve();
- return defer.promise( obj );
- }
-} );
-var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source;
-
-var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" );
-
-
-var cssExpand = [ "Top", "Right", "Bottom", "Left" ];
-
-var isHiddenWithinTree = function( elem, el ) {
-
- // isHiddenWithinTree might be called from jQuery#filter function;
- // in that case, element will be second argument
- elem = el || elem;
-
- // Inline style trumps all
- return elem.style.display === "none" ||
- elem.style.display === "" &&
-
- // Otherwise, check computed style
- // Support: Firefox <=43 - 45
- // Disconnected elements can have computed display: none, so first confirm that elem is
- // in the document.
- jQuery.contains( elem.ownerDocument, elem ) &&
-
- jQuery.css( elem, "display" ) === "none";
- };
-
-var swap = function( elem, options, callback, args ) {
- var ret, name,
- old = {};
-
- // Remember the old values, and insert the new ones
- for ( name in options ) {
- old[ name ] = elem.style[ name ];
- elem.style[ name ] = options[ name ];
- }
-
- ret = callback.apply( elem, args || [] );
-
- // Revert the old values
- for ( name in options ) {
- elem.style[ name ] = old[ name ];
- }
-
- return ret;
-};
-
-
-
-
-function adjustCSS( elem, prop, valueParts, tween ) {
- var adjusted,
- scale = 1,
- maxIterations = 20,
- currentValue = tween ?
- function() {
- return tween.cur();
- } :
- function() {
- return jQuery.css( elem, prop, "" );
- },
- initial = currentValue(),
- unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
-
- // Starting value computation is required for potential unit mismatches
- initialInUnit = ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) &&
- rcssNum.exec( jQuery.css( elem, prop ) );
-
- if ( initialInUnit && initialInUnit[ 3 ] !== unit ) {
-
- // Trust units reported by jQuery.css
- unit = unit || initialInUnit[ 3 ];
-
- // Make sure we update the tween properties later on
- valueParts = valueParts || [];
-
- // Iteratively approximate from a nonzero starting point
- initialInUnit = +initial || 1;
-
- do {
-
- // If previous iteration zeroed out, double until we get *something*.
- // Use string for doubling so we don't accidentally see scale as unchanged below
- scale = scale || ".5";
-
- // Adjust and apply
- initialInUnit = initialInUnit / scale;
- jQuery.style( elem, prop, initialInUnit + unit );
-
- // Update scale, tolerating zero or NaN from tween.cur()
- // Break the loop if scale is unchanged or perfect, or if we've just had enough.
- } while (
- scale !== ( scale = currentValue() / initial ) && scale !== 1 && --maxIterations
- );
- }
-
- if ( valueParts ) {
- initialInUnit = +initialInUnit || +initial || 0;
-
- // Apply relative offset (+=/-=) if specified
- adjusted = valueParts[ 1 ] ?
- initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] :
- +valueParts[ 2 ];
- if ( tween ) {
- tween.unit = unit;
- tween.start = initialInUnit;
- tween.end = adjusted;
- }
- }
- return adjusted;
-}
-
-
-var defaultDisplayMap = {};
-
-function getDefaultDisplay( elem ) {
- var temp,
- doc = elem.ownerDocument,
- nodeName = elem.nodeName,
- display = defaultDisplayMap[ nodeName ];
-
- if ( display ) {
- return display;
- }
-
- temp = doc.body.appendChild( doc.createElement( nodeName ) );
- display = jQuery.css( temp, "display" );
-
- temp.parentNode.removeChild( temp );
-
- if ( display === "none" ) {
- display = "block";
- }
- defaultDisplayMap[ nodeName ] = display;
-
- return display;
-}
-
-function showHide( elements, show ) {
- var display, elem,
- values = [],
- index = 0,
- length = elements.length;
-
- // Determine new display value for elements that need to change
- for ( ; index < length; index++ ) {
- elem = elements[ index ];
- if ( !elem.style ) {
- continue;
- }
-
- display = elem.style.display;
- if ( show ) {
-
- // Since we force visibility upon cascade-hidden elements, an immediate (and slow)
- // check is required in this first loop unless we have a nonempty display value (either
- // inline or about-to-be-restored)
- if ( display === "none" ) {
- values[ index ] = dataPriv.get( elem, "display" ) || null;
- if ( !values[ index ] ) {
- elem.style.display = "";
- }
- }
- if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) {
- values[ index ] = getDefaultDisplay( elem );
- }
- } else {
- if ( display !== "none" ) {
- values[ index ] = "none";
-
- // Remember what we're overwriting
- dataPriv.set( elem, "display", display );
- }
- }
- }
-
- // Set the display of the elements in a second loop to avoid constant reflow
- for ( index = 0; index < length; index++ ) {
- if ( values[ index ] != null ) {
- elements[ index ].style.display = values[ index ];
- }
- }
-
- return elements;
-}
-
-jQuery.fn.extend( {
- show: function() {
- return showHide( this, true );
- },
- hide: function() {
- return showHide( this );
- },
- toggle: function( state ) {
- if ( typeof state === "boolean" ) {
- return state ? this.show() : this.hide();
- }
-
- return this.each( function() {
- if ( isHiddenWithinTree( this ) ) {
- jQuery( this ).show();
- } else {
- jQuery( this ).hide();
- }
- } );
- }
-} );
-var rcheckableType = ( /^(?:checkbox|radio)$/i );
-
-var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]+)/i );
-
-var rscriptType = ( /^$|\/(?:java|ecma)script/i );
-
-
-
-// We have to close these tags to support XHTML (#13200)
-var wrapMap = {
-
- // Support: IE <=9 only
- option: [ 1, "<select multiple='multiple'>", "</select>" ],
-
- // XHTML parsers do not magically insert elements in the
- // same way that tag soup parsers do. So we cannot shorten
- // this by omitting <tbody> or other required elements.
- thead: [ 1, "<table>", "</table>" ],
- col: [ 2, "<table><colgroup>", "</colgroup></table>" ],
- tr: [ 2, "<table><tbody>", "</tbody></table>" ],
- td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
-
- _default: [ 0, "", "" ]
-};
-
-// Support: IE <=9 only
-wrapMap.optgroup = wrapMap.option;
-
-wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
-wrapMap.th = wrapMap.td;
-
-
-function getAll( context, tag ) {
-
- // Support: IE <=9 - 11 only
- // Use typeof to avoid zero-argument method invocation on host objects (#15151)
- var ret;
-
- if ( typeof context.getElementsByTagName !== "undefined" ) {
- ret = context.getElementsByTagName( tag || "*" );
-
- } else if ( typeof context.querySelectorAll !== "undefined" ) {
- ret = context.querySelectorAll( tag || "*" );
-
- } else {
- ret = [];
- }
-
- if ( tag === undefined || tag && nodeName( context, tag ) ) {
- return jQuery.merge( [ context ], ret );
- }
-
- return ret;
-}
-
-
-// Mark scripts as having already been evaluated
-function setGlobalEval( elems, refElements ) {
- var i = 0,
- l = elems.length;
-
- for ( ; i < l; i++ ) {
- dataPriv.set(
- elems[ i ],
- "globalEval",
- !refElements || dataPriv.get( refElements[ i ], "globalEval" )
- );
- }
-}
-
-
-var rhtml = /<|&#?\w+;/;
-
-function buildFragment( elems, context, scripts, selection, ignored ) {
- var elem, tmp, tag, wrap, contains, j,
- fragment = context.createDocumentFragment(),
- nodes = [],
- i = 0,
- l = elems.length;
-
- for ( ; i < l; i++ ) {
- elem = elems[ i ];
-
- if ( elem || elem === 0 ) {
-
- // Add nodes directly
- if ( jQuery.type( elem ) === "object" ) {
-
- // Support: Android <=4.0 only, PhantomJS 1 only
- // push.apply(_, arraylike) throws on ancient WebKit
- jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );
-
- // Convert non-html into a text node
- } else if ( !rhtml.test( elem ) ) {
- nodes.push( context.createTextNode( elem ) );
-
- // Convert html into DOM nodes
- } else {
- tmp = tmp || fragment.appendChild( context.createElement( "div" ) );
-
- // Deserialize a standard representation
- tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase();
- wrap = wrapMap[ tag ] || wrapMap._default;
- tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ];
-
- // Descend through wrappers to the right content
- j = wrap[ 0 ];
- while ( j-- ) {
- tmp = tmp.lastChild;
- }
-
- // Support: Android <=4.0 only, PhantomJS 1 only
- // push.apply(_, arraylike) throws on ancient WebKit
- jQuery.merge( nodes, tmp.childNodes );
-
- // Remember the top-level container
- tmp = fragment.firstChild;
-
- // Ensure the created nodes are orphaned (#12392)
- tmp.textContent = "";
- }
- }
- }
-
- // Remove wrapper from fragment
- fragment.textContent = "";
-
- i = 0;
- while ( ( elem = nodes[ i++ ] ) ) {
-
- // Skip elements already in the context collection (trac-4087)
- if ( selection && jQuery.inArray( elem, selection ) > -1 ) {
- if ( ignored ) {
- ignored.push( elem );
- }
- continue;
- }
-
- contains = jQuery.contains( elem.ownerDocument, elem );
-
- // Append to fragment
- tmp = getAll( fragment.appendChild( elem ), "script" );
-
- // Preserve script evaluation history
- if ( contains ) {
- setGlobalEval( tmp );
- }
-
- // Capture executables
- if ( scripts ) {
- j = 0;
- while ( ( elem = tmp[ j++ ] ) ) {
- if ( rscriptType.test( elem.type || "" ) ) {
- scripts.push( elem );
- }
- }
- }
- }
-
- return fragment;
-}
-
-
-( function() {
- var fragment = document.createDocumentFragment(),
- div = fragment.appendChild( document.createElement( "div" ) ),
- input = document.createElement( "input" );
-
- // Support: Android 4.0 - 4.3 only
- // Check state lost if the name is set (#11217)
- // Support: Windows Web Apps (WWA)
- // `name` and `type` must use .setAttribute for WWA (#14901)
- input.setAttribute( "type", "radio" );
- input.setAttribute( "checked", "checked" );
- input.setAttribute( "name", "t" );
-
- div.appendChild( input );
-
- // Support: Android <=4.1 only
- // Older WebKit doesn't clone checked state correctly in fragments
- support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
-
- // Support: IE <=11 only
- // Make sure textarea (and checkbox) defaultValue is properly cloned
- div.innerHTML = "<textarea>x</textarea>";
- support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
-} )();
-var documentElement = document.documentElement;
-
-
-
-var
- rkeyEvent = /^key/,
- rmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/,
- rtypenamespace = /^([^.]*)(?:\.(.+)|)/;
-
-function returnTrue() {
- return true;
-}
-
-function returnFalse() {
- return false;
-}
-
-// Support: IE <=9 only
-// See #13393 for more info
-function safeActiveElement() {
- try {
- return document.activeElement;
- } catch ( err ) { }
-}
-
-function on( elem, types, selector, data, fn, one ) {
- var origFn, type;
-
- // Types can be a map of types/handlers
- if ( typeof types === "object" ) {
-
- // ( types-Object, selector, data )
- if ( typeof selector !== "string" ) {
-
- // ( types-Object, data )
- data = data || selector;
- selector = undefined;
- }
- for ( type in types ) {
- on( elem, type, selector, data, types[ type ], one );
- }
- return elem;
- }
-
- if ( data == null && fn == null ) {
-
- // ( types, fn )
- fn = selector;
- data = selector = undefined;
- } else if ( fn == null ) {
- if ( typeof selector === "string" ) {
-
- // ( types, selector, fn )
- fn = data;
- data = undefined;
- } else {
-
- // ( types, data, fn )
- fn = data;
- data = selector;
- selector = undefined;
- }
- }
- if ( fn === false ) {
- fn = returnFalse;
- } else if ( !fn ) {
- return elem;
- }
-
- if ( one === 1 ) {
- origFn = fn;
- fn = function( event ) {
-
- // Can use an empty set, since event contains the info
- jQuery().off( event );
- return origFn.apply( this, arguments );
- };
-
- // Use same guid so caller can remove using origFn
- fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
- }
- return elem.each( function() {
- jQuery.event.add( this, types, fn, data, selector );
- } );
-}
-
-/*
- * Helper functions for managing events -- not part of the public interface.
- * Props to Dean Edwards' addEvent library for many of the ideas.
- */
-jQuery.event = {
-
- global: {},
-
- add: function( elem, types, handler, data, selector ) {
-
- var handleObjIn, eventHandle, tmp,
- events, t, handleObj,
- special, handlers, type, namespaces, origType,
- elemData = dataPriv.get( elem );
-
- // Don't attach events to noData or text/comment nodes (but allow plain objects)
- if ( !elemData ) {
- return;
- }
-
- // Caller can pass in an object of custom data in lieu of the handler
- if ( handler.handler ) {
- handleObjIn = handler;
- handler = handleObjIn.handler;
- selector = handleObjIn.selector;
- }
-
- // Ensure that invalid selectors throw exceptions at attach time
- // Evaluate against documentElement in case elem is a non-element node (e.g., document)
- if ( selector ) {
- jQuery.find.matchesSelector( documentElement, selector );
- }
-
- // Make sure that the handler has a unique ID, used to find/remove it later
- if ( !handler.guid ) {
- handler.guid = jQuery.guid++;
- }
-
- // Init the element's event structure and main handler, if this is the first
- if ( !( events = elemData.events ) ) {
- events = elemData.events = {};
- }
- if ( !( eventHandle = elemData.handle ) ) {
- eventHandle = elemData.handle = function( e ) {
-
- // Discard the second event of a jQuery.event.trigger() and
- // when an event is called after a page has unloaded
- return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ?
- jQuery.event.dispatch.apply( elem, arguments ) : undefined;
- };
- }
-
- // Handle multiple events separated by a space
- types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
- t = types.length;
- while ( t-- ) {
- tmp = rtypenamespace.exec( types[ t ] ) || [];
- type = origType = tmp[ 1 ];
- namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
-
- // There *must* be a type, no attaching namespace-only handlers
- if ( !type ) {
- continue;
- }
-
- // If event changes its type, use the special event handlers for the changed type
- special = jQuery.event.special[ type ] || {};
-
- // If selector defined, determine special event api type, otherwise given type
- type = ( selector ? special.delegateType : special.bindType ) || type;
-
- // Update special based on newly reset type
- special = jQuery.event.special[ type ] || {};
-
- // handleObj is passed to all event handlers
- handleObj = jQuery.extend( {
- type: type,
- origType: origType,
- data: data,
- handler: handler,
- guid: handler.guid,
- selector: selector,
- needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
- namespace: namespaces.join( "." )
- }, handleObjIn );
-
- // Init the event handler queue if we're the first
- if ( !( handlers = events[ type ] ) ) {
- handlers = events[ type ] = [];
- handlers.delegateCount = 0;
-
- // Only use addEventListener if the special events handler returns false
- if ( !special.setup ||
- special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
-
- if ( elem.addEventListener ) {
- elem.addEventListener( type, eventHandle );
- }
- }
- }
-
- if ( special.add ) {
- special.add.call( elem, handleObj );
-
- if ( !handleObj.handler.guid ) {
- handleObj.handler.guid = handler.guid;
- }
- }
-
- // Add to the element's handler list, delegates in front
- if ( selector ) {
- handlers.splice( handlers.delegateCount++, 0, handleObj );
- } else {
- handlers.push( handleObj );
- }
-
- // Keep track of which events have ever been used, for event optimization
- jQuery.event.global[ type ] = true;
- }
-
- },
-
- // Detach an event or set of events from an element
- remove: function( elem, types, handler, selector, mappedTypes ) {
-
- var j, origCount, tmp,
- events, t, handleObj,
- special, handlers, type, namespaces, origType,
- elemData = dataPriv.hasData( elem ) && dataPriv.get( elem );
-
- if ( !elemData || !( events = elemData.events ) ) {
- return;
- }
-
- // Once for each type.namespace in types; type may be omitted
- types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
- t = types.length;
- while ( t-- ) {
- tmp = rtypenamespace.exec( types[ t ] ) || [];
- type = origType = tmp[ 1 ];
- namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
-
- // Unbind all events (on this namespace, if provided) for the element
- if ( !type ) {
- for ( type in events ) {
- jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
- }
- continue;
- }
-
- special = jQuery.event.special[ type ] || {};
- type = ( selector ? special.delegateType : special.bindType ) || type;
- handlers = events[ type ] || [];
- tmp = tmp[ 2 ] &&
- new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" );
-
- // Remove matching events
- origCount = j = handlers.length;
- while ( j-- ) {
- handleObj = handlers[ j ];
-
- if ( ( mappedTypes || origType === handleObj.origType ) &&
- ( !handler || handler.guid === handleObj.guid ) &&
- ( !tmp || tmp.test( handleObj.namespace ) ) &&
- ( !selector || selector === handleObj.selector ||
- selector === "**" && handleObj.selector ) ) {
- handlers.splice( j, 1 );
-
- if ( handleObj.selector ) {
- handlers.delegateCount--;
- }
- if ( special.remove ) {
- special.remove.call( elem, handleObj );
- }
- }
- }
-
- // Remove generic event handler if we removed something and no more handlers exist
- // (avoids potential for endless recursion during removal of special event handlers)
- if ( origCount && !handlers.length ) {
- if ( !special.teardown ||
- special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
-
- jQuery.removeEvent( elem, type, elemData.handle );
- }
-
- delete events[ type ];
- }
- }
-
- // Remove data and the expando if it's no longer used
- if ( jQuery.isEmptyObject( events ) ) {
- dataPriv.remove( elem, "handle events" );
- }
- },
-
- dispatch: function( nativeEvent ) {
-
- // Make a writable jQuery.Event from the native event object
- var event = jQuery.event.fix( nativeEvent );
-
- var i, j, ret, matched, handleObj, handlerQueue,
- args = new Array( arguments.length ),
- handlers = ( dataPriv.get( this, "events" ) || {} )[ event.type ] || [],
- special = jQuery.event.special[ event.type ] || {};
-
- // Use the fix-ed jQuery.Event rather than the (read-only) native event
- args[ 0 ] = event;
-
- for ( i = 1; i < arguments.length; i++ ) {
- args[ i ] = arguments[ i ];
- }
-
- event.delegateTarget = this;
-
- // Call the preDispatch hook for the mapped type, and let it bail if desired
- if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
- return;
- }
-
- // Determine handlers
- handlerQueue = jQuery.event.handlers.call( this, event, handlers );
-
- // Run delegates first; they may want to stop propagation beneath us
- i = 0;
- while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) {
- event.currentTarget = matched.elem;
-
- j = 0;
- while ( ( handleObj = matched.handlers[ j++ ] ) &&
- !event.isImmediatePropagationStopped() ) {
-
- // Triggered event must either 1) have no namespace, or 2) have namespace(s)
- // a subset or equal to those in the bound event (both can have no namespace).
- if ( !event.rnamespace || event.rnamespace.test( handleObj.namespace ) ) {
-
- event.handleObj = handleObj;
- event.data = handleObj.data;
-
- ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle ||
- handleObj.handler ).apply( matched.elem, args );
-
- if ( ret !== undefined ) {
- if ( ( event.result = ret ) === false ) {
- event.preventDefault();
- event.stopPropagation();
- }
- }
- }
- }
- }
-
- // Call the postDispatch hook for the mapped type
- if ( special.postDispatch ) {
- special.postDispatch.call( this, event );
- }
-
- return event.result;
- },
-
- handlers: function( event, handlers ) {
- var i, handleObj, sel, matchedHandlers, matchedSelectors,
- handlerQueue = [],
- delegateCount = handlers.delegateCount,
- cur = event.target;
-
- // Find delegate handlers
- if ( delegateCount &&
-
- // Support: IE <=9
- // Black-hole SVG <use> instance trees (trac-13180)
- cur.nodeType &&
-
- // Support: Firefox <=42
- // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861)
- // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click
- // Support: IE 11 only
- // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343)
- !( event.type === "click" && event.button >= 1 ) ) {
-
- for ( ; cur !== this; cur = cur.parentNode || this ) {
-
- // Don't check non-elements (#13208)
- // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
- if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) {
- matchedHandlers = [];
- matchedSelectors = {};
- for ( i = 0; i < delegateCount; i++ ) {
- handleObj = handlers[ i ];
-
- // Don't conflict with Object.prototype properties (#13203)
- sel = handleObj.selector + " ";
-
- if ( matchedSelectors[ sel ] === undefined ) {
- matchedSelectors[ sel ] = handleObj.needsContext ?
- jQuery( sel, this ).index( cur ) > -1 :
- jQuery.find( sel, this, null, [ cur ] ).length;
- }
- if ( matchedSelectors[ sel ] ) {
- matchedHandlers.push( handleObj );
- }
- }
- if ( matchedHandlers.length ) {
- handlerQueue.push( { elem: cur, handlers: matchedHandlers } );
- }
- }
- }
- }
-
- // Add the remaining (directly-bound) handlers
- cur = this;
- if ( delegateCount < handlers.length ) {
- handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } );
- }
-
- return handlerQueue;
- },
-
- addProp: function( name, hook ) {
- Object.defineProperty( jQuery.Event.prototype, name, {
- enumerable: true,
- configurable: true,
-
- get: jQuery.isFunction( hook ) ?
- function() {
- if ( this.originalEvent ) {
- return hook( this.originalEvent );
- }
- } :
- function() {
- if ( this.originalEvent ) {
- return this.originalEvent[ name ];
- }
- },
-
- set: function( value ) {
- Object.defineProperty( this, name, {
- enumerable: true,
- configurable: true,
- writable: true,
- value: value
- } );
- }
- } );
- },
-
- fix: function( originalEvent ) {
- return originalEvent[ jQuery.expando ] ?
- originalEvent :
- new jQuery.Event( originalEvent );
- },
-
- special: {
- load: {
-
- // Prevent triggered image.load events from bubbling to window.load
- noBubble: true
- },
- focus: {
-
- // Fire native event if possible so blur/focus sequence is correct
- trigger: function() {
- if ( this !== safeActiveElement() && this.focus ) {
- this.focus();
- return false;
- }
- },
- delegateType: "focusin"
- },
- blur: {
- trigger: function() {
- if ( this === safeActiveElement() && this.blur ) {
- this.blur();
- return false;
- }
- },
- delegateType: "focusout"
- },
- click: {
-
- // For checkbox, fire native event so checked state will be right
- trigger: function() {
- if ( this.type === "checkbox" && this.click && nodeName( this, "input" ) ) {
- this.click();
- return false;
- }
- },
-
- // For cross-browser consistency, don't fire native .click() on links
- _default: function( event ) {
- return nodeName( event.target, "a" );
- }
- },
-
- beforeunload: {
- postDispatch: function( event ) {
-
- // Support: Firefox 20+
- // Firefox doesn't alert if the returnValue field is not set.
- if ( event.result !== undefined && event.originalEvent ) {
- event.originalEvent.returnValue = event.result;
- }
- }
- }
- }
-};
-
-jQuery.removeEvent = function( elem, type, handle ) {
-
- // This "if" is needed for plain objects
- if ( elem.removeEventListener ) {
- elem.removeEventListener( type, handle );
- }
-};
-
-jQuery.Event = function( src, props ) {
-
- // Allow instantiation without the 'new' keyword
- if ( !( this instanceof jQuery.Event ) ) {
- return new jQuery.Event( src, props );
- }
-
- // Event object
- if ( src && src.type ) {
- this.originalEvent = src;
- this.type = src.type;
-
- // Events bubbling up the document may have been marked as prevented
- // by a handler lower down the tree; reflect the correct value.
- this.isDefaultPrevented = src.defaultPrevented ||
- src.defaultPrevented === undefined &&
-
- // Support: Android <=2.3 only
- src.returnValue === false ?
- returnTrue :
- returnFalse;
-
- // Create target properties
- // Support: Safari <=6 - 7 only
- // Target should not be a text node (#504, #13143)
- this.target = ( src.target && src.target.nodeType === 3 ) ?
- src.target.parentNode :
- src.target;
-
- this.currentTarget = src.currentTarget;
- this.relatedTarget = src.relatedTarget;
-
- // Event type
- } else {
- this.type = src;
- }
-
- // Put explicitly provided properties onto the event object
- if ( props ) {
- jQuery.extend( this, props );
- }
-
- // Create a timestamp if incoming event doesn't have one
- this.timeStamp = src && src.timeStamp || jQuery.now();
-
- // Mark it as fixed
- this[ jQuery.expando ] = true;
-};
-
-// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
-// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
-jQuery.Event.prototype = {
- constructor: jQuery.Event,
- isDefaultPrevented: returnFalse,
- isPropagationStopped: returnFalse,
- isImmediatePropagationStopped: returnFalse,
- isSimulated: false,
-
- preventDefault: function() {
- var e = this.originalEvent;
-
- this.isDefaultPrevented = returnTrue;
-
- if ( e && !this.isSimulated ) {
- e.preventDefault();
- }
- },
- stopPropagation: function() {
- var e = this.originalEvent;
-
- this.isPropagationStopped = returnTrue;
-
- if ( e && !this.isSimulated ) {
- e.stopPropagation();
- }
- },
- stopImmediatePropagation: function() {
- var e = this.originalEvent;
-
- this.isImmediatePropagationStopped = returnTrue;
-
- if ( e && !this.isSimulated ) {
- e.stopImmediatePropagation();
- }
-
- this.stopPropagation();
- }
-};
-
-// Includes all common event props including KeyEvent and MouseEvent specific props
-jQuery.each( {
- altKey: true,
- bubbles: true,
- cancelable: true,
- changedTouches: true,
- ctrlKey: true,
- detail: true,
- eventPhase: true,
- metaKey: true,
- pageX: true,
- pageY: true,
- shiftKey: true,
- view: true,
- "char": true,
- charCode: true,
- key: true,
- keyCode: true,
- button: true,
- buttons: true,
- clientX: true,
- clientY: true,
- offsetX: true,
- offsetY: true,
- pointerId: true,
- pointerType: true,
- screenX: true,
- screenY: true,
- targetTouches: true,
- toElement: true,
- touches: true,
-
- which: function( event ) {
- var button = event.button;
-
- // Add which for key events
- if ( event.which == null && rkeyEvent.test( event.type ) ) {
- return event.charCode != null ? event.charCode : event.keyCode;
- }
-
- // Add which for click: 1 === left; 2 === middle; 3 === right
- if ( !event.which && button !== undefined && rmouseEvent.test( event.type ) ) {
- if ( button & 1 ) {
- return 1;
- }
-
- if ( button & 2 ) {
- return 3;
- }
-
- if ( button & 4 ) {
- return 2;
- }
-
- return 0;
- }
-
- return event.which;
- }
-}, jQuery.event.addProp );
-
-// Create mouseenter/leave events using mouseover/out and event-time checks
-// so that event delegation works in jQuery.
-// Do the same for pointerenter/pointerleave and pointerover/pointerout
-//
-// Support: Safari 7 only
-// Safari sends mouseenter too often; see:
-// https://bugs.chromium.org/p/chromium/issues/detail?id=470258
-// for the description of the bug (it existed in older Chrome versions as well).
-jQuery.each( {
- mouseenter: "mouseover",
- mouseleave: "mouseout",
- pointerenter: "pointerover",
- pointerleave: "pointerout"
-}, function( orig, fix ) {
- jQuery.event.special[ orig ] = {
- delegateType: fix,
- bindType: fix,
-
- handle: function( event ) {
- var ret,
- target = this,
- related = event.relatedTarget,
- handleObj = event.handleObj;
-
- // For mouseenter/leave call the handler if related is outside the target.
- // NB: No relatedTarget if the mouse left/entered the browser window
- if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) {
- event.type = handleObj.origType;
- ret = handleObj.handler.apply( this, arguments );
- event.type = fix;
- }
- return ret;
- }
- };
-} );
-
-jQuery.fn.extend( {
-
- on: function( types, selector, data, fn ) {
- return on( this, types, selector, data, fn );
- },
- one: function( types, selector, data, fn ) {
- return on( this, types, selector, data, fn, 1 );
- },
- off: function( types, selector, fn ) {
- var handleObj, type;
- if ( types && types.preventDefault && types.handleObj ) {
-
- // ( event ) dispatched jQuery.Event
- handleObj = types.handleObj;
- jQuery( types.delegateTarget ).off(
- handleObj.namespace ?
- handleObj.origType + "." + handleObj.namespace :
- handleObj.origType,
- handleObj.selector,
- handleObj.handler
- );
- return this;
- }
- if ( typeof types === "object" ) {
-
- // ( types-object [, selector] )
- for ( type in types ) {
- this.off( type, selector, types[ type ] );
- }
- return this;
- }
- if ( selector === false || typeof selector === "function" ) {
-
- // ( types [, fn] )
- fn = selector;
- selector = undefined;
- }
- if ( fn === false ) {
- fn = returnFalse;
- }
- return this.each( function() {
- jQuery.event.remove( this, types, fn, selector );
- } );
- }
-} );
-
-
-var
-
- /* eslint-disable max-len */
-
- // See https://github.com/eslint/eslint/issues/3229
- rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([a-z][^\/\0>\x20\t\r\n\f]*)[^>]*)\/>/gi,
-
- /* eslint-enable */
-
- // Support: IE <=10 - 11, Edge 12 - 13
- // In IE/Edge using regex groups here causes severe slowdowns.
- // See https://connect.microsoft.com/IE/feedback/details/1736512/
- rnoInnerhtml = /<script|<style|<link/i,
-
- // checked="checked" or checked
- rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
- rscriptTypeMasked = /^true\/(.*)/,
- rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g;
-
-// Prefer a tbody over its parent table for containing new rows
-function manipulationTarget( elem, content ) {
- if ( nodeName( elem, "table" ) &&
- nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) {
-
- return jQuery( ">tbody", elem )[ 0 ] || elem;
- }
-
- return elem;
-}
-
-// Replace/restore the type attribute of script elements for safe DOM manipulation
-function disableScript( elem ) {
- elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type;
- return elem;
-}
-function restoreScript( elem ) {
- var match = rscriptTypeMasked.exec( elem.type );
-
- if ( match ) {
- elem.type = match[ 1 ];
- } else {
- elem.removeAttribute( "type" );
- }
-
- return elem;
-}
-
-function cloneCopyEvent( src, dest ) {
- var i, l, type, pdataOld, pdataCur, udataOld, udataCur, events;
-
- if ( dest.nodeType !== 1 ) {
- return;
- }
-
- // 1. Copy private data: events, handlers, etc.
- if ( dataPriv.hasData( src ) ) {
- pdataOld = dataPriv.access( src );
- pdataCur = dataPriv.set( dest, pdataOld );
- events = pdataOld.events;
-
- if ( events ) {
- delete pdataCur.handle;
- pdataCur.events = {};
-
- for ( type in events ) {
- for ( i = 0, l = events[ type ].length; i < l; i++ ) {
- jQuery.event.add( dest, type, events[ type ][ i ] );
- }
- }
- }
- }
-
- // 2. Copy user data
- if ( dataUser.hasData( src ) ) {
- udataOld = dataUser.access( src );
- udataCur = jQuery.extend( {}, udataOld );
-
- dataUser.set( dest, udataCur );
- }
-}
-
-// Fix IE bugs, see support tests
-function fixInput( src, dest ) {
- var nodeName = dest.nodeName.toLowerCase();
-
- // Fails to persist the checked state of a cloned checkbox or radio button.
- if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
- dest.checked = src.checked;
-
- // Fails to return the selected option to the default selected state when cloning options
- } else if ( nodeName === "input" || nodeName === "textarea" ) {
- dest.defaultValue = src.defaultValue;
- }
-}
-
-function domManip( collection, args, callback, ignored ) {
-
- // Flatten any nested arrays
- args = concat.apply( [], args );
-
- var fragment, first, scripts, hasScripts, node, doc,
- i = 0,
- l = collection.length,
- iNoClone = l - 1,
- value = args[ 0 ],
- isFunction = jQuery.isFunction( value );
-
- // We can't cloneNode fragments that contain checked, in WebKit
- if ( isFunction ||
- ( l > 1 && typeof value === "string" &&
- !support.checkClone && rchecked.test( value ) ) ) {
- return collection.each( function( index ) {
- var self = collection.eq( index );
- if ( isFunction ) {
- args[ 0 ] = value.call( this, index, self.html() );
- }
- domManip( self, args, callback, ignored );
- } );
- }
-
- if ( l ) {
- fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored );
- first = fragment.firstChild;
-
- if ( fragment.childNodes.length === 1 ) {
- fragment = first;
- }
-
- // Require either new content or an interest in ignored elements to invoke the callback
- if ( first || ignored ) {
- scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
- hasScripts = scripts.length;
-
- // Use the original fragment for the last item
- // instead of the first because it can end up
- // being emptied incorrectly in certain situations (#8070).
- for ( ; i < l; i++ ) {
- node = fragment;
-
- if ( i !== iNoClone ) {
- node = jQuery.clone( node, true, true );
-
- // Keep references to cloned scripts for later restoration
- if ( hasScripts ) {
-
- // Support: Android <=4.0 only, PhantomJS 1 only
- // push.apply(_, arraylike) throws on ancient WebKit
- jQuery.merge( scripts, getAll( node, "script" ) );
- }
- }
-
- callback.call( collection[ i ], node, i );
- }
-
- if ( hasScripts ) {
- doc = scripts[ scripts.length - 1 ].ownerDocument;
-
- // Reenable scripts
- jQuery.map( scripts, restoreScript );
-
- // Evaluate executable scripts on first document insertion
- for ( i = 0; i < hasScripts; i++ ) {
- node = scripts[ i ];
- if ( rscriptType.test( node.type || "" ) &&
- !dataPriv.access( node, "globalEval" ) &&
- jQuery.contains( doc, node ) ) {
-
- if ( node.src ) {
-
- // Optional AJAX dependency, but won't run scripts if not present
- if ( jQuery._evalUrl ) {
- jQuery._evalUrl( node.src );
- }
- } else {
- DOMEval( node.textContent.replace( rcleanScript, "" ), doc );
- }
- }
- }
- }
- }
- }
-
- return collection;
-}
-
-function remove( elem, selector, keepData ) {
- var node,
- nodes = selector ? jQuery.filter( selector, elem ) : elem,
- i = 0;
-
- for ( ; ( node = nodes[ i ] ) != null; i++ ) {
- if ( !keepData && node.nodeType === 1 ) {
- jQuery.cleanData( getAll( node ) );
- }
-
- if ( node.parentNode ) {
- if ( keepData && jQuery.contains( node.ownerDocument, node ) ) {
- setGlobalEval( getAll( node, "script" ) );
- }
- node.parentNode.removeChild( node );
- }
- }
-
- return elem;
-}
-
-jQuery.extend( {
- htmlPrefilter: function( html ) {
- return html.replace( rxhtmlTag, "<$1></$2>" );
- },
-
- clone: function( elem, dataAndEvents, deepDataAndEvents ) {
- var i, l, srcElements, destElements,
- clone = elem.cloneNode( true ),
- inPage = jQuery.contains( elem.ownerDocument, elem );
-
- // Fix IE cloning issues
- if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) &&
- !jQuery.isXMLDoc( elem ) ) {
-
- // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2
- destElements = getAll( clone );
- srcElements = getAll( elem );
-
- for ( i = 0, l = srcElements.length; i < l; i++ ) {
- fixInput( srcElements[ i ], destElements[ i ] );
- }
- }
-
- // Copy the events from the original to the clone
- if ( dataAndEvents ) {
- if ( deepDataAndEvents ) {
- srcElements = srcElements || getAll( elem );
- destElements = destElements || getAll( clone );
-
- for ( i = 0, l = srcElements.length; i < l; i++ ) {
- cloneCopyEvent( srcElements[ i ], destElements[ i ] );
- }
- } else {
- cloneCopyEvent( elem, clone );
- }
- }
-
- // Preserve script evaluation history
- destElements = getAll( clone, "script" );
- if ( destElements.length > 0 ) {
- setGlobalEval( destElements, !inPage && getAll( elem, "script" ) );
- }
-
- // Return the cloned set
- return clone;
- },
-
- cleanData: function( elems ) {
- var data, elem, type,
- special = jQuery.event.special,
- i = 0;
-
- for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) {
- if ( acceptData( elem ) ) {
- if ( ( data = elem[ dataPriv.expando ] ) ) {
- if ( data.events ) {
- for ( type in data.events ) {
- if ( special[ type ] ) {
- jQuery.event.remove( elem, type );
-
- // This is a shortcut to avoid jQuery.event.remove's overhead
- } else {
- jQuery.removeEvent( elem, type, data.handle );
- }
- }
- }
-
- // Support: Chrome <=35 - 45+
- // Assign undefined instead of using delete, see Data#remove
- elem[ dataPriv.expando ] = undefined;
- }
- if ( elem[ dataUser.expando ] ) {
-
- // Support: Chrome <=35 - 45+
- // Assign undefined instead of using delete, see Data#remove
- elem[ dataUser.expando ] = undefined;
- }
- }
- }
- }
-} );
-
-jQuery.fn.extend( {
- detach: function( selector ) {
- return remove( this, selector, true );
- },
-
- remove: function( selector ) {
- return remove( this, selector );
- },
-
- text: function( value ) {
- return access( this, function( value ) {
- return value === undefined ?
- jQuery.text( this ) :
- this.empty().each( function() {
- if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
- this.textContent = value;
- }
- } );
- }, null, value, arguments.length );
- },
-
- append: function() {
- return domManip( this, arguments, function( elem ) {
- if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
- var target = manipulationTarget( this, elem );
- target.appendChild( elem );
- }
- } );
- },
-
- prepend: function() {
- return domManip( this, arguments, function( elem ) {
- if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
- var target = manipulationTarget( this, elem );
- target.insertBefore( elem, target.firstChild );
- }
- } );
- },
-
- before: function() {
- return domManip( this, arguments, function( elem ) {
- if ( this.parentNode ) {
- this.parentNode.insertBefore( elem, this );
- }
- } );
- },
-
- after: function() {
- return domManip( this, arguments, function( elem ) {
- if ( this.parentNode ) {
- this.parentNode.insertBefore( elem, this.nextSibling );
- }
- } );
- },
-
- empty: function() {
- var elem,
- i = 0;
-
- for ( ; ( elem = this[ i ] ) != null; i++ ) {
- if ( elem.nodeType === 1 ) {
-
- // Prevent memory leaks
- jQuery.cleanData( getAll( elem, false ) );
-
- // Remove any remaining nodes
- elem.textContent = "";
- }
- }
-
- return this;
- },
-
- clone: function( dataAndEvents, deepDataAndEvents ) {
- dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
- deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
-
- return this.map( function() {
- return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
- } );
- },
-
- html: function( value ) {
- return access( this, function( value ) {
- var elem = this[ 0 ] || {},
- i = 0,
- l = this.length;
-
- if ( value === undefined && elem.nodeType === 1 ) {
- return elem.innerHTML;
- }
-
- // See if we can take a shortcut and just use innerHTML
- if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
- !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) {
-
- value = jQuery.htmlPrefilter( value );
-
- try {
- for ( ; i < l; i++ ) {
- elem = this[ i ] || {};
-
- // Remove element nodes and prevent memory leaks
- if ( elem.nodeType === 1 ) {
- jQuery.cleanData( getAll( elem, false ) );
- elem.innerHTML = value;
- }
- }
-
- elem = 0;
-
- // If using innerHTML throws an exception, use the fallback method
- } catch ( e ) {}
- }
-
- if ( elem ) {
- this.empty().append( value );
- }
- }, null, value, arguments.length );
- },
-
- replaceWith: function() {
- var ignored = [];
-
- // Make the changes, replacing each non-ignored context element with the new content
- return domManip( this, arguments, function( elem ) {
- var parent = this.parentNode;
-
- if ( jQuery.inArray( this, ignored ) < 0 ) {
- jQuery.cleanData( getAll( this ) );
- if ( parent ) {
- parent.replaceChild( elem, this );
- }
- }
-
- // Force callback invocation
- }, ignored );
- }
-} );
-
-jQuery.each( {
- appendTo: "append",
- prependTo: "prepend",
- insertBefore: "before",
- insertAfter: "after",
- replaceAll: "replaceWith"
-}, function( name, original ) {
- jQuery.fn[ name ] = function( selector ) {
- var elems,
- ret = [],
- insert = jQuery( selector ),
- last = insert.length - 1,
- i = 0;
-
- for ( ; i <= last; i++ ) {
- elems = i === last ? this : this.clone( true );
- jQuery( insert[ i ] )[ original ]( elems );
-
- // Support: Android <=4.0 only, PhantomJS 1 only
- // .get() because push.apply(_, arraylike) throws on ancient WebKit
- push.apply( ret, elems.get() );
- }
-
- return this.pushStack( ret );
- };
-} );
-var rmargin = ( /^margin/ );
-
-var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
-
-var getStyles = function( elem ) {
-
- // Support: IE <=11 only, Firefox <=30 (#15098, #14150)
- // IE throws on elements created in popups
- // FF meanwhile throws on frame elements through "defaultView.getComputedStyle"
- var view = elem.ownerDocument.defaultView;
-
- if ( !view || !view.opener ) {
- view = window;
- }
-
- return view.getComputedStyle( elem );
- };
-
-
-
-( function() {
-
- // Executing both pixelPosition & boxSizingReliable tests require only one layout
- // so they're executed at the same time to save the second computation.
- function computeStyleTests() {
-
- // This is a singleton, we need to execute it only once
- if ( !div ) {
- return;
- }
-
- div.style.cssText =
- "box-sizing:border-box;" +
- "position:relative;display:block;" +
- "margin:auto;border:1px;padding:1px;" +
- "top:1%;width:50%";
- div.innerHTML = "";
- documentElement.appendChild( container );
-
- var divStyle = window.getComputedStyle( div );
- pixelPositionVal = divStyle.top !== "1%";
-
- // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44
- reliableMarginLeftVal = divStyle.marginLeft === "2px";
- boxSizingReliableVal = divStyle.width === "4px";
-
- // Support: Android 4.0 - 4.3 only
- // Some styles come back with percentage values, even though they shouldn't
- div.style.marginRight = "50%";
- pixelMarginRightVal = divStyle.marginRight === "4px";
-
- documentElement.removeChild( container );
-
- // Nullify the div so it wouldn't be stored in the memory and
- // it will also be a sign that checks already performed
- div = null;
- }
-
- var pixelPositionVal, boxSizingReliableVal, pixelMarginRightVal, reliableMarginLeftVal,
- container = document.createElement( "div" ),
- div = document.createElement( "div" );
-
- // Finish early in limited (non-browser) environments
- if ( !div.style ) {
- return;
- }
-
- // Support: IE <=9 - 11 only
- // Style of cloned element affects source element cloned (#8908)
- div.style.backgroundClip = "content-box";
- div.cloneNode( true ).style.backgroundClip = "";
- support.clearCloneStyle = div.style.backgroundClip === "content-box";
-
- container.style.cssText = "border:0;width:8px;height:0;top:0;left:-9999px;" +
- "padding:0;margin-top:1px;position:absolute";
- container.appendChild( div );
-
- jQuery.extend( support, {
- pixelPosition: function() {
- computeStyleTests();
- return pixelPositionVal;
- },
- boxSizingReliable: function() {
- computeStyleTests();
- return boxSizingReliableVal;
- },
- pixelMarginRight: function() {
- computeStyleTests();
- return pixelMarginRightVal;
- },
- reliableMarginLeft: function() {
- computeStyleTests();
- return reliableMarginLeftVal;
- }
- } );
-} )();
-
-
-function curCSS( elem, name, computed ) {
- var width, minWidth, maxWidth, ret,
-
- // Support: Firefox 51+
- // Retrieving style before computed somehow
- // fixes an issue with getting wrong values
- // on detached elements
- style = elem.style;
-
- computed = computed || getStyles( elem );
-
- // getPropertyValue is needed for:
- // .css('filter') (IE 9 only, #12537)
- // .css('--customProperty) (#3144)
- if ( computed ) {
- ret = computed.getPropertyValue( name ) || computed[ name ];
-
- if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) {
- ret = jQuery.style( elem, name );
- }
-
- // A tribute to the "awesome hack by Dean Edwards"
- // Android Browser returns percentage for some values,
- // but width seems to be reliably pixels.
- // This is against the CSSOM draft spec:
- // https://drafts.csswg.org/cssom/#resolved-values
- if ( !support.pixelMarginRight() && rnumnonpx.test( ret ) && rmargin.test( name ) ) {
-
- // Remember the original values
- width = style.width;
- minWidth = style.minWidth;
- maxWidth = style.maxWidth;
-
- // Put in the new values to get a computed value out
- style.minWidth = style.maxWidth = style.width = ret;
- ret = computed.width;
-
- // Revert the changed values
- style.width = width;
- style.minWidth = minWidth;
- style.maxWidth = maxWidth;
- }
- }
-
- return ret !== undefined ?
-
- // Support: IE <=9 - 11 only
- // IE returns zIndex value as an integer.
- ret + "" :
- ret;
-}
-
-
-function addGetHookIf( conditionFn, hookFn ) {
-
- // Define the hook, we'll check on the first run if it's really needed.
- return {
- get: function() {
- if ( conditionFn() ) {
-
- // Hook not needed (or it's not possible to use it due
- // to missing dependency), remove it.
- delete this.get;
- return;
- }
-
- // Hook needed; redefine it so that the support test is not executed again.
- return ( this.get = hookFn ).apply( this, arguments );
- }
- };
-}
-
-
-var
-
- // Swappable if display is none or starts with table
- // except "table", "table-cell", or "table-caption"
- // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
- rdisplayswap = /^(none|table(?!-c[ea]).+)/,
- rcustomProp = /^--/,
- cssShow = { position: "absolute", visibility: "hidden", display: "block" },
- cssNormalTransform = {
- letterSpacing: "0",
- fontWeight: "400"
- },
-
- cssPrefixes = [ "Webkit", "Moz", "ms" ],
- emptyStyle = document.createElement( "div" ).style;
-
-// Return a css property mapped to a potentially vendor prefixed property
-function vendorPropName( name ) {
-
- // Shortcut for names that are not vendor prefixed
- if ( name in emptyStyle ) {
- return name;
- }
-
- // Check for vendor prefixed names
- var capName = name[ 0 ].toUpperCase() + name.slice( 1 ),
- i = cssPrefixes.length;
-
- while ( i-- ) {
- name = cssPrefixes[ i ] + capName;
- if ( name in emptyStyle ) {
- return name;
- }
- }
-}
-
-// Return a property mapped along what jQuery.cssProps suggests or to
-// a vendor prefixed property.
-function finalPropName( name ) {
- var ret = jQuery.cssProps[ name ];
- if ( !ret ) {
- ret = jQuery.cssProps[ name ] = vendorPropName( name ) || name;
- }
- return ret;
-}
-
-function setPositiveNumber( elem, value, subtract ) {
-
- // Any relative (+/-) values have already been
- // normalized at this point
- var matches = rcssNum.exec( value );
- return matches ?
-
- // Guard against undefined "subtract", e.g., when used as in cssHooks
- Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) :
- value;
-}
-
-function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) {
- var i,
- val = 0;
-
- // If we already have the right measurement, avoid augmentation
- if ( extra === ( isBorderBox ? "border" : "content" ) ) {
- i = 4;
-
- // Otherwise initialize for horizontal or vertical properties
- } else {
- i = name === "width" ? 1 : 0;
- }
-
- for ( ; i < 4; i += 2 ) {
-
- // Both box models exclude margin, so add it if we want it
- if ( extra === "margin" ) {
- val += jQuery.css( elem, extra + cssExpand[ i ], true, styles );
- }
-
- if ( isBorderBox ) {
-
- // border-box includes padding, so remove it if we want content
- if ( extra === "content" ) {
- val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
- }
-
- // At this point, extra isn't border nor margin, so remove border
- if ( extra !== "margin" ) {
- val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
- }
- } else {
-
- // At this point, extra isn't content, so add padding
- val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
-
- // At this point, extra isn't content nor padding, so add border
- if ( extra !== "padding" ) {
- val += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
- }
- }
- }
-
- return val;
-}
-
-function getWidthOrHeight( elem, name, extra ) {
-
- // Start with computed style
- var valueIsBorderBox,
- styles = getStyles( elem ),
- val = curCSS( elem, name, styles ),
- isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
-
- // Computed unit is not pixels. Stop here and return.
- if ( rnumnonpx.test( val ) ) {
- return val;
- }
-
- // Check for style in case a browser which returns unreliable values
- // for getComputedStyle silently falls back to the reliable elem.style
- valueIsBorderBox = isBorderBox &&
- ( support.boxSizingReliable() || val === elem.style[ name ] );
-
- // Fall back to offsetWidth/Height when value is "auto"
- // This happens for inline elements with no explicit setting (gh-3571)
- if ( val === "auto" ) {
- val = elem[ "offset" + name[ 0 ].toUpperCase() + name.slice( 1 ) ];
- }
-
- // Normalize "", auto, and prepare for extra
- val = parseFloat( val ) || 0;
-
- // Use the active box-sizing model to add/subtract irrelevant styles
- return ( val +
- augmentWidthOrHeight(
- elem,
- name,
- extra || ( isBorderBox ? "border" : "content" ),
- valueIsBorderBox,
- styles
- )
- ) + "px";
-}
-
-jQuery.extend( {
-
- // Add in style property hooks for overriding the default
- // behavior of getting and setting a style property
- cssHooks: {
- opacity: {
- get: function( elem, computed ) {
- if ( computed ) {
-
- // We should always get a number back from opacity
- var ret = curCSS( elem, "opacity" );
- return ret === "" ? "1" : ret;
- }
- }
- }
- },
-
- // Don't automatically add "px" to these possibly-unitless properties
- cssNumber: {
- "animationIterationCount": true,
- "columnCount": true,
- "fillOpacity": true,
- "flexGrow": true,
- "flexShrink": true,
- "fontWeight": true,
- "lineHeight": true,
- "opacity": true,
- "order": true,
- "orphans": true,
- "widows": true,
- "zIndex": true,
- "zoom": true
- },
-
- // Add in properties whose names you wish to fix before
- // setting or getting the value
- cssProps: {
- "float": "cssFloat"
- },
-
- // Get and set the style property on a DOM Node
- style: function( elem, name, value, extra ) {
-
- // Don't set styles on text and comment nodes
- if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
- return;
- }
-
- // Make sure that we're working with the right name
- var ret, type, hooks,
- origName = jQuery.camelCase( name ),
- isCustomProp = rcustomProp.test( name ),
- style = elem.style;
-
- // Make sure that we're working with the right name. We don't
- // want to query the value if it is a CSS custom property
- // since they are user-defined.
- if ( !isCustomProp ) {
- name = finalPropName( origName );
- }
-
- // Gets hook for the prefixed version, then unprefixed version
- hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
-
- // Check if we're setting a value
- if ( value !== undefined ) {
- type = typeof value;
-
- // Convert "+=" or "-=" to relative numbers (#7345)
- if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) {
- value = adjustCSS( elem, name, ret );
-
- // Fixes bug #9237
- type = "number";
- }
-
- // Make sure that null and NaN values aren't set (#7116)
- if ( value == null || value !== value ) {
- return;
- }
-
- // If a number was passed in, add the unit (except for certain CSS properties)
- if ( type === "number" ) {
- value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" );
- }
-
- // background-* props affect original clone's values
- if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) {
- style[ name ] = "inherit";
- }
-
- // If a hook was provided, use that value, otherwise just set the specified value
- if ( !hooks || !( "set" in hooks ) ||
- ( value = hooks.set( elem, value, extra ) ) !== undefined ) {
-
- if ( isCustomProp ) {
- style.setProperty( name, value );
- } else {
- style[ name ] = value;
- }
- }
-
- } else {
-
- // If a hook was provided get the non-computed value from there
- if ( hooks && "get" in hooks &&
- ( ret = hooks.get( elem, false, extra ) ) !== undefined ) {
-
- return ret;
- }
-
- // Otherwise just get the value from the style object
- return style[ name ];
- }
- },
-
- css: function( elem, name, extra, styles ) {
- var val, num, hooks,
- origName = jQuery.camelCase( name ),
- isCustomProp = rcustomProp.test( name );
-
- // Make sure that we're working with the right name. We don't
- // want to modify the value if it is a CSS custom property
- // since they are user-defined.
- if ( !isCustomProp ) {
- name = finalPropName( origName );
- }
-
- // Try prefixed name followed by the unprefixed name
- hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
-
- // If a hook was provided get the computed value from there
- if ( hooks && "get" in hooks ) {
- val = hooks.get( elem, true, extra );
- }
-
- // Otherwise, if a way to get the computed value exists, use that
- if ( val === undefined ) {
- val = curCSS( elem, name, styles );
- }
-
- // Convert "normal" to computed value
- if ( val === "normal" && name in cssNormalTransform ) {
- val = cssNormalTransform[ name ];
- }
-
- // Make numeric if forced or a qualifier was provided and val looks numeric
- if ( extra === "" || extra ) {
- num = parseFloat( val );
- return extra === true || isFinite( num ) ? num || 0 : val;
- }
-
- return val;
- }
-} );
-
-jQuery.each( [ "height", "width" ], function( i, name ) {
- jQuery.cssHooks[ name ] = {
- get: function( elem, computed, extra ) {
- if ( computed ) {
-
- // Certain elements can have dimension info if we invisibly show them
- // but it must have a current display style that would benefit
- return rdisplayswap.test( jQuery.css( elem, "display" ) ) &&
-
- // Support: Safari 8+
- // Table columns in Safari have non-zero offsetWidth & zero
- // getBoundingClientRect().width unless display is changed.
- // Support: IE <=11 only
- // Running getBoundingClientRect on a disconnected node
- // in IE throws an error.
- ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ?
- swap( elem, cssShow, function() {
- return getWidthOrHeight( elem, name, extra );
- } ) :
- getWidthOrHeight( elem, name, extra );
- }
- },
-
- set: function( elem, value, extra ) {
- var matches,
- styles = extra && getStyles( elem ),
- subtract = extra && augmentWidthOrHeight(
- elem,
- name,
- extra,
- jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
- styles
- );
-
- // Convert to pixels if value adjustment is needed
- if ( subtract && ( matches = rcssNum.exec( value ) ) &&
- ( matches[ 3 ] || "px" ) !== "px" ) {
-
- elem.style[ name ] = value;
- value = jQuery.css( elem, name );
- }
-
- return setPositiveNumber( elem, value, subtract );
- }
- };
-} );
-
-jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft,
- function( elem, computed ) {
- if ( computed ) {
- return ( parseFloat( curCSS( elem, "marginLeft" ) ) ||
- elem.getBoundingClientRect().left -
- swap( elem, { marginLeft: 0 }, function() {
- return elem.getBoundingClientRect().left;
- } )
- ) + "px";
- }
- }
-);
-
-// These hooks are used by animate to expand properties
-jQuery.each( {
- margin: "",
- padding: "",
- border: "Width"
-}, function( prefix, suffix ) {
- jQuery.cssHooks[ prefix + suffix ] = {
- expand: function( value ) {
- var i = 0,
- expanded = {},
-
- // Assumes a single number if not a string
- parts = typeof value === "string" ? value.split( " " ) : [ value ];
-
- for ( ; i < 4; i++ ) {
- expanded[ prefix + cssExpand[ i ] + suffix ] =
- parts[ i ] || parts[ i - 2 ] || parts[ 0 ];
- }
-
- return expanded;
- }
- };
-
- if ( !rmargin.test( prefix ) ) {
- jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
- }
-} );
-
-jQuery.fn.extend( {
- css: function( name, value ) {
- return access( this, function( elem, name, value ) {
- var styles, len,
- map = {},
- i = 0;
-
- if ( Array.isArray( name ) ) {
- styles = getStyles( elem );
- len = name.length;
-
- for ( ; i < len; i++ ) {
- map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles );
- }
-
- return map;
- }
-
- return value !== undefined ?
- jQuery.style( elem, name, value ) :
- jQuery.css( elem, name );
- }, name, value, arguments.length > 1 );
- }
-} );
-
-
-function Tween( elem, options, prop, end, easing ) {
- return new Tween.prototype.init( elem, options, prop, end, easing );
-}
-jQuery.Tween = Tween;
-
-Tween.prototype = {
- constructor: Tween,
- init: function( elem, options, prop, end, easing, unit ) {
- this.elem = elem;
- this.prop = prop;
- this.easing = easing || jQuery.easing._default;
- this.options = options;
- this.start = this.now = this.cur();
- this.end = end;
- this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
- },
- cur: function() {
- var hooks = Tween.propHooks[ this.prop ];
-
- return hooks && hooks.get ?
- hooks.get( this ) :
- Tween.propHooks._default.get( this );
- },
- run: function( percent ) {
- var eased,
- hooks = Tween.propHooks[ this.prop ];
-
- if ( this.options.duration ) {
- this.pos = eased = jQuery.easing[ this.easing ](
- percent, this.options.duration * percent, 0, 1, this.options.duration
- );
- } else {
- this.pos = eased = percent;
- }
- this.now = ( this.end - this.start ) * eased + this.start;
-
- if ( this.options.step ) {
- this.options.step.call( this.elem, this.now, this );
- }
-
- if ( hooks && hooks.set ) {
- hooks.set( this );
- } else {
- Tween.propHooks._default.set( this );
- }
- return this;
- }
-};
-
-Tween.prototype.init.prototype = Tween.prototype;
-
-Tween.propHooks = {
- _default: {
- get: function( tween ) {
- var result;
-
- // Use a property on the element directly when it is not a DOM element,
- // or when there is no matching style property that exists.
- if ( tween.elem.nodeType !== 1 ||
- tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) {
- return tween.elem[ tween.prop ];
- }
-
- // Passing an empty string as a 3rd parameter to .css will automatically
- // attempt a parseFloat and fallback to a string if the parse fails.
- // Simple values such as "10px" are parsed to Float;
- // complex values such as "rotate(1rad)" are returned as-is.
- result = jQuery.css( tween.elem, tween.prop, "" );
-
- // Empty strings, null, undefined and "auto" are converted to 0.
- return !result || result === "auto" ? 0 : result;
- },
- set: function( tween ) {
-
- // Use step hook for back compat.
- // Use cssHook if its there.
- // Use .style if available and use plain properties where available.
- if ( jQuery.fx.step[ tween.prop ] ) {
- jQuery.fx.step[ tween.prop ]( tween );
- } else if ( tween.elem.nodeType === 1 &&
- ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null ||
- jQuery.cssHooks[ tween.prop ] ) ) {
- jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
- } else {
- tween.elem[ tween.prop ] = tween.now;
- }
- }
- }
-};
-
-// Support: IE <=9 only
-// Panic based approach to setting things on disconnected nodes
-Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
- set: function( tween ) {
- if ( tween.elem.nodeType && tween.elem.parentNode ) {
- tween.elem[ tween.prop ] = tween.now;
- }
- }
-};
-
-jQuery.easing = {
- linear: function( p ) {
- return p;
- },
- swing: function( p ) {
- return 0.5 - Math.cos( p * Math.PI ) / 2;
- },
- _default: "swing"
-};
-
-jQuery.fx = Tween.prototype.init;
-
-// Back compat <1.8 extension point
-jQuery.fx.step = {};
-
-
-
-
-var
- fxNow, inProgress,
- rfxtypes = /^(?:toggle|show|hide)$/,
- rrun = /queueHooks$/;
-
-function schedule() {
- if ( inProgress ) {
- if ( document.hidden === false && window.requestAnimationFrame ) {
- window.requestAnimationFrame( schedule );
- } else {
- window.setTimeout( schedule, jQuery.fx.interval );
- }
-
- jQuery.fx.tick();
- }
-}
-
-// Animations created synchronously will run synchronously
-function createFxNow() {
- window.setTimeout( function() {
- fxNow = undefined;
- } );
- return ( fxNow = jQuery.now() );
-}
-
-// Generate parameters to create a standard animation
-function genFx( type, includeWidth ) {
- var which,
- i = 0,
- attrs = { height: type };
-
- // If we include width, step value is 1 to do all cssExpand values,
- // otherwise step value is 2 to skip over Left and Right
- includeWidth = includeWidth ? 1 : 0;
- for ( ; i < 4; i += 2 - includeWidth ) {
- which = cssExpand[ i ];
- attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
- }
-
- if ( includeWidth ) {
- attrs.opacity = attrs.width = type;
- }
-
- return attrs;
-}
-
-function createTween( value, prop, animation ) {
- var tween,
- collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ),
- index = 0,
- length = collection.length;
- for ( ; index < length; index++ ) {
- if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) {
-
- // We're done with this property
- return tween;
- }
- }
-}
-
-function defaultPrefilter( elem, props, opts ) {
- var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display,
- isBox = "width" in props || "height" in props,
- anim = this,
- orig = {},
- style = elem.style,
- hidden = elem.nodeType && isHiddenWithinTree( elem ),
- dataShow = dataPriv.get( elem, "fxshow" );
-
- // Queue-skipping animations hijack the fx hooks
- if ( !opts.queue ) {
- hooks = jQuery._queueHooks( elem, "fx" );
- if ( hooks.unqueued == null ) {
- hooks.unqueued = 0;
- oldfire = hooks.empty.fire;
- hooks.empty.fire = function() {
- if ( !hooks.unqueued ) {
- oldfire();
- }
- };
- }
- hooks.unqueued++;
-
- anim.always( function() {
-
- // Ensure the complete handler is called before this completes
- anim.always( function() {
- hooks.unqueued--;
- if ( !jQuery.queue( elem, "fx" ).length ) {
- hooks.empty.fire();
- }
- } );
- } );
- }
-
- // Detect show/hide animations
- for ( prop in props ) {
- value = props[ prop ];
- if ( rfxtypes.test( value ) ) {
- delete props[ prop ];
- toggle = toggle || value === "toggle";
- if ( value === ( hidden ? "hide" : "show" ) ) {
-
- // Pretend to be hidden if this is a "show" and
- // there is still data from a stopped show/hide
- if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) {
- hidden = true;
-
- // Ignore all other no-op show/hide data
- } else {
- continue;
- }
- }
- orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop );
- }
- }
-
- // Bail out if this is a no-op like .hide().hide()
- propTween = !jQuery.isEmptyObject( props );
- if ( !propTween && jQuery.isEmptyObject( orig ) ) {
- return;
- }
-
- // Restrict "overflow" and "display" styles during box animations
- if ( isBox && elem.nodeType === 1 ) {
-
- // Support: IE <=9 - 11, Edge 12 - 13
- // Record all 3 overflow attributes because IE does not infer the shorthand
- // from identically-valued overflowX and overflowY
- opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
-
- // Identify a display type, preferring old show/hide data over the CSS cascade
- restoreDisplay = dataShow && dataShow.display;
- if ( restoreDisplay == null ) {
- restoreDisplay = dataPriv.get( elem, "display" );
- }
- display = jQuery.css( elem, "display" );
- if ( display === "none" ) {
- if ( restoreDisplay ) {
- display = restoreDisplay;
- } else {
-
- // Get nonempty value(s) by temporarily forcing visibility
- showHide( [ elem ], true );
- restoreDisplay = elem.style.display || restoreDisplay;
- display = jQuery.css( elem, "display" );
- showHide( [ elem ] );
- }
- }
-
- // Animate inline elements as inline-block
- if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) {
- if ( jQuery.css( elem, "float" ) === "none" ) {
-
- // Restore the original display value at the end of pure show/hide animations
- if ( !propTween ) {
- anim.done( function() {
- style.display = restoreDisplay;
- } );
- if ( restoreDisplay == null ) {
- display = style.display;
- restoreDisplay = display === "none" ? "" : display;
- }
- }
- style.display = "inline-block";
- }
- }
- }
-
- if ( opts.overflow ) {
- style.overflow = "hidden";
- anim.always( function() {
- style.overflow = opts.overflow[ 0 ];
- style.overflowX = opts.overflow[ 1 ];
- style.overflowY = opts.overflow[ 2 ];
- } );
- }
-
- // Implement show/hide animations
- propTween = false;
- for ( prop in orig ) {
-
- // General show/hide setup for this element animation
- if ( !propTween ) {
- if ( dataShow ) {
- if ( "hidden" in dataShow ) {
- hidden = dataShow.hidden;
- }
- } else {
- dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } );
- }
-
- // Store hidden/visible for toggle so `.stop().toggle()` "reverses"
- if ( toggle ) {
- dataShow.hidden = !hidden;
- }
-
- // Show elements before animating them
- if ( hidden ) {
- showHide( [ elem ], true );
- }
-
- /* eslint-disable no-loop-func */
-
- anim.done( function() {
-
- /* eslint-enable no-loop-func */
-
- // The final step of a "hide" animation is actually hiding the element
- if ( !hidden ) {
- showHide( [ elem ] );
- }
- dataPriv.remove( elem, "fxshow" );
- for ( prop in orig ) {
- jQuery.style( elem, prop, orig[ prop ] );
- }
- } );
- }
-
- // Per-property setup
- propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
- if ( !( prop in dataShow ) ) {
- dataShow[ prop ] = propTween.start;
- if ( hidden ) {
- propTween.end = propTween.start;
- propTween.start = 0;
- }
- }
- }
-}
-
-function propFilter( props, specialEasing ) {
- var index, name, easing, value, hooks;
-
- // camelCase, specialEasing and expand cssHook pass
- for ( index in props ) {
- name = jQuery.camelCase( index );
- easing = specialEasing[ name ];
- value = props[ index ];
- if ( Array.isArray( value ) ) {
- easing = value[ 1 ];
- value = props[ index ] = value[ 0 ];
- }
-
- if ( index !== name ) {
- props[ name ] = value;
- delete props[ index ];
- }
-
- hooks = jQuery.cssHooks[ name ];
- if ( hooks && "expand" in hooks ) {
- value = hooks.expand( value );
- delete props[ name ];
-
- // Not quite $.extend, this won't overwrite existing keys.
- // Reusing 'index' because we have the correct "name"
- for ( index in value ) {
- if ( !( index in props ) ) {
- props[ index ] = value[ index ];
- specialEasing[ index ] = easing;
- }
- }
- } else {
- specialEasing[ name ] = easing;
- }
- }
-}
-
-function Animation( elem, properties, options ) {
- var result,
- stopped,
- index = 0,
- length = Animation.prefilters.length,
- deferred = jQuery.Deferred().always( function() {
-
- // Don't match elem in the :animated selector
- delete tick.elem;
- } ),
- tick = function() {
- if ( stopped ) {
- return false;
- }
- var currentTime = fxNow || createFxNow(),
- remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
-
- // Support: Android 2.3 only
- // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497)
- temp = remaining / animation.duration || 0,
- percent = 1 - temp,
- index = 0,
- length = animation.tweens.length;
-
- for ( ; index < length; index++ ) {
- animation.tweens[ index ].run( percent );
- }
-
- deferred.notifyWith( elem, [ animation, percent, remaining ] );
-
- // If there's more to do, yield
- if ( percent < 1 && length ) {
- return remaining;
- }
-
- // If this was an empty animation, synthesize a final progress notification
- if ( !length ) {
- deferred.notifyWith( elem, [ animation, 1, 0 ] );
- }
-
- // Resolve the animation and report its conclusion
- deferred.resolveWith( elem, [ animation ] );
- return false;
- },
- animation = deferred.promise( {
- elem: elem,
- props: jQuery.extend( {}, properties ),
- opts: jQuery.extend( true, {
- specialEasing: {},
- easing: jQuery.easing._default
- }, options ),
- originalProperties: properties,
- originalOptions: options,
- startTime: fxNow || createFxNow(),
- duration: options.duration,
- tweens: [],
- createTween: function( prop, end ) {
- var tween = jQuery.Tween( elem, animation.opts, prop, end,
- animation.opts.specialEasing[ prop ] || animation.opts.easing );
- animation.tweens.push( tween );
- return tween;
- },
- stop: function( gotoEnd ) {
- var index = 0,
-
- // If we are going to the end, we want to run all the tweens
- // otherwise we skip this part
- length = gotoEnd ? animation.tweens.length : 0;
- if ( stopped ) {
- return this;
- }
- stopped = true;
- for ( ; index < length; index++ ) {
- animation.tweens[ index ].run( 1 );
- }
-
- // Resolve when we played the last frame; otherwise, reject
- if ( gotoEnd ) {
- deferred.notifyWith( elem, [ animation, 1, 0 ] );
- deferred.resolveWith( elem, [ animation, gotoEnd ] );
- } else {
- deferred.rejectWith( elem, [ animation, gotoEnd ] );
- }
- return this;
- }
- } ),
- props = animation.props;
-
- propFilter( props, animation.opts.specialEasing );
-
- for ( ; index < length; index++ ) {
- result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts );
- if ( result ) {
- if ( jQuery.isFunction( result.stop ) ) {
- jQuery._queueHooks( animation.elem, animation.opts.queue ).stop =
- jQuery.proxy( result.stop, result );
- }
- return result;
- }
- }
-
- jQuery.map( props, createTween, animation );
-
- if ( jQuery.isFunction( animation.opts.start ) ) {
- animation.opts.start.call( elem, animation );
- }
-
- // Attach callbacks from options
- animation
- .progress( animation.opts.progress )
- .done( animation.opts.done, animation.opts.complete )
- .fail( animation.opts.fail )
- .always( animation.opts.always );
-
- jQuery.fx.timer(
- jQuery.extend( tick, {
- elem: elem,
- anim: animation,
- queue: animation.opts.queue
- } )
- );
-
- return animation;
-}
-
-jQuery.Animation = jQuery.extend( Animation, {
-
- tweeners: {
- "*": [ function( prop, value ) {
- var tween = this.createTween( prop, value );
- adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween );
- return tween;
- } ]
- },
-
- tweener: function( props, callback ) {
- if ( jQuery.isFunction( props ) ) {
- callback = props;
- props = [ "*" ];
- } else {
- props = props.match( rnothtmlwhite );
- }
-
- var prop,
- index = 0,
- length = props.length;
-
- for ( ; index < length; index++ ) {
- prop = props[ index ];
- Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || [];
- Animation.tweeners[ prop ].unshift( callback );
- }
- },
-
- prefilters: [ defaultPrefilter ],
-
- prefilter: function( callback, prepend ) {
- if ( prepend ) {
- Animation.prefilters.unshift( callback );
- } else {
- Animation.prefilters.push( callback );
- }
- }
-} );
-
-jQuery.speed = function( speed, easing, fn ) {
- var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
- complete: fn || !fn && easing ||
- jQuery.isFunction( speed ) && speed,
- duration: speed,
- easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing
- };
-
- // Go to the end state if fx are off
- if ( jQuery.fx.off ) {
- opt.duration = 0;
-
- } else {
- if ( typeof opt.duration !== "number" ) {
- if ( opt.duration in jQuery.fx.speeds ) {
- opt.duration = jQuery.fx.speeds[ opt.duration ];
-
- } else {
- opt.duration = jQuery.fx.speeds._default;
- }
- }
- }
-
- // Normalize opt.queue - true/undefined/null -> "fx"
- if ( opt.queue == null || opt.queue === true ) {
- opt.queue = "fx";
- }
-
- // Queueing
- opt.old = opt.complete;
-
- opt.complete = function() {
- if ( jQuery.isFunction( opt.old ) ) {
- opt.old.call( this );
- }
-
- if ( opt.queue ) {
- jQuery.dequeue( this, opt.queue );
- }
- };
-
- return opt;
-};
-
-jQuery.fn.extend( {
- fadeTo: function( speed, to, easing, callback ) {
-
- // Show any hidden elements after setting opacity to 0
- return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show()
-
- // Animate to the value specified
- .end().animate( { opacity: to }, speed, easing, callback );
- },
- animate: function( prop, speed, easing, callback ) {
- var empty = jQuery.isEmptyObject( prop ),
- optall = jQuery.speed( speed, easing, callback ),
- doAnimation = function() {
-
- // Operate on a copy of prop so per-property easing won't be lost
- var anim = Animation( this, jQuery.extend( {}, prop ), optall );
-
- // Empty animations, or finishing resolves immediately
- if ( empty || dataPriv.get( this, "finish" ) ) {
- anim.stop( true );
- }
- };
- doAnimation.finish = doAnimation;
-
- return empty || optall.queue === false ?
- this.each( doAnimation ) :
- this.queue( optall.queue, doAnimation );
- },
- stop: function( type, clearQueue, gotoEnd ) {
- var stopQueue = function( hooks ) {
- var stop = hooks.stop;
- delete hooks.stop;
- stop( gotoEnd );
- };
-
- if ( typeof type !== "string" ) {
- gotoEnd = clearQueue;
- clearQueue = type;
- type = undefined;
- }
- if ( clearQueue && type !== false ) {
- this.queue( type || "fx", [] );
- }
-
- return this.each( function() {
- var dequeue = true,
- index = type != null && type + "queueHooks",
- timers = jQuery.timers,
- data = dataPriv.get( this );
-
- if ( index ) {
- if ( data[ index ] && data[ index ].stop ) {
- stopQueue( data[ index ] );
- }
- } else {
- for ( index in data ) {
- if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
- stopQueue( data[ index ] );
- }
- }
- }
-
- for ( index = timers.length; index--; ) {
- if ( timers[ index ].elem === this &&
- ( type == null || timers[ index ].queue === type ) ) {
-
- timers[ index ].anim.stop( gotoEnd );
- dequeue = false;
- timers.splice( index, 1 );
- }
- }
-
- // Start the next in the queue if the last step wasn't forced.
- // Timers currently will call their complete callbacks, which
- // will dequeue but only if they were gotoEnd.
- if ( dequeue || !gotoEnd ) {
- jQuery.dequeue( this, type );
- }
- } );
- },
- finish: function( type ) {
- if ( type !== false ) {
- type = type || "fx";
- }
- return this.each( function() {
- var index,
- data = dataPriv.get( this ),
- queue = data[ type + "queue" ],
- hooks = data[ type + "queueHooks" ],
- timers = jQuery.timers,
- length = queue ? queue.length : 0;
-
- // Enable finishing flag on private data
- data.finish = true;
-
- // Empty the queue first
- jQuery.queue( this, type, [] );
-
- if ( hooks && hooks.stop ) {
- hooks.stop.call( this, true );
- }
-
- // Look for any active animations, and finish them
- for ( index = timers.length; index--; ) {
- if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
- timers[ index ].anim.stop( true );
- timers.splice( index, 1 );
- }
- }
-
- // Look for any animations in the old queue and finish them
- for ( index = 0; index < length; index++ ) {
- if ( queue[ index ] && queue[ index ].finish ) {
- queue[ index ].finish.call( this );
- }
- }
-
- // Turn off finishing flag
- delete data.finish;
- } );
- }
-} );
-
-jQuery.each( [ "toggle", "show", "hide" ], function( i, name ) {
- var cssFn = jQuery.fn[ name ];
- jQuery.fn[ name ] = function( speed, easing, callback ) {
- return speed == null || typeof speed === "boolean" ?
- cssFn.apply( this, arguments ) :
- this.animate( genFx( name, true ), speed, easing, callback );
- };
-} );
-
-// Generate shortcuts for custom animations
-jQuery.each( {
- slideDown: genFx( "show" ),
- slideUp: genFx( "hide" ),
- slideToggle: genFx( "toggle" ),
- fadeIn: { opacity: "show" },
- fadeOut: { opacity: "hide" },
- fadeToggle: { opacity: "toggle" }
-}, function( name, props ) {
- jQuery.fn[ name ] = function( speed, easing, callback ) {
- return this.animate( props, speed, easing, callback );
- };
-} );
-
-jQuery.timers = [];
-jQuery.fx.tick = function() {
- var timer,
- i = 0,
- timers = jQuery.timers;
-
- fxNow = jQuery.now();
-
- for ( ; i < timers.length; i++ ) {
- timer = timers[ i ];
-
- // Run the timer and safely remove it when done (allowing for external removal)
- if ( !timer() && timers[ i ] === timer ) {
- timers.splice( i--, 1 );
- }
- }
-
- if ( !timers.length ) {
- jQuery.fx.stop();
- }
- fxNow = undefined;
-};
-
-jQuery.fx.timer = function( timer ) {
- jQuery.timers.push( timer );
- jQuery.fx.start();
-};
-
-jQuery.fx.interval = 13;
-jQuery.fx.start = function() {
- if ( inProgress ) {
- return;
- }
-
- inProgress = true;
- schedule();
-};
-
-jQuery.fx.stop = function() {
- inProgress = null;
-};
-
-jQuery.fx.speeds = {
- slow: 600,
- fast: 200,
-
- // Default speed
- _default: 400
-};
-
-
-// Based off of the plugin by Clint Helfers, with permission.
-// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/
-jQuery.fn.delay = function( time, type ) {
- time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
- type = type || "fx";
-
- return this.queue( type, function( next, hooks ) {
- var timeout = window.setTimeout( next, time );
- hooks.stop = function() {
- window.clearTimeout( timeout );
- };
- } );
-};
-
-
-( function() {
- var input = document.createElement( "input" ),
- select = document.createElement( "select" ),
- opt = select.appendChild( document.createElement( "option" ) );
-
- input.type = "checkbox";
-
- // Support: Android <=4.3 only
- // Default value for a checkbox should be "on"
- support.checkOn = input.value !== "";
-
- // Support: IE <=11 only
- // Must access selectedIndex to make default options select
- support.optSelected = opt.selected;
-
- // Support: IE <=11 only
- // An input loses its value after becoming a radio
- input = document.createElement( "input" );
- input.value = "t";
- input.type = "radio";
- support.radioValue = input.value === "t";
-} )();
-
-
-var boolHook,
- attrHandle = jQuery.expr.attrHandle;
-
-jQuery.fn.extend( {
- attr: function( name, value ) {
- return access( this, jQuery.attr, name, value, arguments.length > 1 );
- },
-
- removeAttr: function( name ) {
- return this.each( function() {
- jQuery.removeAttr( this, name );
- } );
- }
-} );
-
-jQuery.extend( {
- attr: function( elem, name, value ) {
- var ret, hooks,
- nType = elem.nodeType;
-
- // Don't get/set attributes on text, comment and attribute nodes
- if ( nType === 3 || nType === 8 || nType === 2 ) {
- return;
- }
-
- // Fallback to prop when attributes are not supported
- if ( typeof elem.getAttribute === "undefined" ) {
- return jQuery.prop( elem, name, value );
- }
-
- // Attribute hooks are determined by the lowercase version
- // Grab necessary hook if one is defined
- if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
- hooks = jQuery.attrHooks[ name.toLowerCase() ] ||
- ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined );
- }
-
- if ( value !== undefined ) {
- if ( value === null ) {
- jQuery.removeAttr( elem, name );
- return;
- }
-
- if ( hooks && "set" in hooks &&
- ( ret = hooks.set( elem, value, name ) ) !== undefined ) {
- return ret;
- }
-
- elem.setAttribute( name, value + "" );
- return value;
- }
-
- if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
- return ret;
- }
-
- ret = jQuery.find.attr( elem, name );
-
- // Non-existent attributes return null, we normalize to undefined
- return ret == null ? undefined : ret;
- },
-
- attrHooks: {
- type: {
- set: function( elem, value ) {
- if ( !support.radioValue && value === "radio" &&
- nodeName( elem, "input" ) ) {
- var val = elem.value;
- elem.setAttribute( "type", value );
- if ( val ) {
- elem.value = val;
- }
- return value;
- }
- }
- }
- },
-
- removeAttr: function( elem, value ) {
- var name,
- i = 0,
-
- // Attribute names can contain non-HTML whitespace characters
- // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2
- attrNames = value && value.match( rnothtmlwhite );
-
- if ( attrNames && elem.nodeType === 1 ) {
- while ( ( name = attrNames[ i++ ] ) ) {
- elem.removeAttribute( name );
- }
- }
- }
-} );
-
-// Hooks for boolean attributes
-boolHook = {
- set: function( elem, value, name ) {
- if ( value === false ) {
-
- // Remove boolean attributes when set to false
- jQuery.removeAttr( elem, name );
- } else {
- elem.setAttribute( name, name );
- }
- return name;
- }
-};
-
-jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) {
- var getter = attrHandle[ name ] || jQuery.find.attr;
-
- attrHandle[ name ] = function( elem, name, isXML ) {
- var ret, handle,
- lowercaseName = name.toLowerCase();
-
- if ( !isXML ) {
-
- // Avoid an infinite loop by temporarily removing this function from the getter
- handle = attrHandle[ lowercaseName ];
- attrHandle[ lowercaseName ] = ret;
- ret = getter( elem, name, isXML ) != null ?
- lowercaseName :
- null;
- attrHandle[ lowercaseName ] = handle;
- }
- return ret;
- };
-} );
-
-
-
-
-var rfocusable = /^(?:input|select|textarea|button)$/i,
- rclickable = /^(?:a|area)$/i;
-
-jQuery.fn.extend( {
- prop: function( name, value ) {
- return access( this, jQuery.prop, name, value, arguments.length > 1 );
- },
-
- removeProp: function( name ) {
- return this.each( function() {
- delete this[ jQuery.propFix[ name ] || name ];
- } );
- }
-} );
-
-jQuery.extend( {
- prop: function( elem, name, value ) {
- var ret, hooks,
- nType = elem.nodeType;
-
- // Don't get/set properties on text, comment and attribute nodes
- if ( nType === 3 || nType === 8 || nType === 2 ) {
- return;
- }
-
- if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
-
- // Fix name and attach hooks
- name = jQuery.propFix[ name ] || name;
- hooks = jQuery.propHooks[ name ];
- }
-
- if ( value !== undefined ) {
- if ( hooks && "set" in hooks &&
- ( ret = hooks.set( elem, value, name ) ) !== undefined ) {
- return ret;
- }
-
- return ( elem[ name ] = value );
- }
-
- if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
- return ret;
- }
-
- return elem[ name ];
- },
-
- propHooks: {
- tabIndex: {
- get: function( elem ) {
-
- // Support: IE <=9 - 11 only
- // elem.tabIndex doesn't always return the
- // correct value when it hasn't been explicitly set
- // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
- // Use proper attribute retrieval(#12072)
- var tabindex = jQuery.find.attr( elem, "tabindex" );
-
- if ( tabindex ) {
- return parseInt( tabindex, 10 );
- }
-
- if (
- rfocusable.test( elem.nodeName ) ||
- rclickable.test( elem.nodeName ) &&
- elem.href
- ) {
- return 0;
- }
-
- return -1;
- }
- }
- },
-
- propFix: {
- "for": "htmlFor",
- "class": "className"
- }
-} );
-
-// Support: IE <=11 only
-// Accessing the selectedIndex property
-// forces the browser to respect setting selected
-// on the option
-// The getter ensures a default option is selected
-// when in an optgroup
-// eslint rule "no-unused-expressions" is disabled for this code
-// since it considers such accessions noop
-if ( !support.optSelected ) {
- jQuery.propHooks.selected = {
- get: function( elem ) {
-
- /* eslint no-unused-expressions: "off" */
-
- var parent = elem.parentNode;
- if ( parent && parent.parentNode ) {
- parent.parentNode.selectedIndex;
- }
- return null;
- },
- set: function( elem ) {
-
- /* eslint no-unused-expressions: "off" */
-
- var parent = elem.parentNode;
- if ( parent ) {
- parent.selectedIndex;
-
- if ( parent.parentNode ) {
- parent.parentNode.selectedIndex;
- }
- }
- }
- };
-}
-
-jQuery.each( [
- "tabIndex",
- "readOnly",
- "maxLength",
- "cellSpacing",
- "cellPadding",
- "rowSpan",
- "colSpan",
- "useMap",
- "frameBorder",
- "contentEditable"
-], function() {
- jQuery.propFix[ this.toLowerCase() ] = this;
-} );
-
-
-
-
- // Strip and collapse whitespace according to HTML spec
- // https://html.spec.whatwg.org/multipage/infrastructure.html#strip-and-collapse-whitespace
- function stripAndCollapse( value ) {
- var tokens = value.match( rnothtmlwhite ) || [];
- return tokens.join( " " );
- }
-
-
-function getClass( elem ) {
- return elem.getAttribute && elem.getAttribute( "class" ) || "";
-}
-
-jQuery.fn.extend( {
- addClass: function( value ) {
- var classes, elem, cur, curValue, clazz, j, finalValue,
- i = 0;
-
- if ( jQuery.isFunction( value ) ) {
- return this.each( function( j ) {
- jQuery( this ).addClass( value.call( this, j, getClass( this ) ) );
- } );
- }
-
- if ( typeof value === "string" && value ) {
- classes = value.match( rnothtmlwhite ) || [];
-
- while ( ( elem = this[ i++ ] ) ) {
- curValue = getClass( elem );
- cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
-
- if ( cur ) {
- j = 0;
- while ( ( clazz = classes[ j++ ] ) ) {
- if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
- cur += clazz + " ";
- }
- }
-
- // Only assign if different to avoid unneeded rendering.
- finalValue = stripAndCollapse( cur );
- if ( curValue !== finalValue ) {
- elem.setAttribute( "class", finalValue );
- }
- }
- }
- }
-
- return this;
- },
-
- removeClass: function( value ) {
- var classes, elem, cur, curValue, clazz, j, finalValue,
- i = 0;
-
- if ( jQuery.isFunction( value ) ) {
- return this.each( function( j ) {
- jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) );
- } );
- }
-
- if ( !arguments.length ) {
- return this.attr( "class", "" );
- }
-
- if ( typeof value === "string" && value ) {
- classes = value.match( rnothtmlwhite ) || [];
-
- while ( ( elem = this[ i++ ] ) ) {
- curValue = getClass( elem );
-
- // This expression is here for better compressibility (see addClass)
- cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
-
- if ( cur ) {
- j = 0;
- while ( ( clazz = classes[ j++ ] ) ) {
-
- // Remove *all* instances
- while ( cur.indexOf( " " + clazz + " " ) > -1 ) {
- cur = cur.replace( " " + clazz + " ", " " );
- }
- }
-
- // Only assign if different to avoid unneeded rendering.
- finalValue = stripAndCollapse( cur );
- if ( curValue !== finalValue ) {
- elem.setAttribute( "class", finalValue );
- }
- }
- }
- }
-
- return this;
- },
-
- toggleClass: function( value, stateVal ) {
- var type = typeof value;
-
- if ( typeof stateVal === "boolean" && type === "string" ) {
- return stateVal ? this.addClass( value ) : this.removeClass( value );
- }
-
- if ( jQuery.isFunction( value ) ) {
- return this.each( function( i ) {
- jQuery( this ).toggleClass(
- value.call( this, i, getClass( this ), stateVal ),
- stateVal
- );
- } );
- }
-
- return this.each( function() {
- var className, i, self, classNames;
-
- if ( type === "string" ) {
-
- // Toggle individual class names
- i = 0;
- self = jQuery( this );
- classNames = value.match( rnothtmlwhite ) || [];
-
- while ( ( className = classNames[ i++ ] ) ) {
-
- // Check each className given, space separated list
- if ( self.hasClass( className ) ) {
- self.removeClass( className );
- } else {
- self.addClass( className );
- }
- }
-
- // Toggle whole class name
- } else if ( value === undefined || type === "boolean" ) {
- className = getClass( this );
- if ( className ) {
-
- // Store className if set
- dataPriv.set( this, "__className__", className );
- }
-
- // If the element has a class name or if we're passed `false`,
- // then remove the whole classname (if there was one, the above saved it).
- // Otherwise bring back whatever was previously saved (if anything),
- // falling back to the empty string if nothing was stored.
- if ( this.setAttribute ) {
- this.setAttribute( "class",
- className || value === false ?
- "" :
- dataPriv.get( this, "__className__" ) || ""
- );
- }
- }
- } );
- },
-
- hasClass: function( selector ) {
- var className, elem,
- i = 0;
-
- className = " " + selector + " ";
- while ( ( elem = this[ i++ ] ) ) {
- if ( elem.nodeType === 1 &&
- ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) {
- return true;
- }
- }
-
- return false;
- }
-} );
-
-
-
-
-var rreturn = /\r/g;
-
-jQuery.fn.extend( {
- val: function( value ) {
- var hooks, ret, isFunction,
- elem = this[ 0 ];
-
- if ( !arguments.length ) {
- if ( elem ) {
- hooks = jQuery.valHooks[ elem.type ] ||
- jQuery.valHooks[ elem.nodeName.toLowerCase() ];
-
- if ( hooks &&
- "get" in hooks &&
- ( ret = hooks.get( elem, "value" ) ) !== undefined
- ) {
- return ret;
- }
-
- ret = elem.value;
-
- // Handle most common string cases
- if ( typeof ret === "string" ) {
- return ret.replace( rreturn, "" );
- }
-
- // Handle cases where value is null/undef or number
- return ret == null ? "" : ret;
- }
-
- return;
- }
-
- isFunction = jQuery.isFunction( value );
-
- return this.each( function( i ) {
- var val;
-
- if ( this.nodeType !== 1 ) {
- return;
- }
-
- if ( isFunction ) {
- val = value.call( this, i, jQuery( this ).val() );
- } else {
- val = value;
- }
-
- // Treat null/undefined as ""; convert numbers to string
- if ( val == null ) {
- val = "";
-
- } else if ( typeof val === "number" ) {
- val += "";
-
- } else if ( Array.isArray( val ) ) {
- val = jQuery.map( val, function( value ) {
- return value == null ? "" : value + "";
- } );
- }
-
- hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
-
- // If set returns undefined, fall back to normal setting
- if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) {
- this.value = val;
- }
- } );
- }
-} );
-
-jQuery.extend( {
- valHooks: {
- option: {
- get: function( elem ) {
-
- var val = jQuery.find.attr( elem, "value" );
- return val != null ?
- val :
-
- // Support: IE <=10 - 11 only
- // option.text throws exceptions (#14686, #14858)
- // Strip and collapse whitespace
- // https://html.spec.whatwg.org/#strip-and-collapse-whitespace
- stripAndCollapse( jQuery.text( elem ) );
- }
- },
- select: {
- get: function( elem ) {
- var value, option, i,
- options = elem.options,
- index = elem.selectedIndex,
- one = elem.type === "select-one",
- values = one ? null : [],
- max = one ? index + 1 : options.length;
-
- if ( index < 0 ) {
- i = max;
-
- } else {
- i = one ? index : 0;
- }
-
- // Loop through all the selected options
- for ( ; i < max; i++ ) {
- option = options[ i ];
-
- // Support: IE <=9 only
- // IE8-9 doesn't update selected after form reset (#2551)
- if ( ( option.selected || i === index ) &&
-
- // Don't return options that are disabled or in a disabled optgroup
- !option.disabled &&
- ( !option.parentNode.disabled ||
- !nodeName( option.parentNode, "optgroup" ) ) ) {
-
- // Get the specific value for the option
- value = jQuery( option ).val();
-
- // We don't need an array for one selects
- if ( one ) {
- return value;
- }
-
- // Multi-Selects return an array
- values.push( value );
- }
- }
-
- return values;
- },
-
- set: function( elem, value ) {
- var optionSet, option,
- options = elem.options,
- values = jQuery.makeArray( value ),
- i = options.length;
-
- while ( i-- ) {
- option = options[ i ];
-
- /* eslint-disable no-cond-assign */
-
- if ( option.selected =
- jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1
- ) {
- optionSet = true;
- }
-
- /* eslint-enable no-cond-assign */
- }
-
- // Force browsers to behave consistently when non-matching value is set
- if ( !optionSet ) {
- elem.selectedIndex = -1;
- }
- return values;
- }
- }
- }
-} );
-
-// Radios and checkboxes getter/setter
-jQuery.each( [ "radio", "checkbox" ], function() {
- jQuery.valHooks[ this ] = {
- set: function( elem, value ) {
- if ( Array.isArray( value ) ) {
- return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 );
- }
- }
- };
- if ( !support.checkOn ) {
- jQuery.valHooks[ this ].get = function( elem ) {
- return elem.getAttribute( "value" ) === null ? "on" : elem.value;
- };
- }
-} );
-
-
-
-
-// Return jQuery for attributes-only inclusion
-
-
-var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/;
-
-jQuery.extend( jQuery.event, {
-
- trigger: function( event, data, elem, onlyHandlers ) {
-
- var i, cur, tmp, bubbleType, ontype, handle, special,
- eventPath = [ elem || document ],
- type = hasOwn.call( event, "type" ) ? event.type : event,
- namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : [];
-
- cur = tmp = elem = elem || document;
-
- // Don't do events on text and comment nodes
- if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
- return;
- }
-
- // focus/blur morphs to focusin/out; ensure we're not firing them right now
- if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
- return;
- }
-
- if ( type.indexOf( "." ) > -1 ) {
-
- // Namespaced trigger; create a regexp to match event type in handle()
- namespaces = type.split( "." );
- type = namespaces.shift();
- namespaces.sort();
- }
- ontype = type.indexOf( ":" ) < 0 && "on" + type;
-
- // Caller can pass in a jQuery.Event object, Object, or just an event type string
- event = event[ jQuery.expando ] ?
- event :
- new jQuery.Event( type, typeof event === "object" && event );
-
- // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
- event.isTrigger = onlyHandlers ? 2 : 3;
- event.namespace = namespaces.join( "." );
- event.rnamespace = event.namespace ?
- new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) :
- null;
-
- // Clean up the event in case it is being reused
- event.result = undefined;
- if ( !event.target ) {
- event.target = elem;
- }
-
- // Clone any incoming data and prepend the event, creating the handler arg list
- data = data == null ?
- [ event ] :
- jQuery.makeArray( data, [ event ] );
-
- // Allow special events to draw outside the lines
- special = jQuery.event.special[ type ] || {};
- if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
- return;
- }
-
- // Determine event propagation path in advance, per W3C events spec (#9951)
- // Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
- if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
-
- bubbleType = special.delegateType || type;
- if ( !rfocusMorph.test( bubbleType + type ) ) {
- cur = cur.parentNode;
- }
- for ( ; cur; cur = cur.parentNode ) {
- eventPath.push( cur );
- tmp = cur;
- }
-
- // Only add window if we got to document (e.g., not plain obj or detached DOM)
- if ( tmp === ( elem.ownerDocument || document ) ) {
- eventPath.push( tmp.defaultView || tmp.parentWindow || window );
- }
- }
-
- // Fire handlers on the event path
- i = 0;
- while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) {
-
- event.type = i > 1 ?
- bubbleType :
- special.bindType || type;
-
- // jQuery handler
- handle = ( dataPriv.get( cur, "events" ) || {} )[ event.type ] &&
- dataPriv.get( cur, "handle" );
- if ( handle ) {
- handle.apply( cur, data );
- }
-
- // Native handler
- handle = ontype && cur[ ontype ];
- if ( handle && handle.apply && acceptData( cur ) ) {
- event.result = handle.apply( cur, data );
- if ( event.result === false ) {
- event.preventDefault();
- }
- }
- }
- event.type = type;
-
- // If nobody prevented the default action, do it now
- if ( !onlyHandlers && !event.isDefaultPrevented() ) {
-
- if ( ( !special._default ||
- special._default.apply( eventPath.pop(), data ) === false ) &&
- acceptData( elem ) ) {
-
- // Call a native DOM method on the target with the same name as the event.
- // Don't do default actions on window, that's where global variables be (#6170)
- if ( ontype && jQuery.isFunction( elem[ type ] ) && !jQuery.isWindow( elem ) ) {
-
- // Don't re-trigger an onFOO event when we call its FOO() method
- tmp = elem[ ontype ];
-
- if ( tmp ) {
- elem[ ontype ] = null;
- }
-
- // Prevent re-triggering of the same event, since we already bubbled it above
- jQuery.event.triggered = type;
- elem[ type ]();
- jQuery.event.triggered = undefined;
-
- if ( tmp ) {
- elem[ ontype ] = tmp;
- }
- }
- }
- }
-
- return event.result;
- },
-
- // Piggyback on a donor event to simulate a different one
- // Used only for `focus(in | out)` events
- simulate: function( type, elem, event ) {
- var e = jQuery.extend(
- new jQuery.Event(),
- event,
- {
- type: type,
- isSimulated: true
- }
- );
-
- jQuery.event.trigger( e, null, elem );
- }
-
-} );
-
-jQuery.fn.extend( {
-
- trigger: function( type, data ) {
- return this.each( function() {
- jQuery.event.trigger( type, data, this );
- } );
- },
- triggerHandler: function( type, data ) {
- var elem = this[ 0 ];
- if ( elem ) {
- return jQuery.event.trigger( type, data, elem, true );
- }
- }
-} );
-
-
-jQuery.each( ( "blur focus focusin focusout resize scroll click dblclick " +
- "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
- "change select submit keydown keypress keyup contextmenu" ).split( " " ),
- function( i, name ) {
-
- // Handle event binding
- jQuery.fn[ name ] = function( data, fn ) {
- return arguments.length > 0 ?
- this.on( name, null, data, fn ) :
- this.trigger( name );
- };
-} );
-
-jQuery.fn.extend( {
- hover: function( fnOver, fnOut ) {
- return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
- }
-} );
-
-
-
-
-support.focusin = "onfocusin" in window;
-
-
-// Support: Firefox <=44
-// Firefox doesn't have focus(in | out) events
-// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787
-//
-// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1
-// focus(in | out) events fire after focus & blur events,
-// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order
-// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857
-if ( !support.focusin ) {
- jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) {
-
- // Attach a single capturing handler on the document while someone wants focusin/focusout
- var handler = function( event ) {
- jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) );
- };
-
- jQuery.event.special[ fix ] = {
- setup: function() {
- var doc = this.ownerDocument || this,
- attaches = dataPriv.access( doc, fix );
-
- if ( !attaches ) {
- doc.addEventListener( orig, handler, true );
- }
- dataPriv.access( doc, fix, ( attaches || 0 ) + 1 );
- },
- teardown: function() {
- var doc = this.ownerDocument || this,
- attaches = dataPriv.access( doc, fix ) - 1;
-
- if ( !attaches ) {
- doc.removeEventListener( orig, handler, true );
- dataPriv.remove( doc, fix );
-
- } else {
- dataPriv.access( doc, fix, attaches );
- }
- }
- };
- } );
-}
-var location = window.location;
-
-var nonce = jQuery.now();
-
-var rquery = ( /\?/ );
-
-
-
-// Cross-browser xml parsing
-jQuery.parseXML = function( data ) {
- var xml;
- if ( !data || typeof data !== "string" ) {
- return null;
- }
-
- // Support: IE 9 - 11 only
- // IE throws on parseFromString with invalid input.
- try {
- xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" );
- } catch ( e ) {
- xml = undefined;
- }
-
- if ( !xml || xml.getElementsByTagName( "parsererror" ).length ) {
- jQuery.error( "Invalid XML: " + data );
- }
- return xml;
-};
-
-
-var
- rbracket = /\[\]$/,
- rCRLF = /\r?\n/g,
- rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
- rsubmittable = /^(?:input|select|textarea|keygen)/i;
-
-function buildParams( prefix, obj, traditional, add ) {
- var name;
-
- if ( Array.isArray( obj ) ) {
-
- // Serialize array item.
- jQuery.each( obj, function( i, v ) {
- if ( traditional || rbracket.test( prefix ) ) {
-
- // Treat each array item as a scalar.
- add( prefix, v );
-
- } else {
-
- // Item is non-scalar (array or object), encode its numeric index.
- buildParams(
- prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]",
- v,
- traditional,
- add
- );
- }
- } );
-
- } else if ( !traditional && jQuery.type( obj ) === "object" ) {
-
- // Serialize object item.
- for ( name in obj ) {
- buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
- }
-
- } else {
-
- // Serialize scalar item.
- add( prefix, obj );
- }
-}
-
-// Serialize an array of form elements or a set of
-// key/values into a query string
-jQuery.param = function( a, traditional ) {
- var prefix,
- s = [],
- add = function( key, valueOrFunction ) {
-
- // If value is a function, invoke it and use its return value
- var value = jQuery.isFunction( valueOrFunction ) ?
- valueOrFunction() :
- valueOrFunction;
-
- s[ s.length ] = encodeURIComponent( key ) + "=" +
- encodeURIComponent( value == null ? "" : value );
- };
-
- // If an array was passed in, assume that it is an array of form elements.
- if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
-
- // Serialize the form elements
- jQuery.each( a, function() {
- add( this.name, this.value );
- } );
-
- } else {
-
- // If traditional, encode the "old" way (the way 1.3.2 or older
- // did it), otherwise encode params recursively.
- for ( prefix in a ) {
- buildParams( prefix, a[ prefix ], traditional, add );
- }
- }
-
- // Return the resulting serialization
- return s.join( "&" );
-};
-
-jQuery.fn.extend( {
- serialize: function() {
- return jQuery.param( this.serializeArray() );
- },
- serializeArray: function() {
- return this.map( function() {
-
- // Can add propHook for "elements" to filter or add form elements
- var elements = jQuery.prop( this, "elements" );
- return elements ? jQuery.makeArray( elements ) : this;
- } )
- .filter( function() {
- var type = this.type;
-
- // Use .is( ":disabled" ) so that fieldset[disabled] works
- return this.name && !jQuery( this ).is( ":disabled" ) &&
- rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
- ( this.checked || !rcheckableType.test( type ) );
- } )
- .map( function( i, elem ) {
- var val = jQuery( this ).val();
-
- if ( val == null ) {
- return null;
- }
-
- if ( Array.isArray( val ) ) {
- return jQuery.map( val, function( val ) {
- return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
- } );
- }
-
- return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
- } ).get();
- }
-} );
-
-
-var
- r20 = /%20/g,
- rhash = /#.*$/,
- rantiCache = /([?&])_=[^&]*/,
- rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg,
-
- // #7653, #8125, #8152: local protocol detection
- rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
- rnoContent = /^(?:GET|HEAD)$/,
- rprotocol = /^\/\//,
-
- /* Prefilters
- * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
- * 2) These are called:
- * - BEFORE asking for a transport
- * - AFTER param serialization (s.data is a string if s.processData is true)
- * 3) key is the dataType
- * 4) the catchall symbol "*" can be used
- * 5) execution will start with transport dataType and THEN continue down to "*" if needed
- */
- prefilters = {},
-
- /* Transports bindings
- * 1) key is the dataType
- * 2) the catchall symbol "*" can be used
- * 3) selection will start with transport dataType and THEN go to "*" if needed
- */
- transports = {},
-
- // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
- allTypes = "*/".concat( "*" ),
-
- // Anchor tag for parsing the document origin
- originAnchor = document.createElement( "a" );
- originAnchor.href = location.href;
-
-// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
-function addToPrefiltersOrTransports( structure ) {
-
- // dataTypeExpression is optional and defaults to "*"
- return function( dataTypeExpression, func ) {
-
- if ( typeof dataTypeExpression !== "string" ) {
- func = dataTypeExpression;
- dataTypeExpression = "*";
- }
-
- var dataType,
- i = 0,
- dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || [];
-
- if ( jQuery.isFunction( func ) ) {
-
- // For each dataType in the dataTypeExpression
- while ( ( dataType = dataTypes[ i++ ] ) ) {
-
- // Prepend if requested
- if ( dataType[ 0 ] === "+" ) {
- dataType = dataType.slice( 1 ) || "*";
- ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func );
-
- // Otherwise append
- } else {
- ( structure[ dataType ] = structure[ dataType ] || [] ).push( func );
- }
- }
- }
- };
-}
-
-// Base inspection function for prefilters and transports
-function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) {
-
- var inspected = {},
- seekingTransport = ( structure === transports );
-
- function inspect( dataType ) {
- var selected;
- inspected[ dataType ] = true;
- jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
- var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
- if ( typeof dataTypeOrTransport === "string" &&
- !seekingTransport && !inspected[ dataTypeOrTransport ] ) {
-
- options.dataTypes.unshift( dataTypeOrTransport );
- inspect( dataTypeOrTransport );
- return false;
- } else if ( seekingTransport ) {
- return !( selected = dataTypeOrTransport );
- }
- } );
- return selected;
- }
-
- return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" );
-}
-
-// A special extend for ajax options
-// that takes "flat" options (not to be deep extended)
-// Fixes #9887
-function ajaxExtend( target, src ) {
- var key, deep,
- flatOptions = jQuery.ajaxSettings.flatOptions || {};
-
- for ( key in src ) {
- if ( src[ key ] !== undefined ) {
- ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ];
- }
- }
- if ( deep ) {
- jQuery.extend( true, target, deep );
- }
-
- return target;
-}
-
-/* Handles responses to an ajax request:
- * - finds the right dataType (mediates between content-type and expected dataType)
- * - returns the corresponding response
- */
-function ajaxHandleResponses( s, jqXHR, responses ) {
-
- var ct, type, finalDataType, firstDataType,
- contents = s.contents,
- dataTypes = s.dataTypes;
-
- // Remove auto dataType and get content-type in the process
- while ( dataTypes[ 0 ] === "*" ) {
- dataTypes.shift();
- if ( ct === undefined ) {
- ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" );
- }
- }
-
- // Check if we're dealing with a known content-type
- if ( ct ) {
- for ( type in contents ) {
- if ( contents[ type ] && contents[ type ].test( ct ) ) {
- dataTypes.unshift( type );
- break;
- }
- }
- }
-
- // Check to see if we have a response for the expected dataType
- if ( dataTypes[ 0 ] in responses ) {
- finalDataType = dataTypes[ 0 ];
- } else {
-
- // Try convertible dataTypes
- for ( type in responses ) {
- if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) {
- finalDataType = type;
- break;
- }
- if ( !firstDataType ) {
- firstDataType = type;
- }
- }
-
- // Or just use first one
- finalDataType = finalDataType || firstDataType;
- }
-
- // If we found a dataType
- // We add the dataType to the list if needed
- // and return the corresponding response
- if ( finalDataType ) {
- if ( finalDataType !== dataTypes[ 0 ] ) {
- dataTypes.unshift( finalDataType );
- }
- return responses[ finalDataType ];
- }
-}
-
-/* Chain conversions given the request and the original response
- * Also sets the responseXXX fields on the jqXHR instance
- */
-function ajaxConvert( s, response, jqXHR, isSuccess ) {
- var conv2, current, conv, tmp, prev,
- converters = {},
-
- // Work with a copy of dataTypes in case we need to modify it for conversion
- dataTypes = s.dataTypes.slice();
-
- // Create converters map with lowercased keys
- if ( dataTypes[ 1 ] ) {
- for ( conv in s.converters ) {
- converters[ conv.toLowerCase() ] = s.converters[ conv ];
- }
- }
-
- current = dataTypes.shift();
-
- // Convert to each sequential dataType
- while ( current ) {
-
- if ( s.responseFields[ current ] ) {
- jqXHR[ s.responseFields[ current ] ] = response;
- }
-
- // Apply the dataFilter if provided
- if ( !prev && isSuccess && s.dataFilter ) {
- response = s.dataFilter( response, s.dataType );
- }
-
- prev = current;
- current = dataTypes.shift();
-
- if ( current ) {
-
- // There's only work to do if current dataType is non-auto
- if ( current === "*" ) {
-
- current = prev;
-
- // Convert response if prev dataType is non-auto and differs from current
- } else if ( prev !== "*" && prev !== current ) {
-
- // Seek a direct converter
- conv = converters[ prev + " " + current ] || converters[ "* " + current ];
-
- // If none found, seek a pair
- if ( !conv ) {
- for ( conv2 in converters ) {
-
- // If conv2 outputs current
- tmp = conv2.split( " " );
- if ( tmp[ 1 ] === current ) {
-
- // If prev can be converted to accepted input
- conv = converters[ prev + " " + tmp[ 0 ] ] ||
- converters[ "* " + tmp[ 0 ] ];
- if ( conv ) {
-
- // Condense equivalence converters
- if ( conv === true ) {
- conv = converters[ conv2 ];
-
- // Otherwise, insert the intermediate dataType
- } else if ( converters[ conv2 ] !== true ) {
- current = tmp[ 0 ];
- dataTypes.unshift( tmp[ 1 ] );
- }
- break;
- }
- }
- }
- }
-
- // Apply converter (if not an equivalence)
- if ( conv !== true ) {
-
- // Unless errors are allowed to bubble, catch and return them
- if ( conv && s.throws ) {
- response = conv( response );
- } else {
- try {
- response = conv( response );
- } catch ( e ) {
- return {
- state: "parsererror",
- error: conv ? e : "No conversion from " + prev + " to " + current
- };
- }
- }
- }
- }
- }
- }
-
- return { state: "success", data: response };
-}
-
-jQuery.extend( {
-
- // Counter for holding the number of active queries
- active: 0,
-
- // Last-Modified header cache for next request
- lastModified: {},
- etag: {},
-
- ajaxSettings: {
- url: location.href,
- type: "GET",
- isLocal: rlocalProtocol.test( location.protocol ),
- global: true,
- processData: true,
- async: true,
- contentType: "application/x-www-form-urlencoded; charset=UTF-8",
-
- /*
- timeout: 0,
- data: null,
- dataType: null,
- username: null,
- password: null,
- cache: null,
- throws: false,
- traditional: false,
- headers: {},
- */
-
- accepts: {
- "*": allTypes,
- text: "text/plain",
- html: "text/html",
- xml: "application/xml, text/xml",
- json: "application/json, text/javascript"
- },
-
- contents: {
- xml: /\bxml\b/,
- html: /\bhtml/,
- json: /\bjson\b/
- },
-
- responseFields: {
- xml: "responseXML",
- text: "responseText",
- json: "responseJSON"
- },
-
- // Data converters
- // Keys separate source (or catchall "*") and destination types with a single space
- converters: {
-
- // Convert anything to text
- "* text": String,
-
- // Text to html (true = no transformation)
- "text html": true,
-
- // Evaluate text as a json expression
- "text json": JSON.parse,
-
- // Parse text as xml
- "text xml": jQuery.parseXML
- },
-
- // For options that shouldn't be deep extended:
- // you can add your own custom options here if
- // and when you create one that shouldn't be
- // deep extended (see ajaxExtend)
- flatOptions: {
- url: true,
- context: true
- }
- },
-
- // Creates a full fledged settings object into target
- // with both ajaxSettings and settings fields.
- // If target is omitted, writes into ajaxSettings.
- ajaxSetup: function( target, settings ) {
- return settings ?
-
- // Building a settings object
- ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) :
-
- // Extending ajaxSettings
- ajaxExtend( jQuery.ajaxSettings, target );
- },
-
- ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
- ajaxTransport: addToPrefiltersOrTransports( transports ),
-
- // Main method
- ajax: function( url, options ) {
-
- // If url is an object, simulate pre-1.5 signature
- if ( typeof url === "object" ) {
- options = url;
- url = undefined;
- }
-
- // Force options to be an object
- options = options || {};
-
- var transport,
-
- // URL without anti-cache param
- cacheURL,
-
- // Response headers
- responseHeadersString,
- responseHeaders,
-
- // timeout handle
- timeoutTimer,
-
- // Url cleanup var
- urlAnchor,
-
- // Request state (becomes false upon send and true upon completion)
- completed,
-
- // To know if global events are to be dispatched
- fireGlobals,
-
- // Loop variable
- i,
-
- // uncached part of the url
- uncached,
-
- // Create the final options object
- s = jQuery.ajaxSetup( {}, options ),
-
- // Callbacks context
- callbackContext = s.context || s,
-
- // Context for global events is callbackContext if it is a DOM node or jQuery collection
- globalEventContext = s.context &&
- ( callbackContext.nodeType || callbackContext.jquery ) ?
- jQuery( callbackContext ) :
- jQuery.event,
-
- // Deferreds
- deferred = jQuery.Deferred(),
- completeDeferred = jQuery.Callbacks( "once memory" ),
-
- // Status-dependent callbacks
- statusCode = s.statusCode || {},
-
- // Headers (they are sent all at once)
- requestHeaders = {},
- requestHeadersNames = {},
-
- // Default abort message
- strAbort = "canceled",
-
- // Fake xhr
- jqXHR = {
- readyState: 0,
-
- // Builds headers hashtable if needed
- getResponseHeader: function( key ) {
- var match;
- if ( completed ) {
- if ( !responseHeaders ) {
- responseHeaders = {};
- while ( ( match = rheaders.exec( responseHeadersString ) ) ) {
- responseHeaders[ match[ 1 ].toLowerCase() ] = match[ 2 ];
- }
- }
- match = responseHeaders[ key.toLowerCase() ];
- }
- return match == null ? null : match;
- },
-
- // Raw string
- getAllResponseHeaders: function() {
- return completed ? responseHeadersString : null;
- },
-
- // Caches the header
- setRequestHeader: function( name, value ) {
- if ( completed == null ) {
- name = requestHeadersNames[ name.toLowerCase() ] =
- requestHeadersNames[ name.toLowerCase() ] || name;
- requestHeaders[ name ] = value;
- }
- return this;
- },
-
- // Overrides response content-type header
- overrideMimeType: function( type ) {
- if ( completed == null ) {
- s.mimeType = type;
- }
- return this;
- },
-
- // Status-dependent callbacks
- statusCode: function( map ) {
- var code;
- if ( map ) {
- if ( completed ) {
-
- // Execute the appropriate callbacks
- jqXHR.always( map[ jqXHR.status ] );
- } else {
-
- // Lazy-add the new callbacks in a way that preserves old ones
- for ( code in map ) {
- statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
- }
- }
- }
- return this;
- },
-
- // Cancel the request
- abort: function( statusText ) {
- var finalText = statusText || strAbort;
- if ( transport ) {
- transport.abort( finalText );
- }
- done( 0, finalText );
- return this;
- }
- };
-
- // Attach deferreds
- deferred.promise( jqXHR );
-
- // Add protocol if not provided (prefilters might expect it)
- // Handle falsy url in the settings object (#10093: consistency with old signature)
- // We also use the url parameter if available
- s.url = ( ( url || s.url || location.href ) + "" )
- .replace( rprotocol, location.protocol + "//" );
-
- // Alias method option to type as per ticket #12004
- s.type = options.method || options.type || s.method || s.type;
-
- // Extract dataTypes list
- s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ];
-
- // A cross-domain request is in order when the origin doesn't match the current origin.
- if ( s.crossDomain == null ) {
- urlAnchor = document.createElement( "a" );
-
- // Support: IE <=8 - 11, Edge 12 - 13
- // IE throws exception on accessing the href property if url is malformed,
- // e.g. http://example.com:80x/
- try {
- urlAnchor.href = s.url;
-
- // Support: IE <=8 - 11 only
- // Anchor's host property isn't correctly set when s.url is relative
- urlAnchor.href = urlAnchor.href;
- s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !==
- urlAnchor.protocol + "//" + urlAnchor.host;
- } catch ( e ) {
-
- // If there is an error parsing the URL, assume it is crossDomain,
- // it can be rejected by the transport if it is invalid
- s.crossDomain = true;
- }
- }
-
- // Convert data if not already a string
- if ( s.data && s.processData && typeof s.data !== "string" ) {
- s.data = jQuery.param( s.data, s.traditional );
- }
-
- // Apply prefilters
- inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
-
- // If request was aborted inside a prefilter, stop there
- if ( completed ) {
- return jqXHR;
- }
-
- // We can fire global events as of now if asked to
- // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118)
- fireGlobals = jQuery.event && s.global;
-
- // Watch for a new set of requests
- if ( fireGlobals && jQuery.active++ === 0 ) {
- jQuery.event.trigger( "ajaxStart" );
- }
-
- // Uppercase the type
- s.type = s.type.toUpperCase();
-
- // Determine if request has content
- s.hasContent = !rnoContent.test( s.type );
-
- // Save the URL in case we're toying with the If-Modified-Since
- // and/or If-None-Match header later on
- // Remove hash to simplify url manipulation
- cacheURL = s.url.replace( rhash, "" );
-
- // More options handling for requests with no content
- if ( !s.hasContent ) {
-
- // Remember the hash so we can put it back
- uncached = s.url.slice( cacheURL.length );
-
- // If data is available, append data to url
- if ( s.data ) {
- cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data;
-
- // #9682: remove data so that it's not used in an eventual retry
- delete s.data;
- }
-
- // Add or update anti-cache param if needed
- if ( s.cache === false ) {
- cacheURL = cacheURL.replace( rantiCache, "$1" );
- uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce++ ) + uncached;
- }
-
- // Put hash and anti-cache on the URL that will be requested (gh-1732)
- s.url = cacheURL + uncached;
-
- // Change '%20' to '+' if this is encoded form body content (gh-2658)
- } else if ( s.data && s.processData &&
- ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) {
- s.data = s.data.replace( r20, "+" );
- }
-
- // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
- if ( s.ifModified ) {
- if ( jQuery.lastModified[ cacheURL ] ) {
- jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] );
- }
- if ( jQuery.etag[ cacheURL ] ) {
- jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] );
- }
- }
-
- // Set the correct header, if data is being sent
- if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
- jqXHR.setRequestHeader( "Content-Type", s.contentType );
- }
-
- // Set the Accepts header for the server, depending on the dataType
- jqXHR.setRequestHeader(
- "Accept",
- s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ?
- s.accepts[ s.dataTypes[ 0 ] ] +
- ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
- s.accepts[ "*" ]
- );
-
- // Check for headers option
- for ( i in s.headers ) {
- jqXHR.setRequestHeader( i, s.headers[ i ] );
- }
-
- // Allow custom headers/mimetypes and early abort
- if ( s.beforeSend &&
- ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) {
-
- // Abort if not done already and return
- return jqXHR.abort();
- }
-
- // Aborting is no longer a cancellation
- strAbort = "abort";
-
- // Install callbacks on deferreds
- completeDeferred.add( s.complete );
- jqXHR.done( s.success );
- jqXHR.fail( s.error );
-
- // Get transport
- transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
-
- // If no transport, we auto-abort
- if ( !transport ) {
- done( -1, "No Transport" );
- } else {
- jqXHR.readyState = 1;
-
- // Send global event
- if ( fireGlobals ) {
- globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
- }
-
- // If request was aborted inside ajaxSend, stop there
- if ( completed ) {
- return jqXHR;
- }
-
- // Timeout
- if ( s.async && s.timeout > 0 ) {
- timeoutTimer = window.setTimeout( function() {
- jqXHR.abort( "timeout" );
- }, s.timeout );
- }
-
- try {
- completed = false;
- transport.send( requestHeaders, done );
- } catch ( e ) {
-
- // Rethrow post-completion exceptions
- if ( completed ) {
- throw e;
- }
-
- // Propagate others as results
- done( -1, e );
- }
- }
-
- // Callback for when everything is done
- function done( status, nativeStatusText, responses, headers ) {
- var isSuccess, success, error, response, modified,
- statusText = nativeStatusText;
-
- // Ignore repeat invocations
- if ( completed ) {
- return;
- }
-
- completed = true;
-
- // Clear timeout if it exists
- if ( timeoutTimer ) {
- window.clearTimeout( timeoutTimer );
- }
-
- // Dereference transport for early garbage collection
- // (no matter how long the jqXHR object will be used)
- transport = undefined;
-
- // Cache response headers
- responseHeadersString = headers || "";
-
- // Set readyState
- jqXHR.readyState = status > 0 ? 4 : 0;
-
- // Determine if successful
- isSuccess = status >= 200 && status < 300 || status === 304;
-
- // Get response data
- if ( responses ) {
- response = ajaxHandleResponses( s, jqXHR, responses );
- }
-
- // Convert no matter what (that way responseXXX fields are always set)
- response = ajaxConvert( s, response, jqXHR, isSuccess );
-
- // If successful, handle type chaining
- if ( isSuccess ) {
-
- // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
- if ( s.ifModified ) {
- modified = jqXHR.getResponseHeader( "Last-Modified" );
- if ( modified ) {
- jQuery.lastModified[ cacheURL ] = modified;
- }
- modified = jqXHR.getResponseHeader( "etag" );
- if ( modified ) {
- jQuery.etag[ cacheURL ] = modified;
- }
- }
-
- // if no content
- if ( status === 204 || s.type === "HEAD" ) {
- statusText = "nocontent";
-
- // if not modified
- } else if ( status === 304 ) {
- statusText = "notmodified";
-
- // If we have data, let's convert it
- } else {
- statusText = response.state;
- success = response.data;
- error = response.error;
- isSuccess = !error;
- }
- } else {
-
- // Extract error from statusText and normalize for non-aborts
- error = statusText;
- if ( status || !statusText ) {
- statusText = "error";
- if ( status < 0 ) {
- status = 0;
- }
- }
- }
-
- // Set data for the fake xhr object
- jqXHR.status = status;
- jqXHR.statusText = ( nativeStatusText || statusText ) + "";
-
- // Success/Error
- if ( isSuccess ) {
- deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
- } else {
- deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
- }
-
- // Status-dependent callbacks
- jqXHR.statusCode( statusCode );
- statusCode = undefined;
-
- if ( fireGlobals ) {
- globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError",
- [ jqXHR, s, isSuccess ? success : error ] );
- }
-
- // Complete
- completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
-
- if ( fireGlobals ) {
- globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
-
- // Handle the global AJAX counter
- if ( !( --jQuery.active ) ) {
- jQuery.event.trigger( "ajaxStop" );
- }
- }
- }
-
- return jqXHR;
- },
-
- getJSON: function( url, data, callback ) {
- return jQuery.get( url, data, callback, "json" );
- },
-
- getScript: function( url, callback ) {
- return jQuery.get( url, undefined, callback, "script" );
- }
-} );
-
-jQuery.each( [ "get", "post" ], function( i, method ) {
- jQuery[ method ] = function( url, data, callback, type ) {
-
- // Shift arguments if data argument was omitted
- if ( jQuery.isFunction( data ) ) {
- type = type || callback;
- callback = data;
- data = undefined;
- }
-
- // The url can be an options object (which then must have .url)
- return jQuery.ajax( jQuery.extend( {
- url: url,
- type: method,
- dataType: type,
- data: data,
- success: callback
- }, jQuery.isPlainObject( url ) && url ) );
- };
-} );
-
-
-jQuery._evalUrl = function( url ) {
- return jQuery.ajax( {
- url: url,
-
- // Make this explicit, since user can override this through ajaxSetup (#11264)
- type: "GET",
- dataType: "script",
- cache: true,
- async: false,
- global: false,
- "throws": true
- } );
-};
-
-
-jQuery.fn.extend( {
- wrapAll: function( html ) {
- var wrap;
-
- if ( this[ 0 ] ) {
- if ( jQuery.isFunction( html ) ) {
- html = html.call( this[ 0 ] );
- }
-
- // The elements to wrap the target around
- wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true );
-
- if ( this[ 0 ].parentNode ) {
- wrap.insertBefore( this[ 0 ] );
- }
-
- wrap.map( function() {
- var elem = this;
-
- while ( elem.firstElementChild ) {
- elem = elem.firstElementChild;
- }
-
- return elem;
- } ).append( this );
- }
-
- return this;
- },
-
- wrapInner: function( html ) {
- if ( jQuery.isFunction( html ) ) {
- return this.each( function( i ) {
- jQuery( this ).wrapInner( html.call( this, i ) );
- } );
- }
-
- return this.each( function() {
- var self = jQuery( this ),
- contents = self.contents();
-
- if ( contents.length ) {
- contents.wrapAll( html );
-
- } else {
- self.append( html );
- }
- } );
- },
-
- wrap: function( html ) {
- var isFunction = jQuery.isFunction( html );
-
- return this.each( function( i ) {
- jQuery( this ).wrapAll( isFunction ? html.call( this, i ) : html );
- } );
- },
-
- unwrap: function( selector ) {
- this.parent( selector ).not( "body" ).each( function() {
- jQuery( this ).replaceWith( this.childNodes );
- } );
- return this;
- }
-} );
-
-
-jQuery.expr.pseudos.hidden = function( elem ) {
- return !jQuery.expr.pseudos.visible( elem );
-};
-jQuery.expr.pseudos.visible = function( elem ) {
- return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length );
-};
-
-
-
-
-jQuery.ajaxSettings.xhr = function() {
- try {
- return new window.XMLHttpRequest();
- } catch ( e ) {}
-};
-
-var xhrSuccessStatus = {
-
- // File protocol always yields status code 0, assume 200
- 0: 200,
-
- // Support: IE <=9 only
- // #1450: sometimes IE returns 1223 when it should be 204
- 1223: 204
- },
- xhrSupported = jQuery.ajaxSettings.xhr();
-
-support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
-support.ajax = xhrSupported = !!xhrSupported;
-
-jQuery.ajaxTransport( function( options ) {
- var callback, errorCallback;
-
- // Cross domain only allowed if supported through XMLHttpRequest
- if ( support.cors || xhrSupported && !options.crossDomain ) {
- return {
- send: function( headers, complete ) {
- var i,
- xhr = options.xhr();
-
- xhr.open(
- options.type,
- options.url,
- options.async,
- options.username,
- options.password
- );
-
- // Apply custom fields if provided
- if ( options.xhrFields ) {
- for ( i in options.xhrFields ) {
- xhr[ i ] = options.xhrFields[ i ];
- }
- }
-
- // Override mime type if needed
- if ( options.mimeType && xhr.overrideMimeType ) {
- xhr.overrideMimeType( options.mimeType );
- }
-
- // X-Requested-With header
- // For cross-domain requests, seeing as conditions for a preflight are
- // akin to a jigsaw puzzle, we simply never set it to be sure.
- // (it can always be set on a per-request basis or even using ajaxSetup)
- // For same-domain requests, won't change header if already provided.
- if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) {
- headers[ "X-Requested-With" ] = "XMLHttpRequest";
- }
-
- // Set headers
- for ( i in headers ) {
- xhr.setRequestHeader( i, headers[ i ] );
- }
-
- // Callback
- callback = function( type ) {
- return function() {
- if ( callback ) {
- callback = errorCallback = xhr.onload =
- xhr.onerror = xhr.onabort = xhr.onreadystatechange = null;
-
- if ( type === "abort" ) {
- xhr.abort();
- } else if ( type === "error" ) {
-
- // Support: IE <=9 only
- // On a manual native abort, IE9 throws
- // errors on any property access that is not readyState
- if ( typeof xhr.status !== "number" ) {
- complete( 0, "error" );
- } else {
- complete(
-
- // File: protocol always yields status 0; see #8605, #14207
- xhr.status,
- xhr.statusText
- );
- }
- } else {
- complete(
- xhrSuccessStatus[ xhr.status ] || xhr.status,
- xhr.statusText,
-
- // Support: IE <=9 only
- // IE9 has no XHR2 but throws on binary (trac-11426)
- // For XHR2 non-text, let the caller handle it (gh-2498)
- ( xhr.responseType || "text" ) !== "text" ||
- typeof xhr.responseText !== "string" ?
- { binary: xhr.response } :
- { text: xhr.responseText },
- xhr.getAllResponseHeaders()
- );
- }
- }
- };
- };
-
- // Listen to events
- xhr.onload = callback();
- errorCallback = xhr.onerror = callback( "error" );
-
- // Support: IE 9 only
- // Use onreadystatechange to replace onabort
- // to handle uncaught aborts
- if ( xhr.onabort !== undefined ) {
- xhr.onabort = errorCallback;
- } else {
- xhr.onreadystatechange = function() {
-
- // Check readyState before timeout as it changes
- if ( xhr.readyState === 4 ) {
-
- // Allow onerror to be called first,
- // but that will not handle a native abort
- // Also, save errorCallback to a variable
- // as xhr.onerror cannot be accessed
- window.setTimeout( function() {
- if ( callback ) {
- errorCallback();
- }
- } );
- }
- };
- }
-
- // Create the abort callback
- callback = callback( "abort" );
-
- try {
-
- // Do send the request (this may raise an exception)
- xhr.send( options.hasContent && options.data || null );
- } catch ( e ) {
-
- // #14683: Only rethrow if this hasn't been notified as an error yet
- if ( callback ) {
- throw e;
- }
- }
- },
-
- abort: function() {
- if ( callback ) {
- callback();
- }
- }
- };
- }
-} );
-
-
-
-
-// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432)
-jQuery.ajaxPrefilter( function( s ) {
- if ( s.crossDomain ) {
- s.contents.script = false;
- }
-} );
-
-// Install script dataType
-jQuery.ajaxSetup( {
- accepts: {
- script: "text/javascript, application/javascript, " +
- "application/ecmascript, application/x-ecmascript"
- },
- contents: {
- script: /\b(?:java|ecma)script\b/
- },
- converters: {
- "text script": function( text ) {
- jQuery.globalEval( text );
- return text;
- }
- }
-} );
-
-// Handle cache's special case and crossDomain
-jQuery.ajaxPrefilter( "script", function( s ) {
- if ( s.cache === undefined ) {
- s.cache = false;
- }
- if ( s.crossDomain ) {
- s.type = "GET";
- }
-} );
-
-// Bind script tag hack transport
-jQuery.ajaxTransport( "script", function( s ) {
-
- // This transport only deals with cross domain requests
- if ( s.crossDomain ) {
- var script, callback;
- return {
- send: function( _, complete ) {
- script = jQuery( "<script>" ).prop( {
- charset: s.scriptCharset,
- src: s.url
- } ).on(
- "load error",
- callback = function( evt ) {
- script.remove();
- callback = null;
- if ( evt ) {
- complete( evt.type === "error" ? 404 : 200, evt.type );
- }
- }
- );
-
- // Use native DOM manipulation to avoid our domManip AJAX trickery
- document.head.appendChild( script[ 0 ] );
- },
- abort: function() {
- if ( callback ) {
- callback();
- }
- }
- };
- }
-} );
-
-
-
-
-var oldCallbacks = [],
- rjsonp = /(=)\?(?=&|$)|\?\?/;
-
-// Default jsonp settings
-jQuery.ajaxSetup( {
- jsonp: "callback",
- jsonpCallback: function() {
- var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce++ ) );
- this[ callback ] = true;
- return callback;
- }
-} );
-
-// Detect, normalize options and install callbacks for jsonp requests
-jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
-
- var callbackName, overwritten, responseContainer,
- jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ?
- "url" :
- typeof s.data === "string" &&
- ( s.contentType || "" )
- .indexOf( "application/x-www-form-urlencoded" ) === 0 &&
- rjsonp.test( s.data ) && "data"
- );
-
- // Handle iff the expected data type is "jsonp" or we have a parameter to set
- if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) {
-
- // Get callback name, remembering preexisting value associated with it
- callbackName = s.jsonpCallback = jQuery.isFunction( s.jsonpCallback ) ?
- s.jsonpCallback() :
- s.jsonpCallback;
-
- // Insert callback into url or form data
- if ( jsonProp ) {
- s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName );
- } else if ( s.jsonp !== false ) {
- s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName;
- }
-
- // Use data converter to retrieve json after script execution
- s.converters[ "script json" ] = function() {
- if ( !responseContainer ) {
- jQuery.error( callbackName + " was not called" );
- }
- return responseContainer[ 0 ];
- };
-
- // Force json dataType
- s.dataTypes[ 0 ] = "json";
-
- // Install callback
- overwritten = window[ callbackName ];
- window[ callbackName ] = function() {
- responseContainer = arguments;
- };
-
- // Clean-up function (fires after converters)
- jqXHR.always( function() {
-
- // If previous value didn't exist - remove it
- if ( overwritten === undefined ) {
- jQuery( window ).removeProp( callbackName );
-
- // Otherwise restore preexisting value
- } else {
- window[ callbackName ] = overwritten;
- }
-
- // Save back as free
- if ( s[ callbackName ] ) {
-
- // Make sure that re-using the options doesn't screw things around
- s.jsonpCallback = originalSettings.jsonpCallback;
-
- // Save the callback name for future use
- oldCallbacks.push( callbackName );
- }
-
- // Call if it was a function and we have a response
- if ( responseContainer && jQuery.isFunction( overwritten ) ) {
- overwritten( responseContainer[ 0 ] );
- }
-
- responseContainer = overwritten = undefined;
- } );
-
- // Delegate to script
- return "script";
- }
-} );
-
-
-
-
-// Support: Safari 8 only
-// In Safari 8 documents created via document.implementation.createHTMLDocument
-// collapse sibling forms: the second one becomes a child of the first one.
-// Because of that, this security measure has to be disabled in Safari 8.
-// https://bugs.webkit.org/show_bug.cgi?id=137337
-support.createHTMLDocument = ( function() {
- var body = document.implementation.createHTMLDocument( "" ).body;
- body.innerHTML = "<form></form><form></form>";
- return body.childNodes.length === 2;
-} )();
-
-
-// Argument "data" should be string of html
-// context (optional): If specified, the fragment will be created in this context,
-// defaults to document
-// keepScripts (optional): If true, will include scripts passed in the html string
-jQuery.parseHTML = function( data, context, keepScripts ) {
- if ( typeof data !== "string" ) {
- return [];
- }
- if ( typeof context === "boolean" ) {
- keepScripts = context;
- context = false;
- }
-
- var base, parsed, scripts;
-
- if ( !context ) {
-
- // Stop scripts or inline event handlers from being executed immediately
- // by using document.implementation
- if ( support.createHTMLDocument ) {
- context = document.implementation.createHTMLDocument( "" );
-
- // Set the base href for the created document
- // so any parsed elements with URLs
- // are based on the document's URL (gh-2965)
- base = context.createElement( "base" );
- base.href = document.location.href;
- context.head.appendChild( base );
- } else {
- context = document;
- }
- }
-
- parsed = rsingleTag.exec( data );
- scripts = !keepScripts && [];
-
- // Single tag
- if ( parsed ) {
- return [ context.createElement( parsed[ 1 ] ) ];
- }
-
- parsed = buildFragment( [ data ], context, scripts );
-
- if ( scripts && scripts.length ) {
- jQuery( scripts ).remove();
- }
-
- return jQuery.merge( [], parsed.childNodes );
-};
-
-
-/**
- * Load a url into a page
- */
-jQuery.fn.load = function( url, params, callback ) {
- var selector, type, response,
- self = this,
- off = url.indexOf( " " );
-
- if ( off > -1 ) {
- selector = stripAndCollapse( url.slice( off ) );
- url = url.slice( 0, off );
- }
-
- // If it's a function
- if ( jQuery.isFunction( params ) ) {
-
- // We assume that it's the callback
- callback = params;
- params = undefined;
-
- // Otherwise, build a param string
- } else if ( params && typeof params === "object" ) {
- type = "POST";
- }
-
- // If we have elements to modify, make the request
- if ( self.length > 0 ) {
- jQuery.ajax( {
- url: url,
-
- // If "type" variable is undefined, then "GET" method will be used.
- // Make value of this field explicit since
- // user can override it through ajaxSetup method
- type: type || "GET",
- dataType: "html",
- data: params
- } ).done( function( responseText ) {
-
- // Save response for use in complete callback
- response = arguments;
-
- self.html( selector ?
-
- // If a selector was specified, locate the right elements in a dummy div
- // Exclude scripts to avoid IE 'Permission Denied' errors
- jQuery( "<div>" ).append( jQuery.parseHTML( responseText ) ).find( selector ) :
-
- // Otherwise use the full result
- responseText );
-
- // If the request succeeds, this function gets "data", "status", "jqXHR"
- // but they are ignored because response was set above.
- // If it fails, this function gets "jqXHR", "status", "error"
- } ).always( callback && function( jqXHR, status ) {
- self.each( function() {
- callback.apply( this, response || [ jqXHR.responseText, status, jqXHR ] );
- } );
- } );
- }
-
- return this;
-};
-
-
-
-
-// Attach a bunch of functions for handling common AJAX events
-jQuery.each( [
- "ajaxStart",
- "ajaxStop",
- "ajaxComplete",
- "ajaxError",
- "ajaxSuccess",
- "ajaxSend"
-], function( i, type ) {
- jQuery.fn[ type ] = function( fn ) {
- return this.on( type, fn );
- };
-} );
-
-
-
-
-jQuery.expr.pseudos.animated = function( elem ) {
- return jQuery.grep( jQuery.timers, function( fn ) {
- return elem === fn.elem;
- } ).length;
-};
-
-
-
-
-jQuery.offset = {
- setOffset: function( elem, options, i ) {
- var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition,
- position = jQuery.css( elem, "position" ),
- curElem = jQuery( elem ),
- props = {};
-
- // Set position first, in-case top/left are set even on static elem
- if ( position === "static" ) {
- elem.style.position = "relative";
- }
-
- curOffset = curElem.offset();
- curCSSTop = jQuery.css( elem, "top" );
- curCSSLeft = jQuery.css( elem, "left" );
- calculatePosition = ( position === "absolute" || position === "fixed" ) &&
- ( curCSSTop + curCSSLeft ).indexOf( "auto" ) > -1;
-
- // Need to be able to calculate position if either
- // top or left is auto and position is either absolute or fixed
- if ( calculatePosition ) {
- curPosition = curElem.position();
- curTop = curPosition.top;
- curLeft = curPosition.left;
-
- } else {
- curTop = parseFloat( curCSSTop ) || 0;
- curLeft = parseFloat( curCSSLeft ) || 0;
- }
-
- if ( jQuery.isFunction( options ) ) {
-
- // Use jQuery.extend here to allow modification of coordinates argument (gh-1848)
- options = options.call( elem, i, jQuery.extend( {}, curOffset ) );
- }
-
- if ( options.top != null ) {
- props.top = ( options.top - curOffset.top ) + curTop;
- }
- if ( options.left != null ) {
- props.left = ( options.left - curOffset.left ) + curLeft;
- }
-
- if ( "using" in options ) {
- options.using.call( elem, props );
-
- } else {
- curElem.css( props );
- }
- }
-};
-
-jQuery.fn.extend( {
- offset: function( options ) {
-
- // Preserve chaining for setter
- if ( arguments.length ) {
- return options === undefined ?
- this :
- this.each( function( i ) {
- jQuery.offset.setOffset( this, options, i );
- } );
- }
-
- var doc, docElem, rect, win,
- elem = this[ 0 ];
-
- if ( !elem ) {
- return;
- }
-
- // Return zeros for disconnected and hidden (display: none) elements (gh-2310)
- // Support: IE <=11 only
- // Running getBoundingClientRect on a
- // disconnected node in IE throws an error
- if ( !elem.getClientRects().length ) {
- return { top: 0, left: 0 };
- }
-
- rect = elem.getBoundingClientRect();
-
- doc = elem.ownerDocument;
- docElem = doc.documentElement;
- win = doc.defaultView;
-
- return {
- top: rect.top + win.pageYOffset - docElem.clientTop,
- left: rect.left + win.pageXOffset - docElem.clientLeft
- };
- },
-
- position: function() {
- if ( !this[ 0 ] ) {
- return;
- }
-
- var offsetParent, offset,
- elem = this[ 0 ],
- parentOffset = { top: 0, left: 0 };
-
- // Fixed elements are offset from window (parentOffset = {top:0, left: 0},
- // because it is its only offset parent
- if ( jQuery.css( elem, "position" ) === "fixed" ) {
-
- // Assume getBoundingClientRect is there when computed position is fixed
- offset = elem.getBoundingClientRect();
-
- } else {
-
- // Get *real* offsetParent
- offsetParent = this.offsetParent();
-
- // Get correct offsets
- offset = this.offset();
- if ( !nodeName( offsetParent[ 0 ], "html" ) ) {
- parentOffset = offsetParent.offset();
- }
-
- // Add offsetParent borders
- parentOffset = {
- top: parentOffset.top + jQuery.css( offsetParent[ 0 ], "borderTopWidth", true ),
- left: parentOffset.left + jQuery.css( offsetParent[ 0 ], "borderLeftWidth", true )
- };
- }
-
- // Subtract parent offsets and element margins
- return {
- top: offset.top - parentOffset.top - jQuery.css( elem, "marginTop", true ),
- left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true )
- };
- },
-
- // This method will return documentElement in the following cases:
- // 1) For the element inside the iframe without offsetParent, this method will return
- // documentElement of the parent window
- // 2) For the hidden or detached element
- // 3) For body or html element, i.e. in case of the html node - it will return itself
- //
- // but those exceptions were never presented as a real life use-cases
- // and might be considered as more preferable results.
- //
- // This logic, however, is not guaranteed and can change at any point in the future
- offsetParent: function() {
- return this.map( function() {
- var offsetParent = this.offsetParent;
-
- while ( offsetParent && jQuery.css( offsetParent, "position" ) === "static" ) {
- offsetParent = offsetParent.offsetParent;
- }
-
- return offsetParent || documentElement;
- } );
- }
-} );
-
-// Create scrollLeft and scrollTop methods
-jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) {
- var top = "pageYOffset" === prop;
-
- jQuery.fn[ method ] = function( val ) {
- return access( this, function( elem, method, val ) {
-
- // Coalesce documents and windows
- var win;
- if ( jQuery.isWindow( elem ) ) {
- win = elem;
- } else if ( elem.nodeType === 9 ) {
- win = elem.defaultView;
- }
-
- if ( val === undefined ) {
- return win ? win[ prop ] : elem[ method ];
- }
-
- if ( win ) {
- win.scrollTo(
- !top ? val : win.pageXOffset,
- top ? val : win.pageYOffset
- );
-
- } else {
- elem[ method ] = val;
- }
- }, method, val, arguments.length );
- };
-} );
-
-// Support: Safari <=7 - 9.1, Chrome <=37 - 49
-// Add the top/left cssHooks using jQuery.fn.position
-// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084
-// Blink bug: https://bugs.chromium.org/p/chromium/issues/detail?id=589347
-// getComputedStyle returns percent when specified for top/left/bottom/right;
-// rather than make the css module depend on the offset module, just check for it here
-jQuery.each( [ "top", "left" ], function( i, prop ) {
- jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition,
- function( elem, computed ) {
- if ( computed ) {
- computed = curCSS( elem, prop );
-
- // If curCSS returns percentage, fallback to offset
- return rnumnonpx.test( computed ) ?
- jQuery( elem ).position()[ prop ] + "px" :
- computed;
- }
- }
- );
-} );
-
-
-// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
-jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
- jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name },
- function( defaultExtra, funcName ) {
-
- // Margin is only for outerHeight, outerWidth
- jQuery.fn[ funcName ] = function( margin, value ) {
- var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),
- extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );
-
- return access( this, function( elem, type, value ) {
- var doc;
-
- if ( jQuery.isWindow( elem ) ) {
-
- // $( window ).outerWidth/Height return w/h including scrollbars (gh-1729)
- return funcName.indexOf( "outer" ) === 0 ?
- elem[ "inner" + name ] :
- elem.document.documentElement[ "client" + name ];
- }
-
- // Get document width or height
- if ( elem.nodeType === 9 ) {
- doc = elem.documentElement;
-
- // Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height],
- // whichever is greatest
- return Math.max(
- elem.body[ "scroll" + name ], doc[ "scroll" + name ],
- elem.body[ "offset" + name ], doc[ "offset" + name ],
- doc[ "client" + name ]
- );
- }
-
- return value === undefined ?
-
- // Get width or height on the element, requesting but not forcing parseFloat
- jQuery.css( elem, type, extra ) :
-
- // Set width or height on the element
- jQuery.style( elem, type, value, extra );
- }, type, chainable ? margin : undefined, chainable );
- };
- } );
-} );
-
-
-jQuery.fn.extend( {
-
- bind: function( types, data, fn ) {
- return this.on( types, null, data, fn );
- },
- unbind: function( types, fn ) {
- return this.off( types, null, fn );
- },
-
- delegate: function( selector, types, data, fn ) {
- return this.on( types, selector, data, fn );
- },
- undelegate: function( selector, types, fn ) {
-
- // ( namespace ) or ( selector, types [, fn] )
- return arguments.length === 1 ?
- this.off( selector, "**" ) :
- this.off( types, selector || "**", fn );
- }
-} );
-
-jQuery.holdReady = function( hold ) {
- if ( hold ) {
- jQuery.readyWait++;
- } else {
- jQuery.ready( true );
- }
-};
-jQuery.isArray = Array.isArray;
-jQuery.parseJSON = JSON.parse;
-jQuery.nodeName = nodeName;
-
-
-
-
-// Register as a named AMD module, since jQuery can be concatenated with other
-// files that may use define, but not via a proper concatenation script that
-// understands anonymous AMD modules. A named AMD is safest and most robust
-// way to register. Lowercase jquery is used because AMD module names are
-// derived from file names, and jQuery is normally delivered in a lowercase
-// file name. Do this after creating the global so that if an AMD module wants
-// to call noConflict to hide this version of jQuery, it will work.
-
-// Note that for maximum portability, libraries that are not jQuery should
-// declare themselves as anonymous modules, and avoid setting a global if an
-// AMD loader is present. jQuery is a special case. For more information, see
-// https://github.com/jrburke/requirejs/wiki/Updating-existing-libraries#wiki-anon
-
-if ( typeof define === "function" && define.amd ) {
- define( "jquery", [], function() {
- return jQuery;
- } );
-}
-
-
-
-
-var
-
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diff --git a/doc/html/_static/jquery.js b/doc/html/_static/jquery.js
index 644d35e274fd64ddaf6d12af813e820c424176a9..888a82f32f694cd456e6f31b319c11a47a605bb9 100644
--- a/doc/html/_static/jquery.js
+++ b/doc/html/_static/jquery.js
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+/*!
+ * jQuery JavaScript Library v3.3.1-dfsg
+ * https://jquery.com/
+ *
+ * Includes Sizzle.js
+ * https://sizzlejs.com/
+ *
+ * Copyright JS Foundation and other contributors
+ * Released under the MIT license
+ * https://jquery.org/license
+ *
+ * Date: 2021-03-09T19:42Z
+ */
+( function( global, factory ) {
+
+ "use strict";
+
+ if ( typeof module === "object" && typeof module.exports === "object" ) {
+
+ // For CommonJS and CommonJS-like environments where a proper `window`
+ // is present, execute the factory and get jQuery.
+ // For environments that do not have a `window` with a `document`
+ // (such as Node.js), expose a factory as module.exports.
+ // This accentuates the need for the creation of a real `window`.
+ // e.g. var jQuery = require("jquery")(window);
+ // See ticket #14549 for more info.
+ module.exports = global.document ?
+ factory( global, true ) :
+ function( w ) {
+ if ( !w.document ) {
+ throw new Error( "jQuery requires a window with a document" );
+ }
+ return factory( w );
+ };
+ } else {
+ factory( global );
+ }
+
+// Pass this if window is not defined yet
+} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
+
+// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1
+// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode
+// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common
+// enough that all such attempts are guarded in a try block.
+
+
+var arr = [];
+
+var document = window.document;
+
+var getProto = Object.getPrototypeOf;
+
+var slice = arr.slice;
+
+var concat = arr.concat;
+
+var push = arr.push;
+
+var indexOf = arr.indexOf;
+
+var class2type = {};
+
+var toString = class2type.toString;
+
+var hasOwn = class2type.hasOwnProperty;
+
+var fnToString = hasOwn.toString;
+
+var ObjectFunctionString = fnToString.call( Object );
+
+var support = {};
+
+var isFunction = function isFunction( obj ) {
+
+ // Support: Chrome <=57, Firefox <=52
+ // In some browsers, typeof returns "function" for HTML <object> elements
+ // (i.e., `typeof document.createElement( "object" ) === "function"`).
+ // We don't want to classify *any* DOM node as a function.
+ return typeof obj === "function" && typeof obj.nodeType !== "number";
+ };
+
+
+var isWindow = function isWindow( obj ) {
+ return obj != null && obj === obj.window;
+ };
+
+
+
+
+ var preservedScriptAttributes = {
+ type: true,
+ src: true,
+ noModule: true
+ };
+
+ function DOMEval( code, doc, node ) {
+ doc = doc || document;
+
+ var i,
+ script = doc.createElement( "script" );
+
+ script.text = code;
+ if ( node ) {
+ for ( i in preservedScriptAttributes ) {
+ if ( node[ i ] ) {
+ script[ i ] = node[ i ];
+ }
+ }
+ }
+ doc.head.appendChild( script ).parentNode.removeChild( script );
+ }
+
+
+function toType( obj ) {
+ if ( obj == null ) {
+ return obj + "";
+ }
+
+ // Support: Android <=2.3 only (functionish RegExp)
+ return typeof obj === "object" || typeof obj === "function" ?
+ class2type[ toString.call( obj ) ] || "object" :
+ typeof obj;
+}
+/* global Symbol */
+// Defining this global in .eslintrc.json would create a danger of using the global
+// unguarded in another place, it seems safer to define global only for this module
+
+
+
+var
+ version = "3.3.1",
+
+ // Define a local copy of jQuery
+ jQuery = function( selector, context ) {
+
+ // The jQuery object is actually just the init constructor 'enhanced'
+ // Need init if jQuery is called (just allow error to be thrown if not included)
+ return new jQuery.fn.init( selector, context );
+ },
+
+ // Support: Android <=4.0 only
+ // Make sure we trim BOM and NBSP
+ rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g;
+
+jQuery.fn = jQuery.prototype = {
+
+ // The current version of jQuery being used
+ jquery: version,
+
+ constructor: jQuery,
+
+ // The default length of a jQuery object is 0
+ length: 0,
+
+ toArray: function() {
+ return slice.call( this );
+ },
+
+ // Get the Nth element in the matched element set OR
+ // Get the whole matched element set as a clean array
+ get: function( num ) {
+
+ // Return all the elements in a clean array
+ if ( num == null ) {
+ return slice.call( this );
+ }
+
+ // Return just the one element from the set
+ return num < 0 ? this[ num + this.length ] : this[ num ];
+ },
+
+ // Take an array of elements and push it onto the stack
+ // (returning the new matched element set)
+ pushStack: function( elems ) {
+
+ // Build a new jQuery matched element set
+ var ret = jQuery.merge( this.constructor(), elems );
+
+ // Add the old object onto the stack (as a reference)
+ ret.prevObject = this;
+
+ // Return the newly-formed element set
+ return ret;
+ },
+
+ // Execute a callback for every element in the matched set.
+ each: function( callback ) {
+ return jQuery.each( this, callback );
+ },
+
+ map: function( callback ) {
+ return this.pushStack( jQuery.map( this, function( elem, i ) {
+ return callback.call( elem, i, elem );
+ } ) );
+ },
+
+ slice: function() {
+ return this.pushStack( slice.apply( this, arguments ) );
+ },
+
+ first: function() {
+ return this.eq( 0 );
+ },
+
+ last: function() {
+ return this.eq( -1 );
+ },
+
+ eq: function( i ) {
+ var len = this.length,
+ j = +i + ( i < 0 ? len : 0 );
+ return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] );
+ },
+
+ end: function() {
+ return this.prevObject || this.constructor();
+ },
+
+ // For internal use only.
+ // Behaves like an Array's method, not like a jQuery method.
+ push: push,
+ sort: arr.sort,
+ splice: arr.splice
+};
+
+jQuery.extend = jQuery.fn.extend = function() {
+ var options, name, src, copy, copyIsArray, clone,
+ target = arguments[ 0 ] || {},
+ i = 1,
+ length = arguments.length,
+ deep = false;
+
+ // Handle a deep copy situation
+ if ( typeof target === "boolean" ) {
+ deep = target;
+
+ // Skip the boolean and the target
+ target = arguments[ i ] || {};
+ i++;
+ }
+
+ // Handle case when target is a string or something (possible in deep copy)
+ if ( typeof target !== "object" && !isFunction( target ) ) {
+ target = {};
+ }
+
+ // Extend jQuery itself if only one argument is passed
+ if ( i === length ) {
+ target = this;
+ i--;
+ }
+
+ for ( ; i < length; i++ ) {
+
+ // Only deal with non-null/undefined values
+ if ( ( options = arguments[ i ] ) != null ) {
+
+ // Extend the base object
+ for ( name in options ) {
+ src = target[ name ];
+ copy = options[ name ];
+
+ // Prevent Object.prototype pollution
+ // Prevent never-ending loop
+ if ( name === "__proto__" || target === copy ) {
+ continue;
+ }
+
+ // Recurse if we're merging plain objects or arrays
+ if ( deep && copy && ( jQuery.isPlainObject( copy ) ||
+ ( copyIsArray = Array.isArray( copy ) ) ) ) {
+
+ if ( copyIsArray ) {
+ copyIsArray = false;
+ clone = src && Array.isArray( src ) ? src : [];
+
+ } else {
+ clone = src && jQuery.isPlainObject( src ) ? src : {};
+ }
+
+ // Never move original objects, clone them
+ target[ name ] = jQuery.extend( deep, clone, copy );
+
+ // Don't bring in undefined values
+ } else if ( copy !== undefined ) {
+ target[ name ] = copy;
+ }
+ }
+ }
+ }
+
+ // Return the modified object
+ return target;
+};
+
+jQuery.extend( {
+
+ // Unique for each copy of jQuery on the page
+ expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ),
+
+ // Assume jQuery is ready without the ready module
+ isReady: true,
+
+ error: function( msg ) {
+ throw new Error( msg );
+ },
+
+ noop: function() {},
+
+ isPlainObject: function( obj ) {
+ var proto, Ctor;
+
+ // Detect obvious negatives
+ // Use toString instead of jQuery.type to catch host objects
+ if ( !obj || toString.call( obj ) !== "[object Object]" ) {
+ return false;
+ }
+
+ proto = getProto( obj );
+
+ // Objects with no prototype (e.g., `Object.create( null )`) are plain
+ if ( !proto ) {
+ return true;
+ }
+
+ // Objects with prototype are plain iff they were constructed by a global Object function
+ Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor;
+ return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString;
+ },
+
+ isEmptyObject: function( obj ) {
+
+ /* eslint-disable no-unused-vars */
+ // See https://github.com/eslint/eslint/issues/6125
+ var name;
+
+ for ( name in obj ) {
+ return false;
+ }
+ return true;
+ },
+
+ // Evaluates a script in a global context
+ globalEval: function( code ) {
+ DOMEval( code );
+ },
+
+ each: function( obj, callback ) {
+ var length, i = 0;
+
+ if ( isArrayLike( obj ) ) {
+ length = obj.length;
+ for ( ; i < length; i++ ) {
+ if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
+ break;
+ }
+ }
+ } else {
+ for ( i in obj ) {
+ if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
+ break;
+ }
+ }
+ }
+
+ return obj;
+ },
+
+ // Support: Android <=4.0 only
+ trim: function( text ) {
+ return text == null ?
+ "" :
+ ( text + "" ).replace( rtrim, "" );
+ },
+
+ // results is for internal usage only
+ makeArray: function( arr, results ) {
+ var ret = results || [];
+
+ if ( arr != null ) {
+ if ( isArrayLike( Object( arr ) ) ) {
+ jQuery.merge( ret,
+ typeof arr === "string" ?
+ [ arr ] : arr
+ );
+ } else {
+ push.call( ret, arr );
+ }
+ }
+
+ return ret;
+ },
+
+ inArray: function( elem, arr, i ) {
+ return arr == null ? -1 : indexOf.call( arr, elem, i );
+ },
+
+ // Support: Android <=4.0 only, PhantomJS 1 only
+ // push.apply(_, arraylike) throws on ancient WebKit
+ merge: function( first, second ) {
+ var len = +second.length,
+ j = 0,
+ i = first.length;
+
+ for ( ; j < len; j++ ) {
+ first[ i++ ] = second[ j ];
+ }
+
+ first.length = i;
+
+ return first;
+ },
+
+ grep: function( elems, callback, invert ) {
+ var callbackInverse,
+ matches = [],
+ i = 0,
+ length = elems.length,
+ callbackExpect = !invert;
+
+ // Go through the array, only saving the items
+ // that pass the validator function
+ for ( ; i < length; i++ ) {
+ callbackInverse = !callback( elems[ i ], i );
+ if ( callbackInverse !== callbackExpect ) {
+ matches.push( elems[ i ] );
+ }
+ }
+
+ return matches;
+ },
+
+ // arg is for internal usage only
+ map: function( elems, callback, arg ) {
+ var length, value,
+ i = 0,
+ ret = [];
+
+ // Go through the array, translating each of the items to their new values
+ if ( isArrayLike( elems ) ) {
+ length = elems.length;
+ for ( ; i < length; i++ ) {
+ value = callback( elems[ i ], i, arg );
+
+ if ( value != null ) {
+ ret.push( value );
+ }
+ }
+
+ // Go through every key on the object,
+ } else {
+ for ( i in elems ) {
+ value = callback( elems[ i ], i, arg );
+
+ if ( value != null ) {
+ ret.push( value );
+ }
+ }
+ }
+
+ // Flatten any nested arrays
+ return concat.apply( [], ret );
+ },
+
+ // A global GUID counter for objects
+ guid: 1,
+
+ // jQuery.support is not used in Core but other projects attach their
+ // properties to it so it needs to exist.
+ support: support
+} );
+
+if ( typeof Symbol === "function" ) {
+ jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ];
+}
+
+// Populate the class2type map
+jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ),
+function( i, name ) {
+ class2type[ "[object " + name + "]" ] = name.toLowerCase();
+} );
+
+function isArrayLike( obj ) {
+
+ // Support: real iOS 8.2 only (not reproducible in simulator)
+ // `in` check used to prevent JIT error (gh-2145)
+ // hasOwn isn't used here due to false negatives
+ // regarding Nodelist length in IE
+ var length = !!obj && "length" in obj && obj.length,
+ type = toType( obj );
+
+ if ( isFunction( obj ) || isWindow( obj ) ) {
+ return false;
+ }
+
+ return type === "array" || length === 0 ||
+ typeof length === "number" && length > 0 && ( length - 1 ) in obj;
+}
+var Sizzle =
+/*!
+ * Sizzle CSS Selector Engine v2.3.3
+ * https://sizzlejs.com/
+ *
+ * Copyright jQuery Foundation and other contributors
+ * Released under the MIT license
+ * http://jquery.org/license
+ *
+ * Date: 2016-08-08
+ */
+(function( window ) {
+
+var i,
+ support,
+ Expr,
+ getText,
+ isXML,
+ tokenize,
+ compile,
+ select,
+ outermostContext,
+ sortInput,
+ hasDuplicate,
+
+ // Local document vars
+ setDocument,
+ document,
+ docElem,
+ documentIsHTML,
+ rbuggyQSA,
+ rbuggyMatches,
+ matches,
+ contains,
+
+ // Instance-specific data
+ expando = "sizzle" + 1 * new Date(),
+ preferredDoc = window.document,
+ dirruns = 0,
+ done = 0,
+ classCache = createCache(),
+ tokenCache = createCache(),
+ compilerCache = createCache(),
+ sortOrder = function( a, b ) {
+ if ( a === b ) {
+ hasDuplicate = true;
+ }
+ return 0;
+ },
+
+ // Instance methods
+ hasOwn = ({}).hasOwnProperty,
+ arr = [],
+ pop = arr.pop,
+ push_native = arr.push,
+ push = arr.push,
+ slice = arr.slice,
+ // Use a stripped-down indexOf as it's faster than native
+ // https://jsperf.com/thor-indexof-vs-for/5
+ indexOf = function( list, elem ) {
+ var i = 0,
+ len = list.length;
+ for ( ; i < len; i++ ) {
+ if ( list[i] === elem ) {
+ return i;
+ }
+ }
+ return -1;
+ },
+
+ booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped",
+
+ // Regular expressions
+
+ // http://www.w3.org/TR/css3-selectors/#whitespace
+ whitespace = "[\\x20\\t\\r\\n\\f]",
+
+ // http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
+ identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+",
+
+ // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors
+ attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace +
+ // Operator (capture 2)
+ "*([*^$|!~]?=)" + whitespace +
+ // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]"
+ "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace +
+ "*\\]",
+
+ pseudos = ":(" + identifier + ")(?:\\((" +
+ // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:
+ // 1. quoted (capture 3; capture 4 or capture 5)
+ "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" +
+ // 2. simple (capture 6)
+ "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" +
+ // 3. anything else (capture 2)
+ ".*" +
+ ")\\)|)",
+
+ // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
+ rwhitespace = new RegExp( whitespace + "+", "g" ),
+ rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
+
+ rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
+ rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ),
+
+ rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ),
+
+ rpseudo = new RegExp( pseudos ),
+ ridentifier = new RegExp( "^" + identifier + "$" ),
+
+ matchExpr = {
+ "ID": new RegExp( "^#(" + identifier + ")" ),
+ "CLASS": new RegExp( "^\\.(" + identifier + ")" ),
+ "TAG": new RegExp( "^(" + identifier + "|[*])" ),
+ "ATTR": new RegExp( "^" + attributes ),
+ "PSEUDO": new RegExp( "^" + pseudos ),
+ "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace +
+ "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace +
+ "*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
+ "bool": new RegExp( "^(?:" + booleans + ")$", "i" ),
+ // For use in libraries implementing .is()
+ // We use this for POS matching in `select`
+ "needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" +
+ whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" )
+ },
+
+ rinputs = /^(?:input|select|textarea|button)$/i,
+ rheader = /^h\d$/i,
+
+ rnative = /^[^{]+\{\s*\[native \w/,
+
+ // Easily-parseable/retrievable ID or TAG or CLASS selectors
+ rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
+
+ rsibling = /[+~]/,
+
+ // CSS escapes
+ // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
+ runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ),
+ funescape = function( _, escaped, escapedWhitespace ) {
+ var high = "0x" + escaped - 0x10000;
+ // NaN means non-codepoint
+ // Support: Firefox<24
+ // Workaround erroneous numeric interpretation of +"0x"
+ return high !== high || escapedWhitespace ?
+ escaped :
+ high < 0 ?
+ // BMP codepoint
+ String.fromCharCode( high + 0x10000 ) :
+ // Supplemental Plane codepoint (surrogate pair)
+ String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
+ },
+
+ // CSS string/identifier serialization
+ // https://drafts.csswg.org/cssom/#common-serializing-idioms
+ rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g,
+ fcssescape = function( ch, asCodePoint ) {
+ if ( asCodePoint ) {
+
+ // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER
+ if ( ch === "\0" ) {
+ return "\uFFFD";
+ }
+
+ // Control characters and (dependent upon position) numbers get escaped as code points
+ return ch.slice( 0, -1 ) + "\\" + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " ";
+ }
+
+ // Other potentially-special ASCII characters get backslash-escaped
+ return "\\" + ch;
+ },
+
+ // Used for iframes
+ // See setDocument()
+ // Removing the function wrapper causes a "Permission Denied"
+ // error in IE
+ unloadHandler = function() {
+ setDocument();
+ },
+
+ disabledAncestor = addCombinator(
+ function( elem ) {
+ return elem.disabled === true && ("form" in elem || "label" in elem);
+ },
+ { dir: "parentNode", next: "legend" }
+ );
+
+// Optimize for push.apply( _, NodeList )
+try {
+ push.apply(
+ (arr = slice.call( preferredDoc.childNodes )),
+ preferredDoc.childNodes
+ );
+ // Support: Android<4.0
+ // Detect silently failing push.apply
+ arr[ preferredDoc.childNodes.length ].nodeType;
+} catch ( e ) {
+ push = { apply: arr.length ?
+
+ // Leverage slice if possible
+ function( target, els ) {
+ push_native.apply( target, slice.call(els) );
+ } :
+
+ // Support: IE<9
+ // Otherwise append directly
+ function( target, els ) {
+ var j = target.length,
+ i = 0;
+ // Can't trust NodeList.length
+ while ( (target[j++] = els[i++]) ) {}
+ target.length = j - 1;
+ }
+ };
+}
+
+function Sizzle( selector, context, results, seed ) {
+ var m, i, elem, nid, match, groups, newSelector,
+ newContext = context && context.ownerDocument,
+
+ // nodeType defaults to 9, since context defaults to document
+ nodeType = context ? context.nodeType : 9;
+
+ results = results || [];
+
+ // Return early from calls with invalid selector or context
+ if ( typeof selector !== "string" || !selector ||
+ nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) {
+
+ return results;
+ }
+
+ // Try to shortcut find operations (as opposed to filters) in HTML documents
+ if ( !seed ) {
+
+ if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
+ setDocument( context );
+ }
+ context = context || document;
+
+ if ( documentIsHTML ) {
+
+ // If the selector is sufficiently simple, try using a "get*By*" DOM method
+ // (excepting DocumentFragment context, where the methods don't exist)
+ if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) {
+
+ // ID selector
+ if ( (m = match[1]) ) {
+
+ // Document context
+ if ( nodeType === 9 ) {
+ if ( (elem = context.getElementById( m )) ) {
+
+ // Support: IE, Opera, Webkit
+ // TODO: identify versions
+ // getElementById can match elements by name instead of ID
+ if ( elem.id === m ) {
+ results.push( elem );
+ return results;
+ }
+ } else {
+ return results;
+ }
+
+ // Element context
+ } else {
+
+ // Support: IE, Opera, Webkit
+ // TODO: identify versions
+ // getElementById can match elements by name instead of ID
+ if ( newContext && (elem = newContext.getElementById( m )) &&
+ contains( context, elem ) &&
+ elem.id === m ) {
+
+ results.push( elem );
+ return results;
+ }
+ }
+
+ // Type selector
+ } else if ( match[2] ) {
+ push.apply( results, context.getElementsByTagName( selector ) );
+ return results;
+
+ // Class selector
+ } else if ( (m = match[3]) && support.getElementsByClassName &&
+ context.getElementsByClassName ) {
+
+ push.apply( results, context.getElementsByClassName( m ) );
+ return results;
+ }
+ }
+
+ // Take advantage of querySelectorAll
+ if ( support.qsa &&
+ !compilerCache[ selector + " " ] &&
+ (!rbuggyQSA || !rbuggyQSA.test( selector )) ) {
+
+ if ( nodeType !== 1 ) {
+ newContext = context;
+ newSelector = selector;
+
+ // qSA looks outside Element context, which is not what we want
+ // Thanks to Andrew Dupont for this workaround technique
+ // Support: IE <=8
+ // Exclude object elements
+ } else if ( context.nodeName.toLowerCase() !== "object" ) {
+
+ // Capture the context ID, setting it first if necessary
+ if ( (nid = context.getAttribute( "id" )) ) {
+ nid = nid.replace( rcssescape, fcssescape );
+ } else {
+ context.setAttribute( "id", (nid = expando) );
+ }
+
+ // Prefix every selector in the list
+ groups = tokenize( selector );
+ i = groups.length;
+ while ( i-- ) {
+ groups[i] = "#" + nid + " " + toSelector( groups[i] );
+ }
+ newSelector = groups.join( "," );
+
+ // Expand context for sibling selectors
+ newContext = rsibling.test( selector ) && testContext( context.parentNode ) ||
+ context;
+ }
+
+ if ( newSelector ) {
+ try {
+ push.apply( results,
+ newContext.querySelectorAll( newSelector )
+ );
+ return results;
+ } catch ( qsaError ) {
+ } finally {
+ if ( nid === expando ) {
+ context.removeAttribute( "id" );
+ }
+ }
+ }
+ }
+ }
+ }
+
+ // All others
+ return select( selector.replace( rtrim, "$1" ), context, results, seed );
+}
+
+/**
+ * Create key-value caches of limited size
+ * @returns {function(string, object)} Returns the Object data after storing it on itself with
+ * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
+ * deleting the oldest entry
+ */
+function createCache() {
+ var keys = [];
+
+ function cache( key, value ) {
+ // Use (key + " ") to avoid collision with native prototype properties (see Issue #157)
+ if ( keys.push( key + " " ) > Expr.cacheLength ) {
+ // Only keep the most recent entries
+ delete cache[ keys.shift() ];
+ }
+ return (cache[ key + " " ] = value);
+ }
+ return cache;
+}
+
+/**
+ * Mark a function for special use by Sizzle
+ * @param {Function} fn The function to mark
+ */
+function markFunction( fn ) {
+ fn[ expando ] = true;
+ return fn;
+}
+
+/**
+ * Support testing using an element
+ * @param {Function} fn Passed the created element and returns a boolean result
+ */
+function assert( fn ) {
+ var el = document.createElement("fieldset");
+
+ try {
+ return !!fn( el );
+ } catch (e) {
+ return false;
+ } finally {
+ // Remove from its parent by default
+ if ( el.parentNode ) {
+ el.parentNode.removeChild( el );
+ }
+ // release memory in IE
+ el = null;
+ }
+}
+
+/**
+ * Adds the same handler for all of the specified attrs
+ * @param {String} attrs Pipe-separated list of attributes
+ * @param {Function} handler The method that will be applied
+ */
+function addHandle( attrs, handler ) {
+ var arr = attrs.split("|"),
+ i = arr.length;
+
+ while ( i-- ) {
+ Expr.attrHandle[ arr[i] ] = handler;
+ }
+}
+
+/**
+ * Checks document order of two siblings
+ * @param {Element} a
+ * @param {Element} b
+ * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b
+ */
+function siblingCheck( a, b ) {
+ var cur = b && a,
+ diff = cur && a.nodeType === 1 && b.nodeType === 1 &&
+ a.sourceIndex - b.sourceIndex;
+
+ // Use IE sourceIndex if available on both nodes
+ if ( diff ) {
+ return diff;
+ }
+
+ // Check if b follows a
+ if ( cur ) {
+ while ( (cur = cur.nextSibling) ) {
+ if ( cur === b ) {
+ return -1;
+ }
+ }
+ }
+
+ return a ? 1 : -1;
+}
+
+/**
+ * Returns a function to use in pseudos for input types
+ * @param {String} type
+ */
+function createInputPseudo( type ) {
+ return function( elem ) {
+ var name = elem.nodeName.toLowerCase();
+ return name === "input" && elem.type === type;
+ };
+}
+
+/**
+ * Returns a function to use in pseudos for buttons
+ * @param {String} type
+ */
+function createButtonPseudo( type ) {
+ return function( elem ) {
+ var name = elem.nodeName.toLowerCase();
+ return (name === "input" || name === "button") && elem.type === type;
+ };
+}
+
+/**
+ * Returns a function to use in pseudos for :enabled/:disabled
+ * @param {Boolean} disabled true for :disabled; false for :enabled
+ */
+function createDisabledPseudo( disabled ) {
+
+ // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable
+ return function( elem ) {
+
+ // Only certain elements can match :enabled or :disabled
+ // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled
+ // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled
+ if ( "form" in elem ) {
+
+ // Check for inherited disabledness on relevant non-disabled elements:
+ // * listed form-associated elements in a disabled fieldset
+ // https://html.spec.whatwg.org/multipage/forms.html#category-listed
+ // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled
+ // * option elements in a disabled optgroup
+ // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled
+ // All such elements have a "form" property.
+ if ( elem.parentNode && elem.disabled === false ) {
+
+ // Option elements defer to a parent optgroup if present
+ if ( "label" in elem ) {
+ if ( "label" in elem.parentNode ) {
+ return elem.parentNode.disabled === disabled;
+ } else {
+ return elem.disabled === disabled;
+ }
+ }
+
+ // Support: IE 6 - 11
+ // Use the isDisabled shortcut property to check for disabled fieldset ancestors
+ return elem.isDisabled === disabled ||
+
+ // Where there is no isDisabled, check manually
+ /* jshint -W018 */
+ elem.isDisabled !== !disabled &&
+ disabledAncestor( elem ) === disabled;
+ }
+
+ return elem.disabled === disabled;
+
+ // Try to winnow out elements that can't be disabled before trusting the disabled property.
+ // Some victims get caught in our net (label, legend, menu, track), but it shouldn't
+ // even exist on them, let alone have a boolean value.
+ } else if ( "label" in elem ) {
+ return elem.disabled === disabled;
+ }
+
+ // Remaining elements are neither :enabled nor :disabled
+ return false;
+ };
+}
+
+/**
+ * Returns a function to use in pseudos for positionals
+ * @param {Function} fn
+ */
+function createPositionalPseudo( fn ) {
+ return markFunction(function( argument ) {
+ argument = +argument;
+ return markFunction(function( seed, matches ) {
+ var j,
+ matchIndexes = fn( [], seed.length, argument ),
+ i = matchIndexes.length;
+
+ // Match elements found at the specified indexes
+ while ( i-- ) {
+ if ( seed[ (j = matchIndexes[i]) ] ) {
+ seed[j] = !(matches[j] = seed[j]);
+ }
+ }
+ });
+ });
+}
+
+/**
+ * Checks a node for validity as a Sizzle context
+ * @param {Element|Object=} context
+ * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value
+ */
+function testContext( context ) {
+ return context && typeof context.getElementsByTagName !== "undefined" && context;
+}
+
+// Expose support vars for convenience
+support = Sizzle.support = {};
+
+/**
+ * Detects XML nodes
+ * @param {Element|Object} elem An element or a document
+ * @returns {Boolean} True iff elem is a non-HTML XML node
+ */
+isXML = Sizzle.isXML = function( elem ) {
+ // documentElement is verified for cases where it doesn't yet exist
+ // (such as loading iframes in IE - #4833)
+ var documentElement = elem && (elem.ownerDocument || elem).documentElement;
+ return documentElement ? documentElement.nodeName !== "HTML" : false;
+};
+
+/**
+ * Sets document-related variables once based on the current document
+ * @param {Element|Object} [doc] An element or document object to use to set the document
+ * @returns {Object} Returns the current document
+ */
+setDocument = Sizzle.setDocument = function( node ) {
+ var hasCompare, subWindow,
+ doc = node ? node.ownerDocument || node : preferredDoc;
+
+ // Return early if doc is invalid or already selected
+ if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {
+ return document;
+ }
+
+ // Update global variables
+ document = doc;
+ docElem = document.documentElement;
+ documentIsHTML = !isXML( document );
+
+ // Support: IE 9-11, Edge
+ // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936)
+ if ( preferredDoc !== document &&
+ (subWindow = document.defaultView) && subWindow.top !== subWindow ) {
+
+ // Support: IE 11, Edge
+ if ( subWindow.addEventListener ) {
+ subWindow.addEventListener( "unload", unloadHandler, false );
+
+ // Support: IE 9 - 10 only
+ } else if ( subWindow.attachEvent ) {
+ subWindow.attachEvent( "onunload", unloadHandler );
+ }
+ }
+
+ /* Attributes
+ ---------------------------------------------------------------------- */
+
+ // Support: IE<8
+ // Verify that getAttribute really returns attributes and not properties
+ // (excepting IE8 booleans)
+ support.attributes = assert(function( el ) {
+ el.className = "i";
+ return !el.getAttribute("className");
+ });
+
+ /* getElement(s)By*
+ ---------------------------------------------------------------------- */
+
+ // Check if getElementsByTagName("*") returns only elements
+ support.getElementsByTagName = assert(function( el ) {
+ el.appendChild( document.createComment("") );
+ return !el.getElementsByTagName("*").length;
+ });
+
+ // Support: IE<9
+ support.getElementsByClassName = rnative.test( document.getElementsByClassName );
+
+ // Support: IE<10
+ // Check if getElementById returns elements by name
+ // The broken getElementById methods don't pick up programmatically-set names,
+ // so use a roundabout getElementsByName test
+ support.getById = assert(function( el ) {
+ docElem.appendChild( el ).id = expando;
+ return !document.getElementsByName || !document.getElementsByName( expando ).length;
+ });
+
+ // ID filter and find
+ if ( support.getById ) {
+ Expr.filter["ID"] = function( id ) {
+ var attrId = id.replace( runescape, funescape );
+ return function( elem ) {
+ return elem.getAttribute("id") === attrId;
+ };
+ };
+ Expr.find["ID"] = function( id, context ) {
+ if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
+ var elem = context.getElementById( id );
+ return elem ? [ elem ] : [];
+ }
+ };
+ } else {
+ Expr.filter["ID"] = function( id ) {
+ var attrId = id.replace( runescape, funescape );
+ return function( elem ) {
+ var node = typeof elem.getAttributeNode !== "undefined" &&
+ elem.getAttributeNode("id");
+ return node && node.value === attrId;
+ };
+ };
+
+ // Support: IE 6 - 7 only
+ // getElementById is not reliable as a find shortcut
+ Expr.find["ID"] = function( id, context ) {
+ if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
+ var node, i, elems,
+ elem = context.getElementById( id );
+
+ if ( elem ) {
+
+ // Verify the id attribute
+ node = elem.getAttributeNode("id");
+ if ( node && node.value === id ) {
+ return [ elem ];
+ }
+
+ // Fall back on getElementsByName
+ elems = context.getElementsByName( id );
+ i = 0;
+ while ( (elem = elems[i++]) ) {
+ node = elem.getAttributeNode("id");
+ if ( node && node.value === id ) {
+ return [ elem ];
+ }
+ }
+ }
+
+ return [];
+ }
+ };
+ }
+
+ // Tag
+ Expr.find["TAG"] = support.getElementsByTagName ?
+ function( tag, context ) {
+ if ( typeof context.getElementsByTagName !== "undefined" ) {
+ return context.getElementsByTagName( tag );
+
+ // DocumentFragment nodes don't have gEBTN
+ } else if ( support.qsa ) {
+ return context.querySelectorAll( tag );
+ }
+ } :
+
+ function( tag, context ) {
+ var elem,
+ tmp = [],
+ i = 0,
+ // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too
+ results = context.getElementsByTagName( tag );
+
+ // Filter out possible comments
+ if ( tag === "*" ) {
+ while ( (elem = results[i++]) ) {
+ if ( elem.nodeType === 1 ) {
+ tmp.push( elem );
+ }
+ }
+
+ return tmp;
+ }
+ return results;
+ };
+
+ // Class
+ Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) {
+ if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) {
+ return context.getElementsByClassName( className );
+ }
+ };
+
+ /* QSA/matchesSelector
+ ---------------------------------------------------------------------- */
+
+ // QSA and matchesSelector support
+
+ // matchesSelector(:active) reports false when true (IE9/Opera 11.5)
+ rbuggyMatches = [];
+
+ // qSa(:focus) reports false when true (Chrome 21)
+ // We allow this because of a bug in IE8/9 that throws an error
+ // whenever `document.activeElement` is accessed on an iframe
+ // So, we allow :focus to pass through QSA all the time to avoid the IE error
+ // See https://bugs.jquery.com/ticket/13378
+ rbuggyQSA = [];
+
+ if ( (support.qsa = rnative.test( document.querySelectorAll )) ) {
+ // Build QSA regex
+ // Regex strategy adopted from Diego Perini
+ assert(function( el ) {
+ // Select is set to empty string on purpose
+ // This is to test IE's treatment of not explicitly
+ // setting a boolean content attribute,
+ // since its presence should be enough
+ // https://bugs.jquery.com/ticket/12359
+ docElem.appendChild( el ).innerHTML = "<a id='" + expando + "'></a>" +
+ "<select id='" + expando + "-\r\\' msallowcapture=''>" +
+ "<option selected=''></option></select>";
+
+ // Support: IE8, Opera 11-12.16
+ // Nothing should be selected when empty strings follow ^= or $= or *=
+ // The test attribute must be unknown in Opera but "safe" for WinRT
+ // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
+ if ( el.querySelectorAll("[msallowcapture^='']").length ) {
+ rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
+ }
+
+ // Support: IE8
+ // Boolean attributes and "value" are not treated correctly
+ if ( !el.querySelectorAll("[selected]").length ) {
+ rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" );
+ }
+
+ // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+
+ if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) {
+ rbuggyQSA.push("~=");
+ }
+
+ // Webkit/Opera - :checked should return selected option elements
+ // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+ // IE8 throws error here and will not see later tests
+ if ( !el.querySelectorAll(":checked").length ) {
+ rbuggyQSA.push(":checked");
+ }
+
+ // Support: Safari 8+, iOS 8+
+ // https://bugs.webkit.org/show_bug.cgi?id=136851
+ // In-page `selector#id sibling-combinator selector` fails
+ if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) {
+ rbuggyQSA.push(".#.+[+~]");
+ }
+ });
+
+ assert(function( el ) {
+ el.innerHTML = "<a href='' disabled='disabled'></a>" +
+ "<select disabled='disabled'><option/></select>";
+
+ // Support: Windows 8 Native Apps
+ // The type and name attributes are restricted during .innerHTML assignment
+ var input = document.createElement("input");
+ input.setAttribute( "type", "hidden" );
+ el.appendChild( input ).setAttribute( "name", "D" );
+
+ // Support: IE8
+ // Enforce case-sensitivity of name attribute
+ if ( el.querySelectorAll("[name=d]").length ) {
+ rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" );
+ }
+
+ // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
+ // IE8 throws error here and will not see later tests
+ if ( el.querySelectorAll(":enabled").length !== 2 ) {
+ rbuggyQSA.push( ":enabled", ":disabled" );
+ }
+
+ // Support: IE9-11+
+ // IE's :disabled selector does not pick up the children of disabled fieldsets
+ docElem.appendChild( el ).disabled = true;
+ if ( el.querySelectorAll(":disabled").length !== 2 ) {
+ rbuggyQSA.push( ":enabled", ":disabled" );
+ }
+
+ // Opera 10-11 does not throw on post-comma invalid pseudos
+ el.querySelectorAll("*,:x");
+ rbuggyQSA.push(",.*:");
+ });
+ }
+
+ if ( (support.matchesSelector = rnative.test( (matches = docElem.matches ||
+ docElem.webkitMatchesSelector ||
+ docElem.mozMatchesSelector ||
+ docElem.oMatchesSelector ||
+ docElem.msMatchesSelector) )) ) {
+
+ assert(function( el ) {
+ // Check to see if it's possible to do matchesSelector
+ // on a disconnected node (IE 9)
+ support.disconnectedMatch = matches.call( el, "*" );
+
+ // This should fail with an exception
+ // Gecko does not error, returns false instead
+ matches.call( el, "[s!='']:x" );
+ rbuggyMatches.push( "!=", pseudos );
+ });
+ }
+
+ rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") );
+ rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") );
+
+ /* Contains
+ ---------------------------------------------------------------------- */
+ hasCompare = rnative.test( docElem.compareDocumentPosition );
+
+ // Element contains another
+ // Purposefully self-exclusive
+ // As in, an element does not contain itself
+ contains = hasCompare || rnative.test( docElem.contains ) ?
+ function( a, b ) {
+ var adown = a.nodeType === 9 ? a.documentElement : a,
+ bup = b && b.parentNode;
+ return a === bup || !!( bup && bup.nodeType === 1 && (
+ adown.contains ?
+ adown.contains( bup ) :
+ a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16
+ ));
+ } :
+ function( a, b ) {
+ if ( b ) {
+ while ( (b = b.parentNode) ) {
+ if ( b === a ) {
+ return true;
+ }
+ }
+ }
+ return false;
+ };
+
+ /* Sorting
+ ---------------------------------------------------------------------- */
+
+ // Document order sorting
+ sortOrder = hasCompare ?
+ function( a, b ) {
+
+ // Flag for duplicate removal
+ if ( a === b ) {
+ hasDuplicate = true;
+ return 0;
+ }
+
+ // Sort on method existence if only one input has compareDocumentPosition
+ var compare = !a.compareDocumentPosition - !b.compareDocumentPosition;
+ if ( compare ) {
+ return compare;
+ }
+
+ // Calculate position if both inputs belong to the same document
+ compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ?
+ a.compareDocumentPosition( b ) :
+
+ // Otherwise we know they are disconnected
+ 1;
+
+ // Disconnected nodes
+ if ( compare & 1 ||
+ (!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) {
+
+ // Choose the first element that is related to our preferred document
+ if ( a === document || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) {
+ return -1;
+ }
+ if ( b === document || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) {
+ return 1;
+ }
+
+ // Maintain original order
+ return sortInput ?
+ ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
+ 0;
+ }
+
+ return compare & 4 ? -1 : 1;
+ } :
+ function( a, b ) {
+ // Exit early if the nodes are identical
+ if ( a === b ) {
+ hasDuplicate = true;
+ return 0;
+ }
+
+ var cur,
+ i = 0,
+ aup = a.parentNode,
+ bup = b.parentNode,
+ ap = [ a ],
+ bp = [ b ];
+
+ // Parentless nodes are either documents or disconnected
+ if ( !aup || !bup ) {
+ return a === document ? -1 :
+ b === document ? 1 :
+ aup ? -1 :
+ bup ? 1 :
+ sortInput ?
+ ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
+ 0;
+
+ // If the nodes are siblings, we can do a quick check
+ } else if ( aup === bup ) {
+ return siblingCheck( a, b );
+ }
+
+ // Otherwise we need full lists of their ancestors for comparison
+ cur = a;
+ while ( (cur = cur.parentNode) ) {
+ ap.unshift( cur );
+ }
+ cur = b;
+ while ( (cur = cur.parentNode) ) {
+ bp.unshift( cur );
+ }
+
+ // Walk down the tree looking for a discrepancy
+ while ( ap[i] === bp[i] ) {
+ i++;
+ }
+
+ return i ?
+ // Do a sibling check if the nodes have a common ancestor
+ siblingCheck( ap[i], bp[i] ) :
+
+ // Otherwise nodes in our document sort first
+ ap[i] === preferredDoc ? -1 :
+ bp[i] === preferredDoc ? 1 :
+ 0;
+ };
+
+ return document;
+};
+
+Sizzle.matches = function( expr, elements ) {
+ return Sizzle( expr, null, null, elements );
+};
+
+Sizzle.matchesSelector = function( elem, expr ) {
+ // Set document vars if needed
+ if ( ( elem.ownerDocument || elem ) !== document ) {
+ setDocument( elem );
+ }
+
+ // Make sure that attribute selectors are quoted
+ expr = expr.replace( rattributeQuotes, "='$1']" );
+
+ if ( support.matchesSelector && documentIsHTML &&
+ !compilerCache[ expr + " " ] &&
+ ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) &&
+ ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) {
+
+ try {
+ var ret = matches.call( elem, expr );
+
+ // IE 9's matchesSelector returns false on disconnected nodes
+ if ( ret || support.disconnectedMatch ||
+ // As well, disconnected nodes are said to be in a document
+ // fragment in IE 9
+ elem.document && elem.document.nodeType !== 11 ) {
+ return ret;
+ }
+ } catch (e) {}
+ }
+
+ return Sizzle( expr, document, null, [ elem ] ).length > 0;
+};
+
+Sizzle.contains = function( context, elem ) {
+ // Set document vars if needed
+ if ( ( context.ownerDocument || context ) !== document ) {
+ setDocument( context );
+ }
+ return contains( context, elem );
+};
+
+Sizzle.attr = function( elem, name ) {
+ // Set document vars if needed
+ if ( ( elem.ownerDocument || elem ) !== document ) {
+ setDocument( elem );
+ }
+
+ var fn = Expr.attrHandle[ name.toLowerCase() ],
+ // Don't get fooled by Object.prototype properties (jQuery #13807)
+ val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ?
+ fn( elem, name, !documentIsHTML ) :
+ undefined;
+
+ return val !== undefined ?
+ val :
+ support.attributes || !documentIsHTML ?
+ elem.getAttribute( name ) :
+ (val = elem.getAttributeNode(name)) && val.specified ?
+ val.value :
+ null;
+};
+
+Sizzle.escape = function( sel ) {
+ return (sel + "").replace( rcssescape, fcssescape );
+};
+
+Sizzle.error = function( msg ) {
+ throw new Error( "Syntax error, unrecognized expression: " + msg );
+};
+
+/**
+ * Document sorting and removing duplicates
+ * @param {ArrayLike} results
+ */
+Sizzle.uniqueSort = function( results ) {
+ var elem,
+ duplicates = [],
+ j = 0,
+ i = 0;
+
+ // Unless we *know* we can detect duplicates, assume their presence
+ hasDuplicate = !support.detectDuplicates;
+ sortInput = !support.sortStable && results.slice( 0 );
+ results.sort( sortOrder );
+
+ if ( hasDuplicate ) {
+ while ( (elem = results[i++]) ) {
+ if ( elem === results[ i ] ) {
+ j = duplicates.push( i );
+ }
+ }
+ while ( j-- ) {
+ results.splice( duplicates[ j ], 1 );
+ }
+ }
+
+ // Clear input after sorting to release objects
+ // See https://github.com/jquery/sizzle/pull/225
+ sortInput = null;
+
+ return results;
+};
+
+/**
+ * Utility function for retrieving the text value of an array of DOM nodes
+ * @param {Array|Element} elem
+ */
+getText = Sizzle.getText = function( elem ) {
+ var node,
+ ret = "",
+ i = 0,
+ nodeType = elem.nodeType;
+
+ if ( !nodeType ) {
+ // If no nodeType, this is expected to be an array
+ while ( (node = elem[i++]) ) {
+ // Do not traverse comment nodes
+ ret += getText( node );
+ }
+ } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
+ // Use textContent for elements
+ // innerText usage removed for consistency of new lines (jQuery #11153)
+ if ( typeof elem.textContent === "string" ) {
+ return elem.textContent;
+ } else {
+ // Traverse its children
+ for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+ ret += getText( elem );
+ }
+ }
+ } else if ( nodeType === 3 || nodeType === 4 ) {
+ return elem.nodeValue;
+ }
+ // Do not include comment or processing instruction nodes
+
+ return ret;
+};
+
+Expr = Sizzle.selectors = {
+
+ // Can be adjusted by the user
+ cacheLength: 50,
+
+ createPseudo: markFunction,
+
+ match: matchExpr,
+
+ attrHandle: {},
+
+ find: {},
+
+ relative: {
+ ">": { dir: "parentNode", first: true },
+ " ": { dir: "parentNode" },
+ "+": { dir: "previousSibling", first: true },
+ "~": { dir: "previousSibling" }
+ },
+
+ preFilter: {
+ "ATTR": function( match ) {
+ match[1] = match[1].replace( runescape, funescape );
+
+ // Move the given value to match[3] whether quoted or unquoted
+ match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape );
+
+ if ( match[2] === "~=" ) {
+ match[3] = " " + match[3] + " ";
+ }
+
+ return match.slice( 0, 4 );
+ },
+
+ "CHILD": function( match ) {
+ /* matches from matchExpr["CHILD"]
+ 1 type (only|nth|...)
+ 2 what (child|of-type)
+ 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...)
+ 4 xn-component of xn+y argument ([+-]?\d*n|)
+ 5 sign of xn-component
+ 6 x of xn-component
+ 7 sign of y-component
+ 8 y of y-component
+ */
+ match[1] = match[1].toLowerCase();
+
+ if ( match[1].slice( 0, 3 ) === "nth" ) {
+ // nth-* requires argument
+ if ( !match[3] ) {
+ Sizzle.error( match[0] );
+ }
+
+ // numeric x and y parameters for Expr.filter.CHILD
+ // remember that false/true cast respectively to 0/1
+ match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) );
+ match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" );
+
+ // other types prohibit arguments
+ } else if ( match[3] ) {
+ Sizzle.error( match[0] );
+ }
+
+ return match;
+ },
+
+ "PSEUDO": function( match ) {
+ var excess,
+ unquoted = !match[6] && match[2];
+
+ if ( matchExpr["CHILD"].test( match[0] ) ) {
+ return null;
+ }
+
+ // Accept quoted arguments as-is
+ if ( match[3] ) {
+ match[2] = match[4] || match[5] || "";
+
+ // Strip excess characters from unquoted arguments
+ } else if ( unquoted && rpseudo.test( unquoted ) &&
+ // Get excess from tokenize (recursively)
+ (excess = tokenize( unquoted, true )) &&
+ // advance to the next closing parenthesis
+ (excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) {
+
+ // excess is a negative index
+ match[0] = match[0].slice( 0, excess );
+ match[2] = unquoted.slice( 0, excess );
+ }
+
+ // Return only captures needed by the pseudo filter method (type and argument)
+ return match.slice( 0, 3 );
+ }
+ },
+
+ filter: {
+
+ "TAG": function( nodeNameSelector ) {
+ var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase();
+ return nodeNameSelector === "*" ?
+ function() { return true; } :
+ function( elem ) {
+ return elem.nodeName && elem.nodeName.toLowerCase() === nodeName;
+ };
+ },
+
+ "CLASS": function( className ) {
+ var pattern = classCache[ className + " " ];
+
+ return pattern ||
+ (pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) &&
+ classCache( className, function( elem ) {
+ return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || "" );
+ });
+ },
+
+ "ATTR": function( name, operator, check ) {
+ return function( elem ) {
+ var result = Sizzle.attr( elem, name );
+
+ if ( result == null ) {
+ return operator === "!=";
+ }
+ if ( !operator ) {
+ return true;
+ }
+
+ result += "";
+
+ return operator === "=" ? result === check :
+ operator === "!=" ? result !== check :
+ operator === "^=" ? check && result.indexOf( check ) === 0 :
+ operator === "*=" ? check && result.indexOf( check ) > -1 :
+ operator === "$=" ? check && result.slice( -check.length ) === check :
+ operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 :
+ operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" :
+ false;
+ };
+ },
+
+ "CHILD": function( type, what, argument, first, last ) {
+ var simple = type.slice( 0, 3 ) !== "nth",
+ forward = type.slice( -4 ) !== "last",
+ ofType = what === "of-type";
+
+ return first === 1 && last === 0 ?
+
+ // Shortcut for :nth-*(n)
+ function( elem ) {
+ return !!elem.parentNode;
+ } :
+
+ function( elem, context, xml ) {
+ var cache, uniqueCache, outerCache, node, nodeIndex, start,
+ dir = simple !== forward ? "nextSibling" : "previousSibling",
+ parent = elem.parentNode,
+ name = ofType && elem.nodeName.toLowerCase(),
+ useCache = !xml && !ofType,
+ diff = false;
+
+ if ( parent ) {
+
+ // :(first|last|only)-(child|of-type)
+ if ( simple ) {
+ while ( dir ) {
+ node = elem;
+ while ( (node = node[ dir ]) ) {
+ if ( ofType ?
+ node.nodeName.toLowerCase() === name :
+ node.nodeType === 1 ) {
+
+ return false;
+ }
+ }
+ // Reverse direction for :only-* (if we haven't yet done so)
+ start = dir = type === "only" && !start && "nextSibling";
+ }
+ return true;
+ }
+
+ start = [ forward ? parent.firstChild : parent.lastChild ];
+
+ // non-xml :nth-child(...) stores cache data on `parent`
+ if ( forward && useCache ) {
+
+ // Seek `elem` from a previously-cached index
+
+ // ...in a gzip-friendly way
+ node = parent;
+ outerCache = node[ expando ] || (node[ expando ] = {});
+
+ // Support: IE <9 only
+ // Defend against cloned attroperties (jQuery gh-1709)
+ uniqueCache = outerCache[ node.uniqueID ] ||
+ (outerCache[ node.uniqueID ] = {});
+
+ cache = uniqueCache[ type ] || [];
+ nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];
+ diff = nodeIndex && cache[ 2 ];
+ node = nodeIndex && parent.childNodes[ nodeIndex ];
+
+ while ( (node = ++nodeIndex && node && node[ dir ] ||
+
+ // Fallback to seeking `elem` from the start
+ (diff = nodeIndex = 0) || start.pop()) ) {
+
+ // When found, cache indexes on `parent` and break
+ if ( node.nodeType === 1 && ++diff && node === elem ) {
+ uniqueCache[ type ] = [ dirruns, nodeIndex, diff ];
+ break;
+ }
+ }
+
+ } else {
+ // Use previously-cached element index if available
+ if ( useCache ) {
+ // ...in a gzip-friendly way
+ node = elem;
+ outerCache = node[ expando ] || (node[ expando ] = {});
+
+ // Support: IE <9 only
+ // Defend against cloned attroperties (jQuery gh-1709)
+ uniqueCache = outerCache[ node.uniqueID ] ||
+ (outerCache[ node.uniqueID ] = {});
+
+ cache = uniqueCache[ type ] || [];
+ nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];
+ diff = nodeIndex;
+ }
+
+ // xml :nth-child(...)
+ // or :nth-last-child(...) or :nth(-last)?-of-type(...)
+ if ( diff === false ) {
+ // Use the same loop as above to seek `elem` from the start
+ while ( (node = ++nodeIndex && node && node[ dir ] ||
+ (diff = nodeIndex = 0) || start.pop()) ) {
+
+ if ( ( ofType ?
+ node.nodeName.toLowerCase() === name :
+ node.nodeType === 1 ) &&
+ ++diff ) {
+
+ // Cache the index of each encountered element
+ if ( useCache ) {
+ outerCache = node[ expando ] || (node[ expando ] = {});
+
+ // Support: IE <9 only
+ // Defend against cloned attroperties (jQuery gh-1709)
+ uniqueCache = outerCache[ node.uniqueID ] ||
+ (outerCache[ node.uniqueID ] = {});
+
+ uniqueCache[ type ] = [ dirruns, diff ];
+ }
+
+ if ( node === elem ) {
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ // Incorporate the offset, then check against cycle size
+ diff -= last;
+ return diff === first || ( diff % first === 0 && diff / first >= 0 );
+ }
+ };
+ },
+
+ "PSEUDO": function( pseudo, argument ) {
+ // pseudo-class names are case-insensitive
+ // http://www.w3.org/TR/selectors/#pseudo-classes
+ // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters
+ // Remember that setFilters inherits from pseudos
+ var args,
+ fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||
+ Sizzle.error( "unsupported pseudo: " + pseudo );
+
+ // The user may use createPseudo to indicate that
+ // arguments are needed to create the filter function
+ // just as Sizzle does
+ if ( fn[ expando ] ) {
+ return fn( argument );
+ }
+
+ // But maintain support for old signatures
+ if ( fn.length > 1 ) {
+ args = [ pseudo, pseudo, "", argument ];
+ return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?
+ markFunction(function( seed, matches ) {
+ var idx,
+ matched = fn( seed, argument ),
+ i = matched.length;
+ while ( i-- ) {
+ idx = indexOf( seed, matched[i] );
+ seed[ idx ] = !( matches[ idx ] = matched[i] );
+ }
+ }) :
+ function( elem ) {
+ return fn( elem, 0, args );
+ };
+ }
+
+ return fn;
+ }
+ },
+
+ pseudos: {
+ // Potentially complex pseudos
+ "not": markFunction(function( selector ) {
+ // Trim the selector passed to compile
+ // to avoid treating leading and trailing
+ // spaces as combinators
+ var input = [],
+ results = [],
+ matcher = compile( selector.replace( rtrim, "$1" ) );
+
+ return matcher[ expando ] ?
+ markFunction(function( seed, matches, context, xml ) {
+ var elem,
+ unmatched = matcher( seed, null, xml, [] ),
+ i = seed.length;
+
+ // Match elements unmatched by `matcher`
+ while ( i-- ) {
+ if ( (elem = unmatched[i]) ) {
+ seed[i] = !(matches[i] = elem);
+ }
+ }
+ }) :
+ function( elem, context, xml ) {
+ input[0] = elem;
+ matcher( input, null, xml, results );
+ // Don't keep the element (issue #299)
+ input[0] = null;
+ return !results.pop();
+ };
+ }),
+
+ "has": markFunction(function( selector ) {
+ return function( elem ) {
+ return Sizzle( selector, elem ).length > 0;
+ };
+ }),
+
+ "contains": markFunction(function( text ) {
+ text = text.replace( runescape, funescape );
+ return function( elem ) {
+ return ( elem.textContent || elem.innerText || getText( elem ) ).indexOf( text ) > -1;
+ };
+ }),
+
+ // "Whether an element is represented by a :lang() selector
+ // is based solely on the element's language value
+ // being equal to the identifier C,
+ // or beginning with the identifier C immediately followed by "-".
+ // The matching of C against the element's language value is performed case-insensitively.
+ // The identifier C does not have to be a valid language name."
+ // http://www.w3.org/TR/selectors/#lang-pseudo
+ "lang": markFunction( function( lang ) {
+ // lang value must be a valid identifier
+ if ( !ridentifier.test(lang || "") ) {
+ Sizzle.error( "unsupported lang: " + lang );
+ }
+ lang = lang.replace( runescape, funescape ).toLowerCase();
+ return function( elem ) {
+ var elemLang;
+ do {
+ if ( (elemLang = documentIsHTML ?
+ elem.lang :
+ elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) {
+
+ elemLang = elemLang.toLowerCase();
+ return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0;
+ }
+ } while ( (elem = elem.parentNode) && elem.nodeType === 1 );
+ return false;
+ };
+ }),
+
+ // Miscellaneous
+ "target": function( elem ) {
+ var hash = window.location && window.location.hash;
+ return hash && hash.slice( 1 ) === elem.id;
+ },
+
+ "root": function( elem ) {
+ return elem === docElem;
+ },
+
+ "focus": function( elem ) {
+ return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex);
+ },
+
+ // Boolean properties
+ "enabled": createDisabledPseudo( false ),
+ "disabled": createDisabledPseudo( true ),
+
+ "checked": function( elem ) {
+ // In CSS3, :checked should return both checked and selected elements
+ // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+ var nodeName = elem.nodeName.toLowerCase();
+ return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected);
+ },
+
+ "selected": function( elem ) {
+ // Accessing this property makes selected-by-default
+ // options in Safari work properly
+ if ( elem.parentNode ) {
+ elem.parentNode.selectedIndex;
+ }
+
+ return elem.selected === true;
+ },
+
+ // Contents
+ "empty": function( elem ) {
+ // http://www.w3.org/TR/selectors/#empty-pseudo
+ // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5),
+ // but not by others (comment: 8; processing instruction: 7; etc.)
+ // nodeType < 6 works because attributes (2) do not appear as children
+ for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+ if ( elem.nodeType < 6 ) {
+ return false;
+ }
+ }
+ return true;
+ },
+
+ "parent": function( elem ) {
+ return !Expr.pseudos["empty"]( elem );
+ },
+
+ // Element/input types
+ "header": function( elem ) {
+ return rheader.test( elem.nodeName );
+ },
+
+ "input": function( elem ) {
+ return rinputs.test( elem.nodeName );
+ },
+
+ "button": function( elem ) {
+ var name = elem.nodeName.toLowerCase();
+ return name === "input" && elem.type === "button" || name === "button";
+ },
+
+ "text": function( elem ) {
+ var attr;
+ return elem.nodeName.toLowerCase() === "input" &&
+ elem.type === "text" &&
+
+ // Support: IE<8
+ // New HTML5 attribute values (e.g., "search") appear with elem.type === "text"
+ ( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" );
+ },
+
+ // Position-in-collection
+ "first": createPositionalPseudo(function() {
+ return [ 0 ];
+ }),
+
+ "last": createPositionalPseudo(function( matchIndexes, length ) {
+ return [ length - 1 ];
+ }),
+
+ "eq": createPositionalPseudo(function( matchIndexes, length, argument ) {
+ return [ argument < 0 ? argument + length : argument ];
+ }),
+
+ "even": createPositionalPseudo(function( matchIndexes, length ) {
+ var i = 0;
+ for ( ; i < length; i += 2 ) {
+ matchIndexes.push( i );
+ }
+ return matchIndexes;
+ }),
+
+ "odd": createPositionalPseudo(function( matchIndexes, length ) {
+ var i = 1;
+ for ( ; i < length; i += 2 ) {
+ matchIndexes.push( i );
+ }
+ return matchIndexes;
+ }),
+
+ "lt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+ var i = argument < 0 ? argument + length : argument;
+ for ( ; --i >= 0; ) {
+ matchIndexes.push( i );
+ }
+ return matchIndexes;
+ }),
+
+ "gt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+ var i = argument < 0 ? argument + length : argument;
+ for ( ; ++i < length; ) {
+ matchIndexes.push( i );
+ }
+ return matchIndexes;
+ })
+ }
+};
+
+Expr.pseudos["nth"] = Expr.pseudos["eq"];
+
+// Add button/input type pseudos
+for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) {
+ Expr.pseudos[ i ] = createInputPseudo( i );
+}
+for ( i in { submit: true, reset: true } ) {
+ Expr.pseudos[ i ] = createButtonPseudo( i );
+}
+
+// Easy API for creating new setFilters
+function setFilters() {}
+setFilters.prototype = Expr.filters = Expr.pseudos;
+Expr.setFilters = new setFilters();
+
+tokenize = Sizzle.tokenize = function( selector, parseOnly ) {
+ var matched, match, tokens, type,
+ soFar, groups, preFilters,
+ cached = tokenCache[ selector + " " ];
+
+ if ( cached ) {
+ return parseOnly ? 0 : cached.slice( 0 );
+ }
+
+ soFar = selector;
+ groups = [];
+ preFilters = Expr.preFilter;
+
+ while ( soFar ) {
+
+ // Comma and first run
+ if ( !matched || (match = rcomma.exec( soFar )) ) {
+ if ( match ) {
+ // Don't consume trailing commas as valid
+ soFar = soFar.slice( match[0].length ) || soFar;
+ }
+ groups.push( (tokens = []) );
+ }
+
+ matched = false;
+
+ // Combinators
+ if ( (match = rcombinators.exec( soFar )) ) {
+ matched = match.shift();
+ tokens.push({
+ value: matched,
+ // Cast descendant combinators to space
+ type: match[0].replace( rtrim, " " )
+ });
+ soFar = soFar.slice( matched.length );
+ }
+
+ // Filters
+ for ( type in Expr.filter ) {
+ if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] ||
+ (match = preFilters[ type ]( match ))) ) {
+ matched = match.shift();
+ tokens.push({
+ value: matched,
+ type: type,
+ matches: match
+ });
+ soFar = soFar.slice( matched.length );
+ }
+ }
+
+ if ( !matched ) {
+ break;
+ }
+ }
+
+ // Return the length of the invalid excess
+ // if we're just parsing
+ // Otherwise, throw an error or return tokens
+ return parseOnly ?
+ soFar.length :
+ soFar ?
+ Sizzle.error( selector ) :
+ // Cache the tokens
+ tokenCache( selector, groups ).slice( 0 );
+};
+
+function toSelector( tokens ) {
+ var i = 0,
+ len = tokens.length,
+ selector = "";
+ for ( ; i < len; i++ ) {
+ selector += tokens[i].value;
+ }
+ return selector;
+}
+
+function addCombinator( matcher, combinator, base ) {
+ var dir = combinator.dir,
+ skip = combinator.next,
+ key = skip || dir,
+ checkNonElements = base && key === "parentNode",
+ doneName = done++;
+
+ return combinator.first ?
+ // Check against closest ancestor/preceding element
+ function( elem, context, xml ) {
+ while ( (elem = elem[ dir ]) ) {
+ if ( elem.nodeType === 1 || checkNonElements ) {
+ return matcher( elem, context, xml );
+ }
+ }
+ return false;
+ } :
+
+ // Check against all ancestor/preceding elements
+ function( elem, context, xml ) {
+ var oldCache, uniqueCache, outerCache,
+ newCache = [ dirruns, doneName ];
+
+ // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching
+ if ( xml ) {
+ while ( (elem = elem[ dir ]) ) {
+ if ( elem.nodeType === 1 || checkNonElements ) {
+ if ( matcher( elem, context, xml ) ) {
+ return true;
+ }
+ }
+ }
+ } else {
+ while ( (elem = elem[ dir ]) ) {
+ if ( elem.nodeType === 1 || checkNonElements ) {
+ outerCache = elem[ expando ] || (elem[ expando ] = {});
+
+ // Support: IE <9 only
+ // Defend against cloned attroperties (jQuery gh-1709)
+ uniqueCache = outerCache[ elem.uniqueID ] || (outerCache[ elem.uniqueID ] = {});
+
+ if ( skip && skip === elem.nodeName.toLowerCase() ) {
+ elem = elem[ dir ] || elem;
+ } else if ( (oldCache = uniqueCache[ key ]) &&
+ oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) {
+
+ // Assign to newCache so results back-propagate to previous elements
+ return (newCache[ 2 ] = oldCache[ 2 ]);
+ } else {
+ // Reuse newcache so results back-propagate to previous elements
+ uniqueCache[ key ] = newCache;
+
+ // A match means we're done; a fail means we have to keep checking
+ if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) {
+ return true;
+ }
+ }
+ }
+ }
+ }
+ return false;
+ };
+}
+
+function elementMatcher( matchers ) {
+ return matchers.length > 1 ?
+ function( elem, context, xml ) {
+ var i = matchers.length;
+ while ( i-- ) {
+ if ( !matchers[i]( elem, context, xml ) ) {
+ return false;
+ }
+ }
+ return true;
+ } :
+ matchers[0];
+}
+
+function multipleContexts( selector, contexts, results ) {
+ var i = 0,
+ len = contexts.length;
+ for ( ; i < len; i++ ) {
+ Sizzle( selector, contexts[i], results );
+ }
+ return results;
+}
+
+function condense( unmatched, map, filter, context, xml ) {
+ var elem,
+ newUnmatched = [],
+ i = 0,
+ len = unmatched.length,
+ mapped = map != null;
+
+ for ( ; i < len; i++ ) {
+ if ( (elem = unmatched[i]) ) {
+ if ( !filter || filter( elem, context, xml ) ) {
+ newUnmatched.push( elem );
+ if ( mapped ) {
+ map.push( i );
+ }
+ }
+ }
+ }
+
+ return newUnmatched;
+}
+
+function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
+ if ( postFilter && !postFilter[ expando ] ) {
+ postFilter = setMatcher( postFilter );
+ }
+ if ( postFinder && !postFinder[ expando ] ) {
+ postFinder = setMatcher( postFinder, postSelector );
+ }
+ return markFunction(function( seed, results, context, xml ) {
+ var temp, i, elem,
+ preMap = [],
+ postMap = [],
+ preexisting = results.length,
+
+ // Get initial elements from seed or context
+ elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ),
+
+ // Prefilter to get matcher input, preserving a map for seed-results synchronization
+ matcherIn = preFilter && ( seed || !selector ) ?
+ condense( elems, preMap, preFilter, context, xml ) :
+ elems,
+
+ matcherOut = matcher ?
+ // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,
+ postFinder || ( seed ? preFilter : preexisting || postFilter ) ?
+
+ // ...intermediate processing is necessary
+ [] :
+
+ // ...otherwise use results directly
+ results :
+ matcherIn;
+
+ // Find primary matches
+ if ( matcher ) {
+ matcher( matcherIn, matcherOut, context, xml );
+ }
+
+ // Apply postFilter
+ if ( postFilter ) {
+ temp = condense( matcherOut, postMap );
+ postFilter( temp, [], context, xml );
+
+ // Un-match failing elements by moving them back to matcherIn
+ i = temp.length;
+ while ( i-- ) {
+ if ( (elem = temp[i]) ) {
+ matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem);
+ }
+ }
+ }
+
+ if ( seed ) {
+ if ( postFinder || preFilter ) {
+ if ( postFinder ) {
+ // Get the final matcherOut by condensing this intermediate into postFinder contexts
+ temp = [];
+ i = matcherOut.length;
+ while ( i-- ) {
+ if ( (elem = matcherOut[i]) ) {
+ // Restore matcherIn since elem is not yet a final match
+ temp.push( (matcherIn[i] = elem) );
+ }
+ }
+ postFinder( null, (matcherOut = []), temp, xml );
+ }
+
+ // Move matched elements from seed to results to keep them synchronized
+ i = matcherOut.length;
+ while ( i-- ) {
+ if ( (elem = matcherOut[i]) &&
+ (temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) {
+
+ seed[temp] = !(results[temp] = elem);
+ }
+ }
+ }
+
+ // Add elements to results, through postFinder if defined
+ } else {
+ matcherOut = condense(
+ matcherOut === results ?
+ matcherOut.splice( preexisting, matcherOut.length ) :
+ matcherOut
+ );
+ if ( postFinder ) {
+ postFinder( null, results, matcherOut, xml );
+ } else {
+ push.apply( results, matcherOut );
+ }
+ }
+ });
+}
+
+function matcherFromTokens( tokens ) {
+ var checkContext, matcher, j,
+ len = tokens.length,
+ leadingRelative = Expr.relative[ tokens[0].type ],
+ implicitRelative = leadingRelative || Expr.relative[" "],
+ i = leadingRelative ? 1 : 0,
+
+ // The foundational matcher ensures that elements are reachable from top-level context(s)
+ matchContext = addCombinator( function( elem ) {
+ return elem === checkContext;
+ }, implicitRelative, true ),
+ matchAnyContext = addCombinator( function( elem ) {
+ return indexOf( checkContext, elem ) > -1;
+ }, implicitRelative, true ),
+ matchers = [ function( elem, context, xml ) {
+ var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
+ (checkContext = context).nodeType ?
+ matchContext( elem, context, xml ) :
+ matchAnyContext( elem, context, xml ) );
+ // Avoid hanging onto element (issue #299)
+ checkContext = null;
+ return ret;
+ } ];
+
+ for ( ; i < len; i++ ) {
+ if ( (matcher = Expr.relative[ tokens[i].type ]) ) {
+ matchers = [ addCombinator(elementMatcher( matchers ), matcher) ];
+ } else {
+ matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches );
+
+ // Return special upon seeing a positional matcher
+ if ( matcher[ expando ] ) {
+ // Find the next relative operator (if any) for proper handling
+ j = ++i;
+ for ( ; j < len; j++ ) {
+ if ( Expr.relative[ tokens[j].type ] ) {
+ break;
+ }
+ }
+ return setMatcher(
+ i > 1 && elementMatcher( matchers ),
+ i > 1 && toSelector(
+ // If the preceding token was a descendant combinator, insert an implicit any-element `*`
+ tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" })
+ ).replace( rtrim, "$1" ),
+ matcher,
+ i < j && matcherFromTokens( tokens.slice( i, j ) ),
+ j < len && matcherFromTokens( (tokens = tokens.slice( j )) ),
+ j < len && toSelector( tokens )
+ );
+ }
+ matchers.push( matcher );
+ }
+ }
+
+ return elementMatcher( matchers );
+}
+
+function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
+ var bySet = setMatchers.length > 0,
+ byElement = elementMatchers.length > 0,
+ superMatcher = function( seed, context, xml, results, outermost ) {
+ var elem, j, matcher,
+ matchedCount = 0,
+ i = "0",
+ unmatched = seed && [],
+ setMatched = [],
+ contextBackup = outermostContext,
+ // We must always have either seed elements or outermost context
+ elems = seed || byElement && Expr.find["TAG"]( "*", outermost ),
+ // Use integer dirruns iff this is the outermost matcher
+ dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1),
+ len = elems.length;
+
+ if ( outermost ) {
+ outermostContext = context === document || context || outermost;
+ }
+
+ // Add elements passing elementMatchers directly to results
+ // Support: IE<9, Safari
+ // Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id
+ for ( ; i !== len && (elem = elems[i]) != null; i++ ) {
+ if ( byElement && elem ) {
+ j = 0;
+ if ( !context && elem.ownerDocument !== document ) {
+ setDocument( elem );
+ xml = !documentIsHTML;
+ }
+ while ( (matcher = elementMatchers[j++]) ) {
+ if ( matcher( elem, context || document, xml) ) {
+ results.push( elem );
+ break;
+ }
+ }
+ if ( outermost ) {
+ dirruns = dirrunsUnique;
+ }
+ }
+
+ // Track unmatched elements for set filters
+ if ( bySet ) {
+ // They will have gone through all possible matchers
+ if ( (elem = !matcher && elem) ) {
+ matchedCount--;
+ }
+
+ // Lengthen the array for every element, matched or not
+ if ( seed ) {
+ unmatched.push( elem );
+ }
+ }
+ }
+
+ // `i` is now the count of elements visited above, and adding it to `matchedCount`
+ // makes the latter nonnegative.
+ matchedCount += i;
+
+ // Apply set filters to unmatched elements
+ // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount`
+ // equals `i`), unless we didn't visit _any_ elements in the above loop because we have
+ // no element matchers and no seed.
+ // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that
+ // case, which will result in a "00" `matchedCount` that differs from `i` but is also
+ // numerically zero.
+ if ( bySet && i !== matchedCount ) {
+ j = 0;
+ while ( (matcher = setMatchers[j++]) ) {
+ matcher( unmatched, setMatched, context, xml );
+ }
+
+ if ( seed ) {
+ // Reintegrate element matches to eliminate the need for sorting
+ if ( matchedCount > 0 ) {
+ while ( i-- ) {
+ if ( !(unmatched[i] || setMatched[i]) ) {
+ setMatched[i] = pop.call( results );
+ }
+ }
+ }
+
+ // Discard index placeholder values to get only actual matches
+ setMatched = condense( setMatched );
+ }
+
+ // Add matches to results
+ push.apply( results, setMatched );
+
+ // Seedless set matches succeeding multiple successful matchers stipulate sorting
+ if ( outermost && !seed && setMatched.length > 0 &&
+ ( matchedCount + setMatchers.length ) > 1 ) {
+
+ Sizzle.uniqueSort( results );
+ }
+ }
+
+ // Override manipulation of globals by nested matchers
+ if ( outermost ) {
+ dirruns = dirrunsUnique;
+ outermostContext = contextBackup;
+ }
+
+ return unmatched;
+ };
+
+ return bySet ?
+ markFunction( superMatcher ) :
+ superMatcher;
+}
+
+compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) {
+ var i,
+ setMatchers = [],
+ elementMatchers = [],
+ cached = compilerCache[ selector + " " ];
+
+ if ( !cached ) {
+ // Generate a function of recursive functions that can be used to check each element
+ if ( !match ) {
+ match = tokenize( selector );
+ }
+ i = match.length;
+ while ( i-- ) {
+ cached = matcherFromTokens( match[i] );
+ if ( cached[ expando ] ) {
+ setMatchers.push( cached );
+ } else {
+ elementMatchers.push( cached );
+ }
+ }
+
+ // Cache the compiled function
+ cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );
+
+ // Save selector and tokenization
+ cached.selector = selector;
+ }
+ return cached;
+};
+
+/**
+ * A low-level selection function that works with Sizzle's compiled
+ * selector functions
+ * @param {String|Function} selector A selector or a pre-compiled
+ * selector function built with Sizzle.compile
+ * @param {Element} context
+ * @param {Array} [results]
+ * @param {Array} [seed] A set of elements to match against
+ */
+select = Sizzle.select = function( selector, context, results, seed ) {
+ var i, tokens, token, type, find,
+ compiled = typeof selector === "function" && selector,
+ match = !seed && tokenize( (selector = compiled.selector || selector) );
+
+ results = results || [];
+
+ // Try to minimize operations if there is only one selector in the list and no seed
+ // (the latter of which guarantees us context)
+ if ( match.length === 1 ) {
+
+ // Reduce context if the leading compound selector is an ID
+ tokens = match[0] = match[0].slice( 0 );
+ if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
+ context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[1].type ] ) {
+
+ context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0];
+ if ( !context ) {
+ return results;
+
+ // Precompiled matchers will still verify ancestry, so step up a level
+ } else if ( compiled ) {
+ context = context.parentNode;
+ }
+
+ selector = selector.slice( tokens.shift().value.length );
+ }
+
+ // Fetch a seed set for right-to-left matching
+ i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length;
+ while ( i-- ) {
+ token = tokens[i];
+
+ // Abort if we hit a combinator
+ if ( Expr.relative[ (type = token.type) ] ) {
+ break;
+ }
+ if ( (find = Expr.find[ type ]) ) {
+ // Search, expanding context for leading sibling combinators
+ if ( (seed = find(
+ token.matches[0].replace( runescape, funescape ),
+ rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context
+ )) ) {
+
+ // If seed is empty or no tokens remain, we can return early
+ tokens.splice( i, 1 );
+ selector = seed.length && toSelector( tokens );
+ if ( !selector ) {
+ push.apply( results, seed );
+ return results;
+ }
+
+ break;
+ }
+ }
+ }
+ }
+
+ // Compile and execute a filtering function if one is not provided
+ // Provide `match` to avoid retokenization if we modified the selector above
+ ( compiled || compile( selector, match ) )(
+ seed,
+ context,
+ !documentIsHTML,
+ results,
+ !context || rsibling.test( selector ) && testContext( context.parentNode ) || context
+ );
+ return results;
+};
+
+// One-time assignments
+
+// Sort stability
+support.sortStable = expando.split("").sort( sortOrder ).join("") === expando;
+
+// Support: Chrome 14-35+
+// Always assume duplicates if they aren't passed to the comparison function
+support.detectDuplicates = !!hasDuplicate;
+
+// Initialize against the default document
+setDocument();
+
+// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)
+// Detached nodes confoundingly follow *each other*
+support.sortDetached = assert(function( el ) {
+ // Should return 1, but returns 4 (following)
+ return el.compareDocumentPosition( document.createElement("fieldset") ) & 1;
+});
+
+// Support: IE<8
+// Prevent attribute/property "interpolation"
+// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
+if ( !assert(function( el ) {
+ el.innerHTML = "<a href='#'></a>";
+ return el.firstChild.getAttribute("href") === "#" ;
+}) ) {
+ addHandle( "type|href|height|width", function( elem, name, isXML ) {
+ if ( !isXML ) {
+ return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 );
+ }
+ });
+}
+
+// Support: IE<9
+// Use defaultValue in place of getAttribute("value")
+if ( !support.attributes || !assert(function( el ) {
+ el.innerHTML = "<input/>";
+ el.firstChild.setAttribute( "value", "" );
+ return el.firstChild.getAttribute( "value" ) === "";
+}) ) {
+ addHandle( "value", function( elem, name, isXML ) {
+ if ( !isXML && elem.nodeName.toLowerCase() === "input" ) {
+ return elem.defaultValue;
+ }
+ });
+}
+
+// Support: IE<9
+// Use getAttributeNode to fetch booleans when getAttribute lies
+if ( !assert(function( el ) {
+ return el.getAttribute("disabled") == null;
+}) ) {
+ addHandle( booleans, function( elem, name, isXML ) {
+ var val;
+ if ( !isXML ) {
+ return elem[ name ] === true ? name.toLowerCase() :
+ (val = elem.getAttributeNode( name )) && val.specified ?
+ val.value :
+ null;
+ }
+ });
+}
+
+return Sizzle;
+
+})( window );
+
+
+
+jQuery.find = Sizzle;
+jQuery.expr = Sizzle.selectors;
+
+// Deprecated
+jQuery.expr[ ":" ] = jQuery.expr.pseudos;
+jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort;
+jQuery.text = Sizzle.getText;
+jQuery.isXMLDoc = Sizzle.isXML;
+jQuery.contains = Sizzle.contains;
+jQuery.escapeSelector = Sizzle.escape;
+
+
+
+
+var dir = function( elem, dir, until ) {
+ var matched = [],
+ truncate = until !== undefined;
+
+ while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) {
+ if ( elem.nodeType === 1 ) {
+ if ( truncate && jQuery( elem ).is( until ) ) {
+ break;
+ }
+ matched.push( elem );
+ }
+ }
+ return matched;
+};
+
+
+var siblings = function( n, elem ) {
+ var matched = [];
+
+ for ( ; n; n = n.nextSibling ) {
+ if ( n.nodeType === 1 && n !== elem ) {
+ matched.push( n );
+ }
+ }
+
+ return matched;
+};
+
+
+var rneedsContext = jQuery.expr.match.needsContext;
+
+
+
+function nodeName( elem, name ) {
+
+ return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
+
+};
+var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i );
+
+
+
+// Implement the identical functionality for filter and not
+function winnow( elements, qualifier, not ) {
+ if ( isFunction( qualifier ) ) {
+ return jQuery.grep( elements, function( elem, i ) {
+ return !!qualifier.call( elem, i, elem ) !== not;
+ } );
+ }
+
+ // Single element
+ if ( qualifier.nodeType ) {
+ return jQuery.grep( elements, function( elem ) {
+ return ( elem === qualifier ) !== not;
+ } );
+ }
+
+ // Arraylike of elements (jQuery, arguments, Array)
+ if ( typeof qualifier !== "string" ) {
+ return jQuery.grep( elements, function( elem ) {
+ return ( indexOf.call( qualifier, elem ) > -1 ) !== not;
+ } );
+ }
+
+ // Filtered directly for both simple and complex selectors
+ return jQuery.filter( qualifier, elements, not );
+}
+
+jQuery.filter = function( expr, elems, not ) {
+ var elem = elems[ 0 ];
+
+ if ( not ) {
+ expr = ":not(" + expr + ")";
+ }
+
+ if ( elems.length === 1 && elem.nodeType === 1 ) {
+ return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [];
+ }
+
+ return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {
+ return elem.nodeType === 1;
+ } ) );
+};
+
+jQuery.fn.extend( {
+ find: function( selector ) {
+ var i, ret,
+ len = this.length,
+ self = this;
+
+ if ( typeof selector !== "string" ) {
+ return this.pushStack( jQuery( selector ).filter( function() {
+ for ( i = 0; i < len; i++ ) {
+ if ( jQuery.contains( self[ i ], this ) ) {
+ return true;
+ }
+ }
+ } ) );
+ }
+
+ ret = this.pushStack( [] );
+
+ for ( i = 0; i < len; i++ ) {
+ jQuery.find( selector, self[ i ], ret );
+ }
+
+ return len > 1 ? jQuery.uniqueSort( ret ) : ret;
+ },
+ filter: function( selector ) {
+ return this.pushStack( winnow( this, selector || [], false ) );
+ },
+ not: function( selector ) {
+ return this.pushStack( winnow( this, selector || [], true ) );
+ },
+ is: function( selector ) {
+ return !!winnow(
+ this,
+
+ // If this is a positional/relative selector, check membership in the returned set
+ // so $("p:first").is("p:last") won't return true for a doc with two "p".
+ typeof selector === "string" && rneedsContext.test( selector ) ?
+ jQuery( selector ) :
+ selector || [],
+ false
+ ).length;
+ }
+} );
+
+
+// Initialize a jQuery object
+
+
+// A central reference to the root jQuery(document)
+var rootjQuery,
+
+ // A simple way to check for HTML strings
+ // Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
+ // Strict HTML recognition (#11290: must start with <)
+ // Shortcut simple #id case for speed
+ rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/,
+
+ init = jQuery.fn.init = function( selector, context, root ) {
+ var match, elem;
+
+ // HANDLE: $(""), $(null), $(undefined), $(false)
+ if ( !selector ) {
+ return this;
+ }
+
+ // Method init() accepts an alternate rootjQuery
+ // so migrate can support jQuery.sub (gh-2101)
+ root = root || rootjQuery;
+
+ // Handle HTML strings
+ if ( typeof selector === "string" ) {
+ if ( selector[ 0 ] === "<" &&
+ selector[ selector.length - 1 ] === ">" &&
+ selector.length >= 3 ) {
+
+ // Assume that strings that start and end with <> are HTML and skip the regex check
+ match = [ null, selector, null ];
+
+ } else {
+ match = rquickExpr.exec( selector );
+ }
+
+ // Match html or make sure no context is specified for #id
+ if ( match && ( match[ 1 ] || !context ) ) {
+
+ // HANDLE: $(html) -> $(array)
+ if ( match[ 1 ] ) {
+ context = context instanceof jQuery ? context[ 0 ] : context;
+
+ // Option to run scripts is true for back-compat
+ // Intentionally let the error be thrown if parseHTML is not present
+ jQuery.merge( this, jQuery.parseHTML(
+ match[ 1 ],
+ context && context.nodeType ? context.ownerDocument || context : document,
+ true
+ ) );
+
+ // HANDLE: $(html, props)
+ if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) {
+ for ( match in context ) {
+
+ // Properties of context are called as methods if possible
+ if ( isFunction( this[ match ] ) ) {
+ this[ match ]( context[ match ] );
+
+ // ...and otherwise set as attributes
+ } else {
+ this.attr( match, context[ match ] );
+ }
+ }
+ }
+
+ return this;
+
+ // HANDLE: $(#id)
+ } else {
+ elem = document.getElementById( match[ 2 ] );
+
+ if ( elem ) {
+
+ // Inject the element directly into the jQuery object
+ this[ 0 ] = elem;
+ this.length = 1;
+ }
+ return this;
+ }
+
+ // HANDLE: $(expr, $(...))
+ } else if ( !context || context.jquery ) {
+ return ( context || root ).find( selector );
+
+ // HANDLE: $(expr, context)
+ // (which is just equivalent to: $(context).find(expr)
+ } else {
+ return this.constructor( context ).find( selector );
+ }
+
+ // HANDLE: $(DOMElement)
+ } else if ( selector.nodeType ) {
+ this[ 0 ] = selector;
+ this.length = 1;
+ return this;
+
+ // HANDLE: $(function)
+ // Shortcut for document ready
+ } else if ( isFunction( selector ) ) {
+ return root.ready !== undefined ?
+ root.ready( selector ) :
+
+ // Execute immediately if ready is not present
+ selector( jQuery );
+ }
+
+ return jQuery.makeArray( selector, this );
+ };
+
+// Give the init function the jQuery prototype for later instantiation
+init.prototype = jQuery.fn;
+
+// Initialize central reference
+rootjQuery = jQuery( document );
+
+
+var rparentsprev = /^(?:parents|prev(?:Until|All))/,
+
+ // Methods guaranteed to produce a unique set when starting from a unique set
+ guaranteedUnique = {
+ children: true,
+ contents: true,
+ next: true,
+ prev: true
+ };
+
+jQuery.fn.extend( {
+ has: function( target ) {
+ var targets = jQuery( target, this ),
+ l = targets.length;
+
+ return this.filter( function() {
+ var i = 0;
+ for ( ; i < l; i++ ) {
+ if ( jQuery.contains( this, targets[ i ] ) ) {
+ return true;
+ }
+ }
+ } );
+ },
+
+ closest: function( selectors, context ) {
+ var cur,
+ i = 0,
+ l = this.length,
+ matched = [],
+ targets = typeof selectors !== "string" && jQuery( selectors );
+
+ // Positional selectors never match, since there's no _selection_ context
+ if ( !rneedsContext.test( selectors ) ) {
+ for ( ; i < l; i++ ) {
+ for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) {
+
+ // Always skip document fragments
+ if ( cur.nodeType < 11 && ( targets ?
+ targets.index( cur ) > -1 :
+
+ // Don't pass non-elements to Sizzle
+ cur.nodeType === 1 &&
+ jQuery.find.matchesSelector( cur, selectors ) ) ) {
+
+ matched.push( cur );
+ break;
+ }
+ }
+ }
+ }
+
+ return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched );
+ },
+
+ // Determine the position of an element within the set
+ index: function( elem ) {
+
+ // No argument, return index in parent
+ if ( !elem ) {
+ return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1;
+ }
+
+ // Index in selector
+ if ( typeof elem === "string" ) {
+ return indexOf.call( jQuery( elem ), this[ 0 ] );
+ }
+
+ // Locate the position of the desired element
+ return indexOf.call( this,
+
+ // If it receives a jQuery object, the first element is used
+ elem.jquery ? elem[ 0 ] : elem
+ );
+ },
+
+ add: function( selector, context ) {
+ return this.pushStack(
+ jQuery.uniqueSort(
+ jQuery.merge( this.get(), jQuery( selector, context ) )
+ )
+ );
+ },
+
+ addBack: function( selector ) {
+ return this.add( selector == null ?
+ this.prevObject : this.prevObject.filter( selector )
+ );
+ }
+} );
+
+function sibling( cur, dir ) {
+ while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {}
+ return cur;
+}
+
+jQuery.each( {
+ parent: function( elem ) {
+ var parent = elem.parentNode;
+ return parent && parent.nodeType !== 11 ? parent : null;
+ },
+ parents: function( elem ) {
+ return dir( elem, "parentNode" );
+ },
+ parentsUntil: function( elem, i, until ) {
+ return dir( elem, "parentNode", until );
+ },
+ next: function( elem ) {
+ return sibling( elem, "nextSibling" );
+ },
+ prev: function( elem ) {
+ return sibling( elem, "previousSibling" );
+ },
+ nextAll: function( elem ) {
+ return dir( elem, "nextSibling" );
+ },
+ prevAll: function( elem ) {
+ return dir( elem, "previousSibling" );
+ },
+ nextUntil: function( elem, i, until ) {
+ return dir( elem, "nextSibling", until );
+ },
+ prevUntil: function( elem, i, until ) {
+ return dir( elem, "previousSibling", until );
+ },
+ siblings: function( elem ) {
+ return siblings( ( elem.parentNode || {} ).firstChild, elem );
+ },
+ children: function( elem ) {
+ return siblings( elem.firstChild );
+ },
+ contents: function( elem ) {
+ if ( nodeName( elem, "iframe" ) ) {
+ return elem.contentDocument;
+ }
+
+ // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only
+ // Treat the template element as a regular one in browsers that
+ // don't support it.
+ if ( nodeName( elem, "template" ) ) {
+ elem = elem.content || elem;
+ }
+
+ return jQuery.merge( [], elem.childNodes );
+ }
+}, function( name, fn ) {
+ jQuery.fn[ name ] = function( until, selector ) {
+ var matched = jQuery.map( this, fn, until );
+
+ if ( name.slice( -5 ) !== "Until" ) {
+ selector = until;
+ }
+
+ if ( selector && typeof selector === "string" ) {
+ matched = jQuery.filter( selector, matched );
+ }
+
+ if ( this.length > 1 ) {
+
+ // Remove duplicates
+ if ( !guaranteedUnique[ name ] ) {
+ jQuery.uniqueSort( matched );
+ }
+
+ // Reverse order for parents* and prev-derivatives
+ if ( rparentsprev.test( name ) ) {
+ matched.reverse();
+ }
+ }
+
+ return this.pushStack( matched );
+ };
+} );
+var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g );
+
+
+
+// Convert String-formatted options into Object-formatted ones
+function createOptions( options ) {
+ var object = {};
+ jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) {
+ object[ flag ] = true;
+ } );
+ return object;
+}
+
+/*
+ * Create a callback list using the following parameters:
+ *
+ * options: an optional list of space-separated options that will change how
+ * the callback list behaves or a more traditional option object
+ *
+ * By default a callback list will act like an event callback list and can be
+ * "fired" multiple times.
+ *
+ * Possible options:
+ *
+ * once: will ensure the callback list can only be fired once (like a Deferred)
+ *
+ * memory: will keep track of previous values and will call any callback added
+ * after the list has been fired right away with the latest "memorized"
+ * values (like a Deferred)
+ *
+ * unique: will ensure a callback can only be added once (no duplicate in the list)
+ *
+ * stopOnFalse: interrupt callings when a callback returns false
+ *
+ */
+jQuery.Callbacks = function( options ) {
+
+ // Convert options from String-formatted to Object-formatted if needed
+ // (we check in cache first)
+ options = typeof options === "string" ?
+ createOptions( options ) :
+ jQuery.extend( {}, options );
+
+ var // Flag to know if list is currently firing
+ firing,
+
+ // Last fire value for non-forgettable lists
+ memory,
+
+ // Flag to know if list was already fired
+ fired,
+
+ // Flag to prevent firing
+ locked,
+
+ // Actual callback list
+ list = [],
+
+ // Queue of execution data for repeatable lists
+ queue = [],
+
+ // Index of currently firing callback (modified by add/remove as needed)
+ firingIndex = -1,
+
+ // Fire callbacks
+ fire = function() {
+
+ // Enforce single-firing
+ locked = locked || options.once;
+
+ // Execute callbacks for all pending executions,
+ // respecting firingIndex overrides and runtime changes
+ fired = firing = true;
+ for ( ; queue.length; firingIndex = -1 ) {
+ memory = queue.shift();
+ while ( ++firingIndex < list.length ) {
+
+ // Run callback and check for early termination
+ if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false &&
+ options.stopOnFalse ) {
+
+ // Jump to end and forget the data so .add doesn't re-fire
+ firingIndex = list.length;
+ memory = false;
+ }
+ }
+ }
+
+ // Forget the data if we're done with it
+ if ( !options.memory ) {
+ memory = false;
+ }
+
+ firing = false;
+
+ // Clean up if we're done firing for good
+ if ( locked ) {
+
+ // Keep an empty list if we have data for future add calls
+ if ( memory ) {
+ list = [];
+
+ // Otherwise, this object is spent
+ } else {
+ list = "";
+ }
+ }
+ },
+
+ // Actual Callbacks object
+ self = {
+
+ // Add a callback or a collection of callbacks to the list
+ add: function() {
+ if ( list ) {
+
+ // If we have memory from a past run, we should fire after adding
+ if ( memory && !firing ) {
+ firingIndex = list.length - 1;
+ queue.push( memory );
+ }
+
+ ( function add( args ) {
+ jQuery.each( args, function( _, arg ) {
+ if ( isFunction( arg ) ) {
+ if ( !options.unique || !self.has( arg ) ) {
+ list.push( arg );
+ }
+ } else if ( arg && arg.length && toType( arg ) !== "string" ) {
+
+ // Inspect recursively
+ add( arg );
+ }
+ } );
+ } )( arguments );
+
+ if ( memory && !firing ) {
+ fire();
+ }
+ }
+ return this;
+ },
+
+ // Remove a callback from the list
+ remove: function() {
+ jQuery.each( arguments, function( _, arg ) {
+ var index;
+ while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
+ list.splice( index, 1 );
+
+ // Handle firing indexes
+ if ( index <= firingIndex ) {
+ firingIndex--;
+ }
+ }
+ } );
+ return this;
+ },
+
+ // Check if a given callback is in the list.
+ // If no argument is given, return whether or not list has callbacks attached.
+ has: function( fn ) {
+ return fn ?
+ jQuery.inArray( fn, list ) > -1 :
+ list.length > 0;
+ },
+
+ // Remove all callbacks from the list
+ empty: function() {
+ if ( list ) {
+ list = [];
+ }
+ return this;
+ },
+
+ // Disable .fire and .add
+ // Abort any current/pending executions
+ // Clear all callbacks and values
+ disable: function() {
+ locked = queue = [];
+ list = memory = "";
+ return this;
+ },
+ disabled: function() {
+ return !list;
+ },
+
+ // Disable .fire
+ // Also disable .add unless we have memory (since it would have no effect)
+ // Abort any pending executions
+ lock: function() {
+ locked = queue = [];
+ if ( !memory && !firing ) {
+ list = memory = "";
+ }
+ return this;
+ },
+ locked: function() {
+ return !!locked;
+ },
+
+ // Call all callbacks with the given context and arguments
+ fireWith: function( context, args ) {
+ if ( !locked ) {
+ args = args || [];
+ args = [ context, args.slice ? args.slice() : args ];
+ queue.push( args );
+ if ( !firing ) {
+ fire();
+ }
+ }
+ return this;
+ },
+
+ // Call all the callbacks with the given arguments
+ fire: function() {
+ self.fireWith( this, arguments );
+ return this;
+ },
+
+ // To know if the callbacks have already been called at least once
+ fired: function() {
+ return !!fired;
+ }
+ };
+
+ return self;
+};
+
+
+function Identity( v ) {
+ return v;
+}
+function Thrower( ex ) {
+ throw ex;
+}
+
+function adoptValue( value, resolve, reject, noValue ) {
+ var method;
+
+ try {
+
+ // Check for promise aspect first to privilege synchronous behavior
+ if ( value && isFunction( ( method = value.promise ) ) ) {
+ method.call( value ).done( resolve ).fail( reject );
+
+ // Other thenables
+ } else if ( value && isFunction( ( method = value.then ) ) ) {
+ method.call( value, resolve, reject );
+
+ // Other non-thenables
+ } else {
+
+ // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer:
+ // * false: [ value ].slice( 0 ) => resolve( value )
+ // * true: [ value ].slice( 1 ) => resolve()
+ resolve.apply( undefined, [ value ].slice( noValue ) );
+ }
+
+ // For Promises/A+, convert exceptions into rejections
+ // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in
+ // Deferred#then to conditionally suppress rejection.
+ } catch ( value ) {
+
+ // Support: Android 4.0 only
+ // Strict mode functions invoked without .call/.apply get global-object context
+ reject.apply( undefined, [ value ] );
+ }
+}
+
+jQuery.extend( {
+
+ Deferred: function( func ) {
+ var tuples = [
+
+ // action, add listener, callbacks,
+ // ... .then handlers, argument index, [final state]
+ [ "notify", "progress", jQuery.Callbacks( "memory" ),
+ jQuery.Callbacks( "memory" ), 2 ],
+ [ "resolve", "done", jQuery.Callbacks( "once memory" ),
+ jQuery.Callbacks( "once memory" ), 0, "resolved" ],
+ [ "reject", "fail", jQuery.Callbacks( "once memory" ),
+ jQuery.Callbacks( "once memory" ), 1, "rejected" ]
+ ],
+ state = "pending",
+ promise = {
+ state: function() {
+ return state;
+ },
+ always: function() {
+ deferred.done( arguments ).fail( arguments );
+ return this;
+ },
+ "catch": function( fn ) {
+ return promise.then( null, fn );
+ },
+
+ // Keep pipe for back-compat
+ pipe: function( /* fnDone, fnFail, fnProgress */ ) {
+ var fns = arguments;
+
+ return jQuery.Deferred( function( newDefer ) {
+ jQuery.each( tuples, function( i, tuple ) {
+
+ // Map tuples (progress, done, fail) to arguments (done, fail, progress)
+ var fn = isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ];
+
+ // deferred.progress(function() { bind to newDefer or newDefer.notify })
+ // deferred.done(function() { bind to newDefer or newDefer.resolve })
+ // deferred.fail(function() { bind to newDefer or newDefer.reject })
+ deferred[ tuple[ 1 ] ]( function() {
+ var returned = fn && fn.apply( this, arguments );
+ if ( returned && isFunction( returned.promise ) ) {
+ returned.promise()
+ .progress( newDefer.notify )
+ .done( newDefer.resolve )
+ .fail( newDefer.reject );
+ } else {
+ newDefer[ tuple[ 0 ] + "With" ](
+ this,
+ fn ? [ returned ] : arguments
+ );
+ }
+ } );
+ } );
+ fns = null;
+ } ).promise();
+ },
+ then: function( onFulfilled, onRejected, onProgress ) {
+ var maxDepth = 0;
+ function resolve( depth, deferred, handler, special ) {
+ return function() {
+ var that = this,
+ args = arguments,
+ mightThrow = function() {
+ var returned, then;
+
+ // Support: Promises/A+ section 2.3.3.3.3
+ // https://promisesaplus.com/#point-59
+ // Ignore double-resolution attempts
+ if ( depth < maxDepth ) {
+ return;
+ }
+
+ returned = handler.apply( that, args );
+
+ // Support: Promises/A+ section 2.3.1
+ // https://promisesaplus.com/#point-48
+ if ( returned === deferred.promise() ) {
+ throw new TypeError( "Thenable self-resolution" );
+ }
+
+ // Support: Promises/A+ sections 2.3.3.1, 3.5
+ // https://promisesaplus.com/#point-54
+ // https://promisesaplus.com/#point-75
+ // Retrieve `then` only once
+ then = returned &&
+
+ // Support: Promises/A+ section 2.3.4
+ // https://promisesaplus.com/#point-64
+ // Only check objects and functions for thenability
+ ( typeof returned === "object" ||
+ typeof returned === "function" ) &&
+ returned.then;
+
+ // Handle a returned thenable
+ if ( isFunction( then ) ) {
+
+ // Special processors (notify) just wait for resolution
+ if ( special ) {
+ then.call(
+ returned,
+ resolve( maxDepth, deferred, Identity, special ),
+ resolve( maxDepth, deferred, Thrower, special )
+ );
+
+ // Normal processors (resolve) also hook into progress
+ } else {
+
+ // ...and disregard older resolution values
+ maxDepth++;
+
+ then.call(
+ returned,
+ resolve( maxDepth, deferred, Identity, special ),
+ resolve( maxDepth, deferred, Thrower, special ),
+ resolve( maxDepth, deferred, Identity,
+ deferred.notifyWith )
+ );
+ }
+
+ // Handle all other returned values
+ } else {
+
+ // Only substitute handlers pass on context
+ // and multiple values (non-spec behavior)
+ if ( handler !== Identity ) {
+ that = undefined;
+ args = [ returned ];
+ }
+
+ // Process the value(s)
+ // Default process is resolve
+ ( special || deferred.resolveWith )( that, args );
+ }
+ },
+
+ // Only normal processors (resolve) catch and reject exceptions
+ process = special ?
+ mightThrow :
+ function() {
+ try {
+ mightThrow();
+ } catch ( e ) {
+
+ if ( jQuery.Deferred.exceptionHook ) {
+ jQuery.Deferred.exceptionHook( e,
+ process.stackTrace );
+ }
+
+ // Support: Promises/A+ section 2.3.3.3.4.1
+ // https://promisesaplus.com/#point-61
+ // Ignore post-resolution exceptions
+ if ( depth + 1 >= maxDepth ) {
+
+ // Only substitute handlers pass on context
+ // and multiple values (non-spec behavior)
+ if ( handler !== Thrower ) {
+ that = undefined;
+ args = [ e ];
+ }
+
+ deferred.rejectWith( that, args );
+ }
+ }
+ };
+
+ // Support: Promises/A+ section 2.3.3.3.1
+ // https://promisesaplus.com/#point-57
+ // Re-resolve promises immediately to dodge false rejection from
+ // subsequent errors
+ if ( depth ) {
+ process();
+ } else {
+
+ // Call an optional hook to record the stack, in case of exception
+ // since it's otherwise lost when execution goes async
+ if ( jQuery.Deferred.getStackHook ) {
+ process.stackTrace = jQuery.Deferred.getStackHook();
+ }
+ window.setTimeout( process );
+ }
+ };
+ }
+
+ return jQuery.Deferred( function( newDefer ) {
+
+ // progress_handlers.add( ... )
+ tuples[ 0 ][ 3 ].add(
+ resolve(
+ 0,
+ newDefer,
+ isFunction( onProgress ) ?
+ onProgress :
+ Identity,
+ newDefer.notifyWith
+ )
+ );
+
+ // fulfilled_handlers.add( ... )
+ tuples[ 1 ][ 3 ].add(
+ resolve(
+ 0,
+ newDefer,
+ isFunction( onFulfilled ) ?
+ onFulfilled :
+ Identity
+ )
+ );
+
+ // rejected_handlers.add( ... )
+ tuples[ 2 ][ 3 ].add(
+ resolve(
+ 0,
+ newDefer,
+ isFunction( onRejected ) ?
+ onRejected :
+ Thrower
+ )
+ );
+ } ).promise();
+ },
+
+ // Get a promise for this deferred
+ // If obj is provided, the promise aspect is added to the object
+ promise: function( obj ) {
+ return obj != null ? jQuery.extend( obj, promise ) : promise;
+ }
+ },
+ deferred = {};
+
+ // Add list-specific methods
+ jQuery.each( tuples, function( i, tuple ) {
+ var list = tuple[ 2 ],
+ stateString = tuple[ 5 ];
+
+ // promise.progress = list.add
+ // promise.done = list.add
+ // promise.fail = list.add
+ promise[ tuple[ 1 ] ] = list.add;
+
+ // Handle state
+ if ( stateString ) {
+ list.add(
+ function() {
+
+ // state = "resolved" (i.e., fulfilled)
+ // state = "rejected"
+ state = stateString;
+ },
+
+ // rejected_callbacks.disable
+ // fulfilled_callbacks.disable
+ tuples[ 3 - i ][ 2 ].disable,
+
+ // rejected_handlers.disable
+ // fulfilled_handlers.disable
+ tuples[ 3 - i ][ 3 ].disable,
+
+ // progress_callbacks.lock
+ tuples[ 0 ][ 2 ].lock,
+
+ // progress_handlers.lock
+ tuples[ 0 ][ 3 ].lock
+ );
+ }
+
+ // progress_handlers.fire
+ // fulfilled_handlers.fire
+ // rejected_handlers.fire
+ list.add( tuple[ 3 ].fire );
+
+ // deferred.notify = function() { deferred.notifyWith(...) }
+ // deferred.resolve = function() { deferred.resolveWith(...) }
+ // deferred.reject = function() { deferred.rejectWith(...) }
+ deferred[ tuple[ 0 ] ] = function() {
+ deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments );
+ return this;
+ };
+
+ // deferred.notifyWith = list.fireWith
+ // deferred.resolveWith = list.fireWith
+ // deferred.rejectWith = list.fireWith
+ deferred[ tuple[ 0 ] + "With" ] = list.fireWith;
+ } );
+
+ // Make the deferred a promise
+ promise.promise( deferred );
+
+ // Call given func if any
+ if ( func ) {
+ func.call( deferred, deferred );
+ }
+
+ // All done!
+ return deferred;
+ },
+
+ // Deferred helper
+ when: function( singleValue ) {
+ var
+
+ // count of uncompleted subordinates
+ remaining = arguments.length,
+
+ // count of unprocessed arguments
+ i = remaining,
+
+ // subordinate fulfillment data
+ resolveContexts = Array( i ),
+ resolveValues = slice.call( arguments ),
+
+ // the master Deferred
+ master = jQuery.Deferred(),
+
+ // subordinate callback factory
+ updateFunc = function( i ) {
+ return function( value ) {
+ resolveContexts[ i ] = this;
+ resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
+ if ( !( --remaining ) ) {
+ master.resolveWith( resolveContexts, resolveValues );
+ }
+ };
+ };
+
+ // Single- and empty arguments are adopted like Promise.resolve
+ if ( remaining <= 1 ) {
+ adoptValue( singleValue, master.done( updateFunc( i ) ).resolve, master.reject,
+ !remaining );
+
+ // Use .then() to unwrap secondary thenables (cf. gh-3000)
+ if ( master.state() === "pending" ||
+ isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) {
+
+ return master.then();
+ }
+ }
+
+ // Multiple arguments are aggregated like Promise.all array elements
+ while ( i-- ) {
+ adoptValue( resolveValues[ i ], updateFunc( i ), master.reject );
+ }
+
+ return master.promise();
+ }
+} );
+
+
+// These usually indicate a programmer mistake during development,
+// warn about them ASAP rather than swallowing them by default.
+var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/;
+
+jQuery.Deferred.exceptionHook = function( error, stack ) {
+
+ // Support: IE 8 - 9 only
+ // Console exists when dev tools are open, which can happen at any time
+ if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) {
+ window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack );
+ }
+};
+
+
+
+
+jQuery.readyException = function( error ) {
+ window.setTimeout( function() {
+ throw error;
+ } );
+};
+
+
+
+
+// The deferred used on DOM ready
+var readyList = jQuery.Deferred();
+
+jQuery.fn.ready = function( fn ) {
+
+ readyList
+ .then( fn )
+
+ // Wrap jQuery.readyException in a function so that the lookup
+ // happens at the time of error handling instead of callback
+ // registration.
+ .catch( function( error ) {
+ jQuery.readyException( error );
+ } );
+
+ return this;
+};
+
+jQuery.extend( {
+
+ // Is the DOM ready to be used? Set to true once it occurs.
+ isReady: false,
+
+ // A counter to track how many items to wait for before
+ // the ready event fires. See #6781
+ readyWait: 1,
+
+ // Handle when the DOM is ready
+ ready: function( wait ) {
+
+ // Abort if there are pending holds or we're already ready
+ if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
+ return;
+ }
+
+ // Remember that the DOM is ready
+ jQuery.isReady = true;
+
+ // If a normal DOM Ready event fired, decrement, and wait if need be
+ if ( wait !== true && --jQuery.readyWait > 0 ) {
+ return;
+ }
+
+ // If there are functions bound, to execute
+ readyList.resolveWith( document, [ jQuery ] );
+ }
+} );
+
+jQuery.ready.then = readyList.then;
+
+// The ready event handler and self cleanup method
+function completed() {
+ document.removeEventListener( "DOMContentLoaded", completed );
+ window.removeEventListener( "load", completed );
+ jQuery.ready();
+}
+
+// Catch cases where $(document).ready() is called
+// after the browser event has already occurred.
+// Support: IE <=9 - 10 only
+// Older IE sometimes signals "interactive" too soon
+if ( document.readyState === "complete" ||
+ ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) {
+
+ // Handle it asynchronously to allow scripts the opportunity to delay ready
+ window.setTimeout( jQuery.ready );
+
+} else {
+
+ // Use the handy event callback
+ document.addEventListener( "DOMContentLoaded", completed );
+
+ // A fallback to window.onload, that will always work
+ window.addEventListener( "load", completed );
+}
+
+
+
+
+// Multifunctional method to get and set values of a collection
+// The value/s can optionally be executed if it's a function
+var access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
+ var i = 0,
+ len = elems.length,
+ bulk = key == null;
+
+ // Sets many values
+ if ( toType( key ) === "object" ) {
+ chainable = true;
+ for ( i in key ) {
+ access( elems, fn, i, key[ i ], true, emptyGet, raw );
+ }
+
+ // Sets one value
+ } else if ( value !== undefined ) {
+ chainable = true;
+
+ if ( !isFunction( value ) ) {
+ raw = true;
+ }
+
+ if ( bulk ) {
+
+ // Bulk operations run against the entire set
+ if ( raw ) {
+ fn.call( elems, value );
+ fn = null;
+
+ // ...except when executing function values
+ } else {
+ bulk = fn;
+ fn = function( elem, key, value ) {
+ return bulk.call( jQuery( elem ), value );
+ };
+ }
+ }
+
+ if ( fn ) {
+ for ( ; i < len; i++ ) {
+ fn(
+ elems[ i ], key, raw ?
+ value :
+ value.call( elems[ i ], i, fn( elems[ i ], key ) )
+ );
+ }
+ }
+ }
+
+ if ( chainable ) {
+ return elems;
+ }
+
+ // Gets
+ if ( bulk ) {
+ return fn.call( elems );
+ }
+
+ return len ? fn( elems[ 0 ], key ) : emptyGet;
+};
+
+
+// Matches dashed string for camelizing
+var rmsPrefix = /^-ms-/,
+ rdashAlpha = /-([a-z])/g;
+
+// Used by camelCase as callback to replace()
+function fcamelCase( all, letter ) {
+ return letter.toUpperCase();
+}
+
+// Convert dashed to camelCase; used by the css and data modules
+// Support: IE <=9 - 11, Edge 12 - 15
+// Microsoft forgot to hump their vendor prefix (#9572)
+function camelCase( string ) {
+ return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
+}
+var acceptData = function( owner ) {
+
+ // Accepts only:
+ // - Node
+ // - Node.ELEMENT_NODE
+ // - Node.DOCUMENT_NODE
+ // - Object
+ // - Any
+ return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType );
+};
+
+
+
+
+function Data() {
+ this.expando = jQuery.expando + Data.uid++;
+}
+
+Data.uid = 1;
+
+Data.prototype = {
+
+ cache: function( owner ) {
+
+ // Check if the owner object already has a cache
+ var value = owner[ this.expando ];
+
+ // If not, create one
+ if ( !value ) {
+ value = {};
+
+ // We can accept data for non-element nodes in modern browsers,
+ // but we should not, see #8335.
+ // Always return an empty object.
+ if ( acceptData( owner ) ) {
+
+ // If it is a node unlikely to be stringify-ed or looped over
+ // use plain assignment
+ if ( owner.nodeType ) {
+ owner[ this.expando ] = value;
+
+ // Otherwise secure it in a non-enumerable property
+ // configurable must be true to allow the property to be
+ // deleted when data is removed
+ } else {
+ Object.defineProperty( owner, this.expando, {
+ value: value,
+ configurable: true
+ } );
+ }
+ }
+ }
+
+ return value;
+ },
+ set: function( owner, data, value ) {
+ var prop,
+ cache = this.cache( owner );
+
+ // Handle: [ owner, key, value ] args
+ // Always use camelCase key (gh-2257)
+ if ( typeof data === "string" ) {
+ cache[ camelCase( data ) ] = value;
+
+ // Handle: [ owner, { properties } ] args
+ } else {
+
+ // Copy the properties one-by-one to the cache object
+ for ( prop in data ) {
+ cache[ camelCase( prop ) ] = data[ prop ];
+ }
+ }
+ return cache;
+ },
+ get: function( owner, key ) {
+ return key === undefined ?
+ this.cache( owner ) :
+
+ // Always use camelCase key (gh-2257)
+ owner[ this.expando ] && owner[ this.expando ][ camelCase( key ) ];
+ },
+ access: function( owner, key, value ) {
+
+ // In cases where either:
+ //
+ // 1. No key was specified
+ // 2. A string key was specified, but no value provided
+ //
+ // Take the "read" path and allow the get method to determine
+ // which value to return, respectively either:
+ //
+ // 1. The entire cache object
+ // 2. The data stored at the key
+ //
+ if ( key === undefined ||
+ ( ( key && typeof key === "string" ) && value === undefined ) ) {
+
+ return this.get( owner, key );
+ }
+
+ // When the key is not a string, or both a key and value
+ // are specified, set or extend (existing objects) with either:
+ //
+ // 1. An object of properties
+ // 2. A key and value
+ //
+ this.set( owner, key, value );
+
+ // Since the "set" path can have two possible entry points
+ // return the expected data based on which path was taken[*]
+ return value !== undefined ? value : key;
+ },
+ remove: function( owner, key ) {
+ var i,
+ cache = owner[ this.expando ];
+
+ if ( cache === undefined ) {
+ return;
+ }
+
+ if ( key !== undefined ) {
+
+ // Support array or space separated string of keys
+ if ( Array.isArray( key ) ) {
+
+ // If key is an array of keys...
+ // We always set camelCase keys, so remove that.
+ key = key.map( camelCase );
+ } else {
+ key = camelCase( key );
+
+ // If a key with the spaces exists, use it.
+ // Otherwise, create an array by matching non-whitespace
+ key = key in cache ?
+ [ key ] :
+ ( key.match( rnothtmlwhite ) || [] );
+ }
+
+ i = key.length;
+
+ while ( i-- ) {
+ delete cache[ key[ i ] ];
+ }
+ }
+
+ // Remove the expando if there's no more data
+ if ( key === undefined || jQuery.isEmptyObject( cache ) ) {
+
+ // Support: Chrome <=35 - 45
+ // Webkit & Blink performance suffers when deleting properties
+ // from DOM nodes, so set to undefined instead
+ // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted)
+ if ( owner.nodeType ) {
+ owner[ this.expando ] = undefined;
+ } else {
+ delete owner[ this.expando ];
+ }
+ }
+ },
+ hasData: function( owner ) {
+ var cache = owner[ this.expando ];
+ return cache !== undefined && !jQuery.isEmptyObject( cache );
+ }
+};
+var dataPriv = new Data();
+
+var dataUser = new Data();
+
+
+
+// Implementation Summary
+//
+// 1. Enforce API surface and semantic compatibility with 1.9.x branch
+// 2. Improve the module's maintainability by reducing the storage
+// paths to a single mechanism.
+// 3. Use the same single mechanism to support "private" and "user" data.
+// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData)
+// 5. Avoid exposing implementation details on user objects (eg. expando properties)
+// 6. Provide a clear path for implementation upgrade to WeakMap in 2014
+
+var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
+ rmultiDash = /[A-Z]/g;
+
+function getData( data ) {
+ if ( data === "true" ) {
+ return true;
+ }
+
+ if ( data === "false" ) {
+ return false;
+ }
+
+ if ( data === "null" ) {
+ return null;
+ }
+
+ // Only convert to a number if it doesn't change the string
+ if ( data === +data + "" ) {
+ return +data;
+ }
+
+ if ( rbrace.test( data ) ) {
+ return JSON.parse( data );
+ }
+
+ return data;
+}
+
+function dataAttr( elem, key, data ) {
+ var name;
+
+ // If nothing was found internally, try to fetch any
+ // data from the HTML5 data-* attribute
+ if ( data === undefined && elem.nodeType === 1 ) {
+ name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase();
+ data = elem.getAttribute( name );
+
+ if ( typeof data === "string" ) {
+ try {
+ data = getData( data );
+ } catch ( e ) {}
+
+ // Make sure we set the data so it isn't changed later
+ dataUser.set( elem, key, data );
+ } else {
+ data = undefined;
+ }
+ }
+ return data;
+}
+
+jQuery.extend( {
+ hasData: function( elem ) {
+ return dataUser.hasData( elem ) || dataPriv.hasData( elem );
+ },
+
+ data: function( elem, name, data ) {
+ return dataUser.access( elem, name, data );
+ },
+
+ removeData: function( elem, name ) {
+ dataUser.remove( elem, name );
+ },
+
+ // TODO: Now that all calls to _data and _removeData have been replaced
+ // with direct calls to dataPriv methods, these can be deprecated.
+ _data: function( elem, name, data ) {
+ return dataPriv.access( elem, name, data );
+ },
+
+ _removeData: function( elem, name ) {
+ dataPriv.remove( elem, name );
+ }
+} );
+
+jQuery.fn.extend( {
+ data: function( key, value ) {
+ var i, name, data,
+ elem = this[ 0 ],
+ attrs = elem && elem.attributes;
+
+ // Gets all values
+ if ( key === undefined ) {
+ if ( this.length ) {
+ data = dataUser.get( elem );
+
+ if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) {
+ i = attrs.length;
+ while ( i-- ) {
+
+ // Support: IE 11 only
+ // The attrs elements can be null (#14894)
+ if ( attrs[ i ] ) {
+ name = attrs[ i ].name;
+ if ( name.indexOf( "data-" ) === 0 ) {
+ name = camelCase( name.slice( 5 ) );
+ dataAttr( elem, name, data[ name ] );
+ }
+ }
+ }
+ dataPriv.set( elem, "hasDataAttrs", true );
+ }
+ }
+
+ return data;
+ }
+
+ // Sets multiple values
+ if ( typeof key === "object" ) {
+ return this.each( function() {
+ dataUser.set( this, key );
+ } );
+ }
+
+ return access( this, function( value ) {
+ var data;
+
+ // The calling jQuery object (element matches) is not empty
+ // (and therefore has an element appears at this[ 0 ]) and the
+ // `value` parameter was not undefined. An empty jQuery object
+ // will result in `undefined` for elem = this[ 0 ] which will
+ // throw an exception if an attempt to read a data cache is made.
+ if ( elem && value === undefined ) {
+
+ // Attempt to get data from the cache
+ // The key will always be camelCased in Data
+ data = dataUser.get( elem, key );
+ if ( data !== undefined ) {
+ return data;
+ }
+
+ // Attempt to "discover" the data in
+ // HTML5 custom data-* attrs
+ data = dataAttr( elem, key );
+ if ( data !== undefined ) {
+ return data;
+ }
+
+ // We tried really hard, but the data doesn't exist.
+ return;
+ }
+
+ // Set the data...
+ this.each( function() {
+
+ // We always store the camelCased key
+ dataUser.set( this, key, value );
+ } );
+ }, null, value, arguments.length > 1, null, true );
+ },
+
+ removeData: function( key ) {
+ return this.each( function() {
+ dataUser.remove( this, key );
+ } );
+ }
+} );
+
+
+jQuery.extend( {
+ queue: function( elem, type, data ) {
+ var queue;
+
+ if ( elem ) {
+ type = ( type || "fx" ) + "queue";
+ queue = dataPriv.get( elem, type );
+
+ // Speed up dequeue by getting out quickly if this is just a lookup
+ if ( data ) {
+ if ( !queue || Array.isArray( data ) ) {
+ queue = dataPriv.access( elem, type, jQuery.makeArray( data ) );
+ } else {
+ queue.push( data );
+ }
+ }
+ return queue || [];
+ }
+ },
+
+ dequeue: function( elem, type ) {
+ type = type || "fx";
+
+ var queue = jQuery.queue( elem, type ),
+ startLength = queue.length,
+ fn = queue.shift(),
+ hooks = jQuery._queueHooks( elem, type ),
+ next = function() {
+ jQuery.dequeue( elem, type );
+ };
+
+ // If the fx queue is dequeued, always remove the progress sentinel
+ if ( fn === "inprogress" ) {
+ fn = queue.shift();
+ startLength--;
+ }
+
+ if ( fn ) {
+
+ // Add a progress sentinel to prevent the fx queue from being
+ // automatically dequeued
+ if ( type === "fx" ) {
+ queue.unshift( "inprogress" );
+ }
+
+ // Clear up the last queue stop function
+ delete hooks.stop;
+ fn.call( elem, next, hooks );
+ }
+
+ if ( !startLength && hooks ) {
+ hooks.empty.fire();
+ }
+ },
+
+ // Not public - generate a queueHooks object, or return the current one
+ _queueHooks: function( elem, type ) {
+ var key = type + "queueHooks";
+ return dataPriv.get( elem, key ) || dataPriv.access( elem, key, {
+ empty: jQuery.Callbacks( "once memory" ).add( function() {
+ dataPriv.remove( elem, [ type + "queue", key ] );
+ } )
+ } );
+ }
+} );
+
+jQuery.fn.extend( {
+ queue: function( type, data ) {
+ var setter = 2;
+
+ if ( typeof type !== "string" ) {
+ data = type;
+ type = "fx";
+ setter--;
+ }
+
+ if ( arguments.length < setter ) {
+ return jQuery.queue( this[ 0 ], type );
+ }
+
+ return data === undefined ?
+ this :
+ this.each( function() {
+ var queue = jQuery.queue( this, type, data );
+
+ // Ensure a hooks for this queue
+ jQuery._queueHooks( this, type );
+
+ if ( type === "fx" && queue[ 0 ] !== "inprogress" ) {
+ jQuery.dequeue( this, type );
+ }
+ } );
+ },
+ dequeue: function( type ) {
+ return this.each( function() {
+ jQuery.dequeue( this, type );
+ } );
+ },
+ clearQueue: function( type ) {
+ return this.queue( type || "fx", [] );
+ },
+
+ // Get a promise resolved when queues of a certain type
+ // are emptied (fx is the type by default)
+ promise: function( type, obj ) {
+ var tmp,
+ count = 1,
+ defer = jQuery.Deferred(),
+ elements = this,
+ i = this.length,
+ resolve = function() {
+ if ( !( --count ) ) {
+ defer.resolveWith( elements, [ elements ] );
+ }
+ };
+
+ if ( typeof type !== "string" ) {
+ obj = type;
+ type = undefined;
+ }
+ type = type || "fx";
+
+ while ( i-- ) {
+ tmp = dataPriv.get( elements[ i ], type + "queueHooks" );
+ if ( tmp && tmp.empty ) {
+ count++;
+ tmp.empty.add( resolve );
+ }
+ }
+ resolve();
+ return defer.promise( obj );
+ }
+} );
+var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source;
+
+var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" );
+
+
+var cssExpand = [ "Top", "Right", "Bottom", "Left" ];
+
+var isHiddenWithinTree = function( elem, el ) {
+
+ // isHiddenWithinTree might be called from jQuery#filter function;
+ // in that case, element will be second argument
+ elem = el || elem;
+
+ // Inline style trumps all
+ return elem.style.display === "none" ||
+ elem.style.display === "" &&
+
+ // Otherwise, check computed style
+ // Support: Firefox <=43 - 45
+ // Disconnected elements can have computed display: none, so first confirm that elem is
+ // in the document.
+ jQuery.contains( elem.ownerDocument, elem ) &&
+
+ jQuery.css( elem, "display" ) === "none";
+ };
+
+var swap = function( elem, options, callback, args ) {
+ var ret, name,
+ old = {};
+
+ // Remember the old values, and insert the new ones
+ for ( name in options ) {
+ old[ name ] = elem.style[ name ];
+ elem.style[ name ] = options[ name ];
+ }
+
+ ret = callback.apply( elem, args || [] );
+
+ // Revert the old values
+ for ( name in options ) {
+ elem.style[ name ] = old[ name ];
+ }
+
+ return ret;
+};
+
+
+
+
+function adjustCSS( elem, prop, valueParts, tween ) {
+ var adjusted, scale,
+ maxIterations = 20,
+ currentValue = tween ?
+ function() {
+ return tween.cur();
+ } :
+ function() {
+ return jQuery.css( elem, prop, "" );
+ },
+ initial = currentValue(),
+ unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
+
+ // Starting value computation is required for potential unit mismatches
+ initialInUnit = ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) &&
+ rcssNum.exec( jQuery.css( elem, prop ) );
+
+ if ( initialInUnit && initialInUnit[ 3 ] !== unit ) {
+
+ // Support: Firefox <=54
+ // Halve the iteration target value to prevent interference from CSS upper bounds (gh-2144)
+ initial = initial / 2;
+
+ // Trust units reported by jQuery.css
+ unit = unit || initialInUnit[ 3 ];
+
+ // Iteratively approximate from a nonzero starting point
+ initialInUnit = +initial || 1;
+
+ while ( maxIterations-- ) {
+
+ // Evaluate and update our best guess (doubling guesses that zero out).
+ // Finish if the scale equals or crosses 1 (making the old*new product non-positive).
+ jQuery.style( elem, prop, initialInUnit + unit );
+ if ( ( 1 - scale ) * ( 1 - ( scale = currentValue() / initial || 0.5 ) ) <= 0 ) {
+ maxIterations = 0;
+ }
+ initialInUnit = initialInUnit / scale;
+
+ }
+
+ initialInUnit = initialInUnit * 2;
+ jQuery.style( elem, prop, initialInUnit + unit );
+
+ // Make sure we update the tween properties later on
+ valueParts = valueParts || [];
+ }
+
+ if ( valueParts ) {
+ initialInUnit = +initialInUnit || +initial || 0;
+
+ // Apply relative offset (+=/-=) if specified
+ adjusted = valueParts[ 1 ] ?
+ initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] :
+ +valueParts[ 2 ];
+ if ( tween ) {
+ tween.unit = unit;
+ tween.start = initialInUnit;
+ tween.end = adjusted;
+ }
+ }
+ return adjusted;
+}
+
+
+var defaultDisplayMap = {};
+
+function getDefaultDisplay( elem ) {
+ var temp,
+ doc = elem.ownerDocument,
+ nodeName = elem.nodeName,
+ display = defaultDisplayMap[ nodeName ];
+
+ if ( display ) {
+ return display;
+ }
+
+ temp = doc.body.appendChild( doc.createElement( nodeName ) );
+ display = jQuery.css( temp, "display" );
+
+ temp.parentNode.removeChild( temp );
+
+ if ( display === "none" ) {
+ display = "block";
+ }
+ defaultDisplayMap[ nodeName ] = display;
+
+ return display;
+}
+
+function showHide( elements, show ) {
+ var display, elem,
+ values = [],
+ index = 0,
+ length = elements.length;
+
+ // Determine new display value for elements that need to change
+ for ( ; index < length; index++ ) {
+ elem = elements[ index ];
+ if ( !elem.style ) {
+ continue;
+ }
+
+ display = elem.style.display;
+ if ( show ) {
+
+ // Since we force visibility upon cascade-hidden elements, an immediate (and slow)
+ // check is required in this first loop unless we have a nonempty display value (either
+ // inline or about-to-be-restored)
+ if ( display === "none" ) {
+ values[ index ] = dataPriv.get( elem, "display" ) || null;
+ if ( !values[ index ] ) {
+ elem.style.display = "";
+ }
+ }
+ if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) {
+ values[ index ] = getDefaultDisplay( elem );
+ }
+ } else {
+ if ( display !== "none" ) {
+ values[ index ] = "none";
+
+ // Remember what we're overwriting
+ dataPriv.set( elem, "display", display );
+ }
+ }
+ }
+
+ // Set the display of the elements in a second loop to avoid constant reflow
+ for ( index = 0; index < length; index++ ) {
+ if ( values[ index ] != null ) {
+ elements[ index ].style.display = values[ index ];
+ }
+ }
+
+ return elements;
+}
+
+jQuery.fn.extend( {
+ show: function() {
+ return showHide( this, true );
+ },
+ hide: function() {
+ return showHide( this );
+ },
+ toggle: function( state ) {
+ if ( typeof state === "boolean" ) {
+ return state ? this.show() : this.hide();
+ }
+
+ return this.each( function() {
+ if ( isHiddenWithinTree( this ) ) {
+ jQuery( this ).show();
+ } else {
+ jQuery( this ).hide();
+ }
+ } );
+ }
+} );
+var rcheckableType = ( /^(?:checkbox|radio)$/i );
+
+var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]+)/i );
+
+var rscriptType = ( /^$|^module$|\/(?:java|ecma)script/i );
+
+
+
+( function() {
+ var fragment = document.createDocumentFragment(),
+ div = fragment.appendChild( document.createElement( "div" ) ),
+ input = document.createElement( "input" );
+
+ // Support: Android 4.0 - 4.3 only
+ // Check state lost if the name is set (#11217)
+ // Support: Windows Web Apps (WWA)
+ // `name` and `type` must use .setAttribute for WWA (#14901)
+ input.setAttribute( "type", "radio" );
+ input.setAttribute( "checked", "checked" );
+ input.setAttribute( "name", "t" );
+
+ div.appendChild( input );
+
+ // Support: Android <=4.1 only
+ // Older WebKit doesn't clone checked state correctly in fragments
+ support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
+
+ // Support: IE <=11 only
+ // Make sure textarea (and checkbox) defaultValue is properly cloned
+ div.innerHTML = "<textarea>x</textarea>";
+ support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
+
+ // Support: IE <=9 only
+ // IE <=9 replaces <option> tags with their contents when inserted outside of
+ // the select element.
+ div.innerHTML = "<option></option>";
+ support.option = !!div.lastChild;
+} )();
+
+
+// We have to close these tags to support XHTML (#13200)
+var wrapMap = {
+
+ // XHTML parsers do not magically insert elements in the
+ // same way that tag soup parsers do. So we cannot shorten
+ // this by omitting <tbody> or other required elements.
+ thead: [ 1, "<table>", "</table>" ],
+ col: [ 2, "<table><colgroup>", "</colgroup></table>" ],
+ tr: [ 2, "<table><tbody>", "</tbody></table>" ],
+ td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
+
+ _default: [ 0, "", "" ]
+};
+
+wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
+wrapMap.th = wrapMap.td;
+
+// Support: IE <=9 only
+if ( !support.option ) {
+ wrapMap.optgroup = wrapMap.option = [ 1, "<select multiple='multiple'>", "</select>" ];
+}
+
+
+function getAll( context, tag ) {
+
+ // Support: IE <=9 - 11 only
+ // Use typeof to avoid zero-argument method invocation on host objects (#15151)
+ var ret;
+
+ if ( typeof context.getElementsByTagName !== "undefined" ) {
+ ret = context.getElementsByTagName( tag || "*" );
+
+ } else if ( typeof context.querySelectorAll !== "undefined" ) {
+ ret = context.querySelectorAll( tag || "*" );
+
+ } else {
+ ret = [];
+ }
+
+ if ( tag === undefined || tag && nodeName( context, tag ) ) {
+ return jQuery.merge( [ context ], ret );
+ }
+
+ return ret;
+}
+
+
+// Mark scripts as having already been evaluated
+function setGlobalEval( elems, refElements ) {
+ var i = 0,
+ l = elems.length;
+
+ for ( ; i < l; i++ ) {
+ dataPriv.set(
+ elems[ i ],
+ "globalEval",
+ !refElements || dataPriv.get( refElements[ i ], "globalEval" )
+ );
+ }
+}
+
+
+var rhtml = /<|&#?\w+;/;
+
+function buildFragment( elems, context, scripts, selection, ignored ) {
+ var elem, tmp, tag, wrap, contains, j,
+ fragment = context.createDocumentFragment(),
+ nodes = [],
+ i = 0,
+ l = elems.length;
+
+ for ( ; i < l; i++ ) {
+ elem = elems[ i ];
+
+ if ( elem || elem === 0 ) {
+
+ // Add nodes directly
+ if ( toType( elem ) === "object" ) {
+
+ // Support: Android <=4.0 only, PhantomJS 1 only
+ // push.apply(_, arraylike) throws on ancient WebKit
+ jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );
+
+ // Convert non-html into a text node
+ } else if ( !rhtml.test( elem ) ) {
+ nodes.push( context.createTextNode( elem ) );
+
+ // Convert html into DOM nodes
+ } else {
+ tmp = tmp || fragment.appendChild( context.createElement( "div" ) );
+
+ // Deserialize a standard representation
+ tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase();
+ wrap = wrapMap[ tag ] || wrapMap._default;
+ tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ];
+
+ // Descend through wrappers to the right content
+ j = wrap[ 0 ];
+ while ( j-- ) {
+ tmp = tmp.lastChild;
+ }
+
+ // Support: Android <=4.0 only, PhantomJS 1 only
+ // push.apply(_, arraylike) throws on ancient WebKit
+ jQuery.merge( nodes, tmp.childNodes );
+
+ // Remember the top-level container
+ tmp = fragment.firstChild;
+
+ // Ensure the created nodes are orphaned (#12392)
+ tmp.textContent = "";
+ }
+ }
+ }
+
+ // Remove wrapper from fragment
+ fragment.textContent = "";
+
+ i = 0;
+ while ( ( elem = nodes[ i++ ] ) ) {
+
+ // Skip elements already in the context collection (trac-4087)
+ if ( selection && jQuery.inArray( elem, selection ) > -1 ) {
+ if ( ignored ) {
+ ignored.push( elem );
+ }
+ continue;
+ }
+
+ contains = jQuery.contains( elem.ownerDocument, elem );
+
+ // Append to fragment
+ tmp = getAll( fragment.appendChild( elem ), "script" );
+
+ // Preserve script evaluation history
+ if ( contains ) {
+ setGlobalEval( tmp );
+ }
+
+ // Capture executables
+ if ( scripts ) {
+ j = 0;
+ while ( ( elem = tmp[ j++ ] ) ) {
+ if ( rscriptType.test( elem.type || "" ) ) {
+ scripts.push( elem );
+ }
+ }
+ }
+ }
+
+ return fragment;
+}
+var documentElement = document.documentElement;
+
+
+
+var
+ rkeyEvent = /^key/,
+ rmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/,
+ rtypenamespace = /^([^.]*)(?:\.(.+)|)/;
+
+function returnTrue() {
+ return true;
+}
+
+function returnFalse() {
+ return false;
+}
+
+// Support: IE <=9 only
+// See #13393 for more info
+function safeActiveElement() {
+ try {
+ return document.activeElement;
+ } catch ( err ) { }
+}
+
+function on( elem, types, selector, data, fn, one ) {
+ var origFn, type;
+
+ // Types can be a map of types/handlers
+ if ( typeof types === "object" ) {
+
+ // ( types-Object, selector, data )
+ if ( typeof selector !== "string" ) {
+
+ // ( types-Object, data )
+ data = data || selector;
+ selector = undefined;
+ }
+ for ( type in types ) {
+ on( elem, type, selector, data, types[ type ], one );
+ }
+ return elem;
+ }
+
+ if ( data == null && fn == null ) {
+
+ // ( types, fn )
+ fn = selector;
+ data = selector = undefined;
+ } else if ( fn == null ) {
+ if ( typeof selector === "string" ) {
+
+ // ( types, selector, fn )
+ fn = data;
+ data = undefined;
+ } else {
+
+ // ( types, data, fn )
+ fn = data;
+ data = selector;
+ selector = undefined;
+ }
+ }
+ if ( fn === false ) {
+ fn = returnFalse;
+ } else if ( !fn ) {
+ return elem;
+ }
+
+ if ( one === 1 ) {
+ origFn = fn;
+ fn = function( event ) {
+
+ // Can use an empty set, since event contains the info
+ jQuery().off( event );
+ return origFn.apply( this, arguments );
+ };
+
+ // Use same guid so caller can remove using origFn
+ fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
+ }
+ return elem.each( function() {
+ jQuery.event.add( this, types, fn, data, selector );
+ } );
+}
+
+/*
+ * Helper functions for managing events -- not part of the public interface.
+ * Props to Dean Edwards' addEvent library for many of the ideas.
+ */
+jQuery.event = {
+
+ global: {},
+
+ add: function( elem, types, handler, data, selector ) {
+
+ var handleObjIn, eventHandle, tmp,
+ events, t, handleObj,
+ special, handlers, type, namespaces, origType,
+ elemData = dataPriv.get( elem );
+
+ // Don't attach events to noData or text/comment nodes (but allow plain objects)
+ if ( !elemData ) {
+ return;
+ }
+
+ // Caller can pass in an object of custom data in lieu of the handler
+ if ( handler.handler ) {
+ handleObjIn = handler;
+ handler = handleObjIn.handler;
+ selector = handleObjIn.selector;
+ }
+
+ // Ensure that invalid selectors throw exceptions at attach time
+ // Evaluate against documentElement in case elem is a non-element node (e.g., document)
+ if ( selector ) {
+ jQuery.find.matchesSelector( documentElement, selector );
+ }
+
+ // Make sure that the handler has a unique ID, used to find/remove it later
+ if ( !handler.guid ) {
+ handler.guid = jQuery.guid++;
+ }
+
+ // Init the element's event structure and main handler, if this is the first
+ if ( !( events = elemData.events ) ) {
+ events = elemData.events = {};
+ }
+ if ( !( eventHandle = elemData.handle ) ) {
+ eventHandle = elemData.handle = function( e ) {
+
+ // Discard the second event of a jQuery.event.trigger() and
+ // when an event is called after a page has unloaded
+ return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ?
+ jQuery.event.dispatch.apply( elem, arguments ) : undefined;
+ };
+ }
+
+ // Handle multiple events separated by a space
+ types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
+ t = types.length;
+ while ( t-- ) {
+ tmp = rtypenamespace.exec( types[ t ] ) || [];
+ type = origType = tmp[ 1 ];
+ namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
+
+ // There *must* be a type, no attaching namespace-only handlers
+ if ( !type ) {
+ continue;
+ }
+
+ // If event changes its type, use the special event handlers for the changed type
+ special = jQuery.event.special[ type ] || {};
+
+ // If selector defined, determine special event api type, otherwise given type
+ type = ( selector ? special.delegateType : special.bindType ) || type;
+
+ // Update special based on newly reset type
+ special = jQuery.event.special[ type ] || {};
+
+ // handleObj is passed to all event handlers
+ handleObj = jQuery.extend( {
+ type: type,
+ origType: origType,
+ data: data,
+ handler: handler,
+ guid: handler.guid,
+ selector: selector,
+ needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
+ namespace: namespaces.join( "." )
+ }, handleObjIn );
+
+ // Init the event handler queue if we're the first
+ if ( !( handlers = events[ type ] ) ) {
+ handlers = events[ type ] = [];
+ handlers.delegateCount = 0;
+
+ // Only use addEventListener if the special events handler returns false
+ if ( !special.setup ||
+ special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
+
+ if ( elem.addEventListener ) {
+ elem.addEventListener( type, eventHandle );
+ }
+ }
+ }
+
+ if ( special.add ) {
+ special.add.call( elem, handleObj );
+
+ if ( !handleObj.handler.guid ) {
+ handleObj.handler.guid = handler.guid;
+ }
+ }
+
+ // Add to the element's handler list, delegates in front
+ if ( selector ) {
+ handlers.splice( handlers.delegateCount++, 0, handleObj );
+ } else {
+ handlers.push( handleObj );
+ }
+
+ // Keep track of which events have ever been used, for event optimization
+ jQuery.event.global[ type ] = true;
+ }
+
+ },
+
+ // Detach an event or set of events from an element
+ remove: function( elem, types, handler, selector, mappedTypes ) {
+
+ var j, origCount, tmp,
+ events, t, handleObj,
+ special, handlers, type, namespaces, origType,
+ elemData = dataPriv.hasData( elem ) && dataPriv.get( elem );
+
+ if ( !elemData || !( events = elemData.events ) ) {
+ return;
+ }
+
+ // Once for each type.namespace in types; type may be omitted
+ types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
+ t = types.length;
+ while ( t-- ) {
+ tmp = rtypenamespace.exec( types[ t ] ) || [];
+ type = origType = tmp[ 1 ];
+ namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
+
+ // Unbind all events (on this namespace, if provided) for the element
+ if ( !type ) {
+ for ( type in events ) {
+ jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
+ }
+ continue;
+ }
+
+ special = jQuery.event.special[ type ] || {};
+ type = ( selector ? special.delegateType : special.bindType ) || type;
+ handlers = events[ type ] || [];
+ tmp = tmp[ 2 ] &&
+ new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" );
+
+ // Remove matching events
+ origCount = j = handlers.length;
+ while ( j-- ) {
+ handleObj = handlers[ j ];
+
+ if ( ( mappedTypes || origType === handleObj.origType ) &&
+ ( !handler || handler.guid === handleObj.guid ) &&
+ ( !tmp || tmp.test( handleObj.namespace ) ) &&
+ ( !selector || selector === handleObj.selector ||
+ selector === "**" && handleObj.selector ) ) {
+ handlers.splice( j, 1 );
+
+ if ( handleObj.selector ) {
+ handlers.delegateCount--;
+ }
+ if ( special.remove ) {
+ special.remove.call( elem, handleObj );
+ }
+ }
+ }
+
+ // Remove generic event handler if we removed something and no more handlers exist
+ // (avoids potential for endless recursion during removal of special event handlers)
+ if ( origCount && !handlers.length ) {
+ if ( !special.teardown ||
+ special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
+
+ jQuery.removeEvent( elem, type, elemData.handle );
+ }
+
+ delete events[ type ];
+ }
+ }
+
+ // Remove data and the expando if it's no longer used
+ if ( jQuery.isEmptyObject( events ) ) {
+ dataPriv.remove( elem, "handle events" );
+ }
+ },
+
+ dispatch: function( nativeEvent ) {
+
+ // Make a writable jQuery.Event from the native event object
+ var event = jQuery.event.fix( nativeEvent );
+
+ var i, j, ret, matched, handleObj, handlerQueue,
+ args = new Array( arguments.length ),
+ handlers = ( dataPriv.get( this, "events" ) || {} )[ event.type ] || [],
+ special = jQuery.event.special[ event.type ] || {};
+
+ // Use the fix-ed jQuery.Event rather than the (read-only) native event
+ args[ 0 ] = event;
+
+ for ( i = 1; i < arguments.length; i++ ) {
+ args[ i ] = arguments[ i ];
+ }
+
+ event.delegateTarget = this;
+
+ // Call the preDispatch hook for the mapped type, and let it bail if desired
+ if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
+ return;
+ }
+
+ // Determine handlers
+ handlerQueue = jQuery.event.handlers.call( this, event, handlers );
+
+ // Run delegates first; they may want to stop propagation beneath us
+ i = 0;
+ while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) {
+ event.currentTarget = matched.elem;
+
+ j = 0;
+ while ( ( handleObj = matched.handlers[ j++ ] ) &&
+ !event.isImmediatePropagationStopped() ) {
+
+ // Triggered event must either 1) have no namespace, or 2) have namespace(s)
+ // a subset or equal to those in the bound event (both can have no namespace).
+ if ( !event.rnamespace || event.rnamespace.test( handleObj.namespace ) ) {
+
+ event.handleObj = handleObj;
+ event.data = handleObj.data;
+
+ ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle ||
+ handleObj.handler ).apply( matched.elem, args );
+
+ if ( ret !== undefined ) {
+ if ( ( event.result = ret ) === false ) {
+ event.preventDefault();
+ event.stopPropagation();
+ }
+ }
+ }
+ }
+ }
+
+ // Call the postDispatch hook for the mapped type
+ if ( special.postDispatch ) {
+ special.postDispatch.call( this, event );
+ }
+
+ return event.result;
+ },
+
+ handlers: function( event, handlers ) {
+ var i, handleObj, sel, matchedHandlers, matchedSelectors,
+ handlerQueue = [],
+ delegateCount = handlers.delegateCount,
+ cur = event.target;
+
+ // Find delegate handlers
+ if ( delegateCount &&
+
+ // Support: IE <=9
+ // Black-hole SVG <use> instance trees (trac-13180)
+ cur.nodeType &&
+
+ // Support: Firefox <=42
+ // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861)
+ // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click
+ // Support: IE 11 only
+ // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343)
+ !( event.type === "click" && event.button >= 1 ) ) {
+
+ for ( ; cur !== this; cur = cur.parentNode || this ) {
+
+ // Don't check non-elements (#13208)
+ // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
+ if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) {
+ matchedHandlers = [];
+ matchedSelectors = {};
+ for ( i = 0; i < delegateCount; i++ ) {
+ handleObj = handlers[ i ];
+
+ // Don't conflict with Object.prototype properties (#13203)
+ sel = handleObj.selector + " ";
+
+ if ( matchedSelectors[ sel ] === undefined ) {
+ matchedSelectors[ sel ] = handleObj.needsContext ?
+ jQuery( sel, this ).index( cur ) > -1 :
+ jQuery.find( sel, this, null, [ cur ] ).length;
+ }
+ if ( matchedSelectors[ sel ] ) {
+ matchedHandlers.push( handleObj );
+ }
+ }
+ if ( matchedHandlers.length ) {
+ handlerQueue.push( { elem: cur, handlers: matchedHandlers } );
+ }
+ }
+ }
+ }
+
+ // Add the remaining (directly-bound) handlers
+ cur = this;
+ if ( delegateCount < handlers.length ) {
+ handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } );
+ }
+
+ return handlerQueue;
+ },
+
+ addProp: function( name, hook ) {
+ Object.defineProperty( jQuery.Event.prototype, name, {
+ enumerable: true,
+ configurable: true,
+
+ get: isFunction( hook ) ?
+ function() {
+ if ( this.originalEvent ) {
+ return hook( this.originalEvent );
+ }
+ } :
+ function() {
+ if ( this.originalEvent ) {
+ return this.originalEvent[ name ];
+ }
+ },
+
+ set: function( value ) {
+ Object.defineProperty( this, name, {
+ enumerable: true,
+ configurable: true,
+ writable: true,
+ value: value
+ } );
+ }
+ } );
+ },
+
+ fix: function( originalEvent ) {
+ return originalEvent[ jQuery.expando ] ?
+ originalEvent :
+ new jQuery.Event( originalEvent );
+ },
+
+ special: {
+ load: {
+
+ // Prevent triggered image.load events from bubbling to window.load
+ noBubble: true
+ },
+ focus: {
+
+ // Fire native event if possible so blur/focus sequence is correct
+ trigger: function() {
+ if ( this !== safeActiveElement() && this.focus ) {
+ this.focus();
+ return false;
+ }
+ },
+ delegateType: "focusin"
+ },
+ blur: {
+ trigger: function() {
+ if ( this === safeActiveElement() && this.blur ) {
+ this.blur();
+ return false;
+ }
+ },
+ delegateType: "focusout"
+ },
+ click: {
+
+ // For checkbox, fire native event so checked state will be right
+ trigger: function() {
+ if ( this.type === "checkbox" && this.click && nodeName( this, "input" ) ) {
+ this.click();
+ return false;
+ }
+ },
+
+ // For cross-browser consistency, don't fire native .click() on links
+ _default: function( event ) {
+ return nodeName( event.target, "a" );
+ }
+ },
+
+ beforeunload: {
+ postDispatch: function( event ) {
+
+ // Support: Firefox 20+
+ // Firefox doesn't alert if the returnValue field is not set.
+ if ( event.result !== undefined && event.originalEvent ) {
+ event.originalEvent.returnValue = event.result;
+ }
+ }
+ }
+ }
+};
+
+jQuery.removeEvent = function( elem, type, handle ) {
+
+ // This "if" is needed for plain objects
+ if ( elem.removeEventListener ) {
+ elem.removeEventListener( type, handle );
+ }
+};
+
+jQuery.Event = function( src, props ) {
+
+ // Allow instantiation without the 'new' keyword
+ if ( !( this instanceof jQuery.Event ) ) {
+ return new jQuery.Event( src, props );
+ }
+
+ // Event object
+ if ( src && src.type ) {
+ this.originalEvent = src;
+ this.type = src.type;
+
+ // Events bubbling up the document may have been marked as prevented
+ // by a handler lower down the tree; reflect the correct value.
+ this.isDefaultPrevented = src.defaultPrevented ||
+ src.defaultPrevented === undefined &&
+
+ // Support: Android <=2.3 only
+ src.returnValue === false ?
+ returnTrue :
+ returnFalse;
+
+ // Create target properties
+ // Support: Safari <=6 - 7 only
+ // Target should not be a text node (#504, #13143)
+ this.target = ( src.target && src.target.nodeType === 3 ) ?
+ src.target.parentNode :
+ src.target;
+
+ this.currentTarget = src.currentTarget;
+ this.relatedTarget = src.relatedTarget;
+
+ // Event type
+ } else {
+ this.type = src;
+ }
+
+ // Put explicitly provided properties onto the event object
+ if ( props ) {
+ jQuery.extend( this, props );
+ }
+
+ // Create a timestamp if incoming event doesn't have one
+ this.timeStamp = src && src.timeStamp || Date.now();
+
+ // Mark it as fixed
+ this[ jQuery.expando ] = true;
+};
+
+// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
+// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
+jQuery.Event.prototype = {
+ constructor: jQuery.Event,
+ isDefaultPrevented: returnFalse,
+ isPropagationStopped: returnFalse,
+ isImmediatePropagationStopped: returnFalse,
+ isSimulated: false,
+
+ preventDefault: function() {
+ var e = this.originalEvent;
+
+ this.isDefaultPrevented = returnTrue;
+
+ if ( e && !this.isSimulated ) {
+ e.preventDefault();
+ }
+ },
+ stopPropagation: function() {
+ var e = this.originalEvent;
+
+ this.isPropagationStopped = returnTrue;
+
+ if ( e && !this.isSimulated ) {
+ e.stopPropagation();
+ }
+ },
+ stopImmediatePropagation: function() {
+ var e = this.originalEvent;
+
+ this.isImmediatePropagationStopped = returnTrue;
+
+ if ( e && !this.isSimulated ) {
+ e.stopImmediatePropagation();
+ }
+
+ this.stopPropagation();
+ }
+};
+
+// Includes all common event props including KeyEvent and MouseEvent specific props
+jQuery.each( {
+ altKey: true,
+ bubbles: true,
+ cancelable: true,
+ changedTouches: true,
+ ctrlKey: true,
+ detail: true,
+ eventPhase: true,
+ metaKey: true,
+ pageX: true,
+ pageY: true,
+ shiftKey: true,
+ view: true,
+ "char": true,
+ charCode: true,
+ key: true,
+ keyCode: true,
+ button: true,
+ buttons: true,
+ clientX: true,
+ clientY: true,
+ offsetX: true,
+ offsetY: true,
+ pointerId: true,
+ pointerType: true,
+ screenX: true,
+ screenY: true,
+ targetTouches: true,
+ toElement: true,
+ touches: true,
+
+ which: function( event ) {
+ var button = event.button;
+
+ // Add which for key events
+ if ( event.which == null && rkeyEvent.test( event.type ) ) {
+ return event.charCode != null ? event.charCode : event.keyCode;
+ }
+
+ // Add which for click: 1 === left; 2 === middle; 3 === right
+ if ( !event.which && button !== undefined && rmouseEvent.test( event.type ) ) {
+ if ( button & 1 ) {
+ return 1;
+ }
+
+ if ( button & 2 ) {
+ return 3;
+ }
+
+ if ( button & 4 ) {
+ return 2;
+ }
+
+ return 0;
+ }
+
+ return event.which;
+ }
+}, jQuery.event.addProp );
+
+// Create mouseenter/leave events using mouseover/out and event-time checks
+// so that event delegation works in jQuery.
+// Do the same for pointerenter/pointerleave and pointerover/pointerout
+//
+// Support: Safari 7 only
+// Safari sends mouseenter too often; see:
+// https://bugs.chromium.org/p/chromium/issues/detail?id=470258
+// for the description of the bug (it existed in older Chrome versions as well).
+jQuery.each( {
+ mouseenter: "mouseover",
+ mouseleave: "mouseout",
+ pointerenter: "pointerover",
+ pointerleave: "pointerout"
+}, function( orig, fix ) {
+ jQuery.event.special[ orig ] = {
+ delegateType: fix,
+ bindType: fix,
+
+ handle: function( event ) {
+ var ret,
+ target = this,
+ related = event.relatedTarget,
+ handleObj = event.handleObj;
+
+ // For mouseenter/leave call the handler if related is outside the target.
+ // NB: No relatedTarget if the mouse left/entered the browser window
+ if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) {
+ event.type = handleObj.origType;
+ ret = handleObj.handler.apply( this, arguments );
+ event.type = fix;
+ }
+ return ret;
+ }
+ };
+} );
+
+jQuery.fn.extend( {
+
+ on: function( types, selector, data, fn ) {
+ return on( this, types, selector, data, fn );
+ },
+ one: function( types, selector, data, fn ) {
+ return on( this, types, selector, data, fn, 1 );
+ },
+ off: function( types, selector, fn ) {
+ var handleObj, type;
+ if ( types && types.preventDefault && types.handleObj ) {
+
+ // ( event ) dispatched jQuery.Event
+ handleObj = types.handleObj;
+ jQuery( types.delegateTarget ).off(
+ handleObj.namespace ?
+ handleObj.origType + "." + handleObj.namespace :
+ handleObj.origType,
+ handleObj.selector,
+ handleObj.handler
+ );
+ return this;
+ }
+ if ( typeof types === "object" ) {
+
+ // ( types-object [, selector] )
+ for ( type in types ) {
+ this.off( type, selector, types[ type ] );
+ }
+ return this;
+ }
+ if ( selector === false || typeof selector === "function" ) {
+
+ // ( types [, fn] )
+ fn = selector;
+ selector = undefined;
+ }
+ if ( fn === false ) {
+ fn = returnFalse;
+ }
+ return this.each( function() {
+ jQuery.event.remove( this, types, fn, selector );
+ } );
+ }
+} );
+
+
+var
+
+ // Support: IE <=10 - 11, Edge 12 - 13 only
+ // In IE/Edge using regex groups here causes severe slowdowns.
+ // See https://connect.microsoft.com/IE/feedback/details/1736512/
+ rnoInnerhtml = /<script|<style|<link/i,
+
+ // checked="checked" or checked
+ rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
+ rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g;
+
+// Prefer a tbody over its parent table for containing new rows
+function manipulationTarget( elem, content ) {
+ if ( nodeName( elem, "table" ) &&
+ nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) {
+
+ return jQuery( elem ).children( "tbody" )[ 0 ] || elem;
+ }
+
+ return elem;
+}
+
+// Replace/restore the type attribute of script elements for safe DOM manipulation
+function disableScript( elem ) {
+ elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type;
+ return elem;
+}
+function restoreScript( elem ) {
+ if ( ( elem.type || "" ).slice( 0, 5 ) === "true/" ) {
+ elem.type = elem.type.slice( 5 );
+ } else {
+ elem.removeAttribute( "type" );
+ }
+
+ return elem;
+}
+
+function cloneCopyEvent( src, dest ) {
+ var i, l, type, pdataOld, pdataCur, udataOld, udataCur, events;
+
+ if ( dest.nodeType !== 1 ) {
+ return;
+ }
+
+ // 1. Copy private data: events, handlers, etc.
+ if ( dataPriv.hasData( src ) ) {
+ pdataOld = dataPriv.access( src );
+ pdataCur = dataPriv.set( dest, pdataOld );
+ events = pdataOld.events;
+
+ if ( events ) {
+ delete pdataCur.handle;
+ pdataCur.events = {};
+
+ for ( type in events ) {
+ for ( i = 0, l = events[ type ].length; i < l; i++ ) {
+ jQuery.event.add( dest, type, events[ type ][ i ] );
+ }
+ }
+ }
+ }
+
+ // 2. Copy user data
+ if ( dataUser.hasData( src ) ) {
+ udataOld = dataUser.access( src );
+ udataCur = jQuery.extend( {}, udataOld );
+
+ dataUser.set( dest, udataCur );
+ }
+}
+
+// Fix IE bugs, see support tests
+function fixInput( src, dest ) {
+ var nodeName = dest.nodeName.toLowerCase();
+
+ // Fails to persist the checked state of a cloned checkbox or radio button.
+ if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
+ dest.checked = src.checked;
+
+ // Fails to return the selected option to the default selected state when cloning options
+ } else if ( nodeName === "input" || nodeName === "textarea" ) {
+ dest.defaultValue = src.defaultValue;
+ }
+}
+
+function domManip( collection, args, callback, ignored ) {
+
+ // Flatten any nested arrays
+ args = concat.apply( [], args );
+
+ var fragment, first, scripts, hasScripts, node, doc,
+ i = 0,
+ l = collection.length,
+ iNoClone = l - 1,
+ value = args[ 0 ],
+ valueIsFunction = isFunction( value );
+
+ // We can't cloneNode fragments that contain checked, in WebKit
+ if ( valueIsFunction ||
+ ( l > 1 && typeof value === "string" &&
+ !support.checkClone && rchecked.test( value ) ) ) {
+ return collection.each( function( index ) {
+ var self = collection.eq( index );
+ if ( valueIsFunction ) {
+ args[ 0 ] = value.call( this, index, self.html() );
+ }
+ domManip( self, args, callback, ignored );
+ } );
+ }
+
+ if ( l ) {
+ fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored );
+ first = fragment.firstChild;
+
+ if ( fragment.childNodes.length === 1 ) {
+ fragment = first;
+ }
+
+ // Require either new content or an interest in ignored elements to invoke the callback
+ if ( first || ignored ) {
+ scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
+ hasScripts = scripts.length;
+
+ // Use the original fragment for the last item
+ // instead of the first because it can end up
+ // being emptied incorrectly in certain situations (#8070).
+ for ( ; i < l; i++ ) {
+ node = fragment;
+
+ if ( i !== iNoClone ) {
+ node = jQuery.clone( node, true, true );
+
+ // Keep references to cloned scripts for later restoration
+ if ( hasScripts ) {
+
+ // Support: Android <=4.0 only, PhantomJS 1 only
+ // push.apply(_, arraylike) throws on ancient WebKit
+ jQuery.merge( scripts, getAll( node, "script" ) );
+ }
+ }
+
+ callback.call( collection[ i ], node, i );
+ }
+
+ if ( hasScripts ) {
+ doc = scripts[ scripts.length - 1 ].ownerDocument;
+
+ // Reenable scripts
+ jQuery.map( scripts, restoreScript );
+
+ // Evaluate executable scripts on first document insertion
+ for ( i = 0; i < hasScripts; i++ ) {
+ node = scripts[ i ];
+ if ( rscriptType.test( node.type || "" ) &&
+ !dataPriv.access( node, "globalEval" ) &&
+ jQuery.contains( doc, node ) ) {
+
+ if ( node.src && ( node.type || "" ).toLowerCase() !== "module" ) {
+
+ // Optional AJAX dependency, but won't run scripts if not present
+ if ( jQuery._evalUrl ) {
+ jQuery._evalUrl( node.src );
+ }
+ } else {
+ DOMEval( node.textContent.replace( rcleanScript, "" ), doc, node );
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return collection;
+}
+
+function remove( elem, selector, keepData ) {
+ var node,
+ nodes = selector ? jQuery.filter( selector, elem ) : elem,
+ i = 0;
+
+ for ( ; ( node = nodes[ i ] ) != null; i++ ) {
+ if ( !keepData && node.nodeType === 1 ) {
+ jQuery.cleanData( getAll( node ) );
+ }
+
+ if ( node.parentNode ) {
+ if ( keepData && jQuery.contains( node.ownerDocument, node ) ) {
+ setGlobalEval( getAll( node, "script" ) );
+ }
+ node.parentNode.removeChild( node );
+ }
+ }
+
+ return elem;
+}
+
+jQuery.extend( {
+ htmlPrefilter: function( html ) {
+ return html;
+ },
+
+ clone: function( elem, dataAndEvents, deepDataAndEvents ) {
+ var i, l, srcElements, destElements,
+ clone = elem.cloneNode( true ),
+ inPage = jQuery.contains( elem.ownerDocument, elem );
+
+ // Fix IE cloning issues
+ if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) &&
+ !jQuery.isXMLDoc( elem ) ) {
+
+ // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2
+ destElements = getAll( clone );
+ srcElements = getAll( elem );
+
+ for ( i = 0, l = srcElements.length; i < l; i++ ) {
+ fixInput( srcElements[ i ], destElements[ i ] );
+ }
+ }
+
+ // Copy the events from the original to the clone
+ if ( dataAndEvents ) {
+ if ( deepDataAndEvents ) {
+ srcElements = srcElements || getAll( elem );
+ destElements = destElements || getAll( clone );
+
+ for ( i = 0, l = srcElements.length; i < l; i++ ) {
+ cloneCopyEvent( srcElements[ i ], destElements[ i ] );
+ }
+ } else {
+ cloneCopyEvent( elem, clone );
+ }
+ }
+
+ // Preserve script evaluation history
+ destElements = getAll( clone, "script" );
+ if ( destElements.length > 0 ) {
+ setGlobalEval( destElements, !inPage && getAll( elem, "script" ) );
+ }
+
+ // Return the cloned set
+ return clone;
+ },
+
+ cleanData: function( elems ) {
+ var data, elem, type,
+ special = jQuery.event.special,
+ i = 0;
+
+ for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) {
+ if ( acceptData( elem ) ) {
+ if ( ( data = elem[ dataPriv.expando ] ) ) {
+ if ( data.events ) {
+ for ( type in data.events ) {
+ if ( special[ type ] ) {
+ jQuery.event.remove( elem, type );
+
+ // This is a shortcut to avoid jQuery.event.remove's overhead
+ } else {
+ jQuery.removeEvent( elem, type, data.handle );
+ }
+ }
+ }
+
+ // Support: Chrome <=35 - 45+
+ // Assign undefined instead of using delete, see Data#remove
+ elem[ dataPriv.expando ] = undefined;
+ }
+ if ( elem[ dataUser.expando ] ) {
+
+ // Support: Chrome <=35 - 45+
+ // Assign undefined instead of using delete, see Data#remove
+ elem[ dataUser.expando ] = undefined;
+ }
+ }
+ }
+ }
+} );
+
+jQuery.fn.extend( {
+ detach: function( selector ) {
+ return remove( this, selector, true );
+ },
+
+ remove: function( selector ) {
+ return remove( this, selector );
+ },
+
+ text: function( value ) {
+ return access( this, function( value ) {
+ return value === undefined ?
+ jQuery.text( this ) :
+ this.empty().each( function() {
+ if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+ this.textContent = value;
+ }
+ } );
+ }, null, value, arguments.length );
+ },
+
+ append: function() {
+ return domManip( this, arguments, function( elem ) {
+ if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+ var target = manipulationTarget( this, elem );
+ target.appendChild( elem );
+ }
+ } );
+ },
+
+ prepend: function() {
+ return domManip( this, arguments, function( elem ) {
+ if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+ var target = manipulationTarget( this, elem );
+ target.insertBefore( elem, target.firstChild );
+ }
+ } );
+ },
+
+ before: function() {
+ return domManip( this, arguments, function( elem ) {
+ if ( this.parentNode ) {
+ this.parentNode.insertBefore( elem, this );
+ }
+ } );
+ },
+
+ after: function() {
+ return domManip( this, arguments, function( elem ) {
+ if ( this.parentNode ) {
+ this.parentNode.insertBefore( elem, this.nextSibling );
+ }
+ } );
+ },
+
+ empty: function() {
+ var elem,
+ i = 0;
+
+ for ( ; ( elem = this[ i ] ) != null; i++ ) {
+ if ( elem.nodeType === 1 ) {
+
+ // Prevent memory leaks
+ jQuery.cleanData( getAll( elem, false ) );
+
+ // Remove any remaining nodes
+ elem.textContent = "";
+ }
+ }
+
+ return this;
+ },
+
+ clone: function( dataAndEvents, deepDataAndEvents ) {
+ dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
+ deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
+
+ return this.map( function() {
+ return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
+ } );
+ },
+
+ html: function( value ) {
+ return access( this, function( value ) {
+ var elem = this[ 0 ] || {},
+ i = 0,
+ l = this.length;
+
+ if ( value === undefined && elem.nodeType === 1 ) {
+ return elem.innerHTML;
+ }
+
+ // See if we can take a shortcut and just use innerHTML
+ if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
+ !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) {
+
+ value = jQuery.htmlPrefilter( value );
+
+ try {
+ for ( ; i < l; i++ ) {
+ elem = this[ i ] || {};
+
+ // Remove element nodes and prevent memory leaks
+ if ( elem.nodeType === 1 ) {
+ jQuery.cleanData( getAll( elem, false ) );
+ elem.innerHTML = value;
+ }
+ }
+
+ elem = 0;
+
+ // If using innerHTML throws an exception, use the fallback method
+ } catch ( e ) {}
+ }
+
+ if ( elem ) {
+ this.empty().append( value );
+ }
+ }, null, value, arguments.length );
+ },
+
+ replaceWith: function() {
+ var ignored = [];
+
+ // Make the changes, replacing each non-ignored context element with the new content
+ return domManip( this, arguments, function( elem ) {
+ var parent = this.parentNode;
+
+ if ( jQuery.inArray( this, ignored ) < 0 ) {
+ jQuery.cleanData( getAll( this ) );
+ if ( parent ) {
+ parent.replaceChild( elem, this );
+ }
+ }
+
+ // Force callback invocation
+ }, ignored );
+ }
+} );
+
+jQuery.each( {
+ appendTo: "append",
+ prependTo: "prepend",
+ insertBefore: "before",
+ insertAfter: "after",
+ replaceAll: "replaceWith"
+}, function( name, original ) {
+ jQuery.fn[ name ] = function( selector ) {
+ var elems,
+ ret = [],
+ insert = jQuery( selector ),
+ last = insert.length - 1,
+ i = 0;
+
+ for ( ; i <= last; i++ ) {
+ elems = i === last ? this : this.clone( true );
+ jQuery( insert[ i ] )[ original ]( elems );
+
+ // Support: Android <=4.0 only, PhantomJS 1 only
+ // .get() because push.apply(_, arraylike) throws on ancient WebKit
+ push.apply( ret, elems.get() );
+ }
+
+ return this.pushStack( ret );
+ };
+} );
+var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
+
+var getStyles = function( elem ) {
+
+ // Support: IE <=11 only, Firefox <=30 (#15098, #14150)
+ // IE throws on elements created in popups
+ // FF meanwhile throws on frame elements through "defaultView.getComputedStyle"
+ var view = elem.ownerDocument.defaultView;
+
+ if ( !view || !view.opener ) {
+ view = window;
+ }
+
+ return view.getComputedStyle( elem );
+ };
+
+var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" );
+
+
+
+( function() {
+
+ // Executing both pixelPosition & boxSizingReliable tests require only one layout
+ // so they're executed at the same time to save the second computation.
+ function computeStyleTests() {
+
+ // This is a singleton, we need to execute it only once
+ if ( !div ) {
+ return;
+ }
+
+ container.style.cssText = "position:absolute;left:-11111px;width:60px;" +
+ "margin-top:1px;padding:0;border:0";
+ div.style.cssText =
+ "position:relative;display:block;box-sizing:border-box;overflow:scroll;" +
+ "margin:auto;border:1px;padding:1px;" +
+ "width:60%;top:1%";
+ documentElement.appendChild( container ).appendChild( div );
+
+ var divStyle = window.getComputedStyle( div );
+ pixelPositionVal = divStyle.top !== "1%";
+
+ // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44
+ reliableMarginLeftVal = roundPixelMeasures( divStyle.marginLeft ) === 12;
+
+ // Support: Android 4.0 - 4.3 only, Safari <=9.1 - 10.1, iOS <=7.0 - 9.3
+ // Some styles come back with percentage values, even though they shouldn't
+ div.style.right = "60%";
+ pixelBoxStylesVal = roundPixelMeasures( divStyle.right ) === 36;
+
+ // Support: IE 9 - 11 only
+ // Detect misreporting of content dimensions for box-sizing:border-box elements
+ boxSizingReliableVal = roundPixelMeasures( divStyle.width ) === 36;
+
+ // Support: IE 9 only
+ // Detect overflow:scroll screwiness (gh-3699)
+ div.style.position = "absolute";
+ scrollboxSizeVal = div.offsetWidth === 36 || "absolute";
+
+ documentElement.removeChild( container );
+
+ // Nullify the div so it wouldn't be stored in the memory and
+ // it will also be a sign that checks already performed
+ div = null;
+ }
+
+ function roundPixelMeasures( measure ) {
+ return Math.round( parseFloat( measure ) );
+ }
+
+ var pixelPositionVal, boxSizingReliableVal, scrollboxSizeVal, pixelBoxStylesVal,
+ reliableMarginLeftVal,
+ container = document.createElement( "div" ),
+ div = document.createElement( "div" );
+
+ // Finish early in limited (non-browser) environments
+ if ( !div.style ) {
+ return;
+ }
+
+ // Support: IE <=9 - 11 only
+ // Style of cloned element affects source element cloned (#8908)
+ div.style.backgroundClip = "content-box";
+ div.cloneNode( true ).style.backgroundClip = "";
+ support.clearCloneStyle = div.style.backgroundClip === "content-box";
+
+ jQuery.extend( support, {
+ boxSizingReliable: function() {
+ computeStyleTests();
+ return boxSizingReliableVal;
+ },
+ pixelBoxStyles: function() {
+ computeStyleTests();
+ return pixelBoxStylesVal;
+ },
+ pixelPosition: function() {
+ computeStyleTests();
+ return pixelPositionVal;
+ },
+ reliableMarginLeft: function() {
+ computeStyleTests();
+ return reliableMarginLeftVal;
+ },
+ scrollboxSize: function() {
+ computeStyleTests();
+ return scrollboxSizeVal;
+ }
+ } );
+} )();
+
+
+function curCSS( elem, name, computed ) {
+ var width, minWidth, maxWidth, ret,
+
+ // Support: Firefox 51+
+ // Retrieving style before computed somehow
+ // fixes an issue with getting wrong values
+ // on detached elements
+ style = elem.style;
+
+ computed = computed || getStyles( elem );
+
+ // getPropertyValue is needed for:
+ // .css('filter') (IE 9 only, #12537)
+ // .css('--customProperty) (#3144)
+ if ( computed ) {
+ ret = computed.getPropertyValue( name ) || computed[ name ];
+
+ if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) {
+ ret = jQuery.style( elem, name );
+ }
+
+ // A tribute to the "awesome hack by Dean Edwards"
+ // Android Browser returns percentage for some values,
+ // but width seems to be reliably pixels.
+ // This is against the CSSOM draft spec:
+ // https://drafts.csswg.org/cssom/#resolved-values
+ if ( !support.pixelBoxStyles() && rnumnonpx.test( ret ) && rboxStyle.test( name ) ) {
+
+ // Remember the original values
+ width = style.width;
+ minWidth = style.minWidth;
+ maxWidth = style.maxWidth;
+
+ // Put in the new values to get a computed value out
+ style.minWidth = style.maxWidth = style.width = ret;
+ ret = computed.width;
+
+ // Revert the changed values
+ style.width = width;
+ style.minWidth = minWidth;
+ style.maxWidth = maxWidth;
+ }
+ }
+
+ return ret !== undefined ?
+
+ // Support: IE <=9 - 11 only
+ // IE returns zIndex value as an integer.
+ ret + "" :
+ ret;
+}
+
+
+function addGetHookIf( conditionFn, hookFn ) {
+
+ // Define the hook, we'll check on the first run if it's really needed.
+ return {
+ get: function() {
+ if ( conditionFn() ) {
+
+ // Hook not needed (or it's not possible to use it due
+ // to missing dependency), remove it.
+ delete this.get;
+ return;
+ }
+
+ // Hook needed; redefine it so that the support test is not executed again.
+ return ( this.get = hookFn ).apply( this, arguments );
+ }
+ };
+}
+
+
+var
+
+ // Swappable if display is none or starts with table
+ // except "table", "table-cell", or "table-caption"
+ // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
+ rdisplayswap = /^(none|table(?!-c[ea]).+)/,
+ rcustomProp = /^--/,
+ cssShow = { position: "absolute", visibility: "hidden", display: "block" },
+ cssNormalTransform = {
+ letterSpacing: "0",
+ fontWeight: "400"
+ },
+
+ cssPrefixes = [ "Webkit", "Moz", "ms" ],
+ emptyStyle = document.createElement( "div" ).style;
+
+// Return a css property mapped to a potentially vendor prefixed property
+function vendorPropName( name ) {
+
+ // Shortcut for names that are not vendor prefixed
+ if ( name in emptyStyle ) {
+ return name;
+ }
+
+ // Check for vendor prefixed names
+ var capName = name[ 0 ].toUpperCase() + name.slice( 1 ),
+ i = cssPrefixes.length;
+
+ while ( i-- ) {
+ name = cssPrefixes[ i ] + capName;
+ if ( name in emptyStyle ) {
+ return name;
+ }
+ }
+}
+
+// Return a property mapped along what jQuery.cssProps suggests or to
+// a vendor prefixed property.
+function finalPropName( name ) {
+ var ret = jQuery.cssProps[ name ];
+ if ( !ret ) {
+ ret = jQuery.cssProps[ name ] = vendorPropName( name ) || name;
+ }
+ return ret;
+}
+
+function setPositiveNumber( elem, value, subtract ) {
+
+ // Any relative (+/-) values have already been
+ // normalized at this point
+ var matches = rcssNum.exec( value );
+ return matches ?
+
+ // Guard against undefined "subtract", e.g., when used as in cssHooks
+ Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) :
+ value;
+}
+
+function boxModelAdjustment( elem, dimension, box, isBorderBox, styles, computedVal ) {
+ var i = dimension === "width" ? 1 : 0,
+ extra = 0,
+ delta = 0;
+
+ // Adjustment may not be necessary
+ if ( box === ( isBorderBox ? "border" : "content" ) ) {
+ return 0;
+ }
+
+ for ( ; i < 4; i += 2 ) {
+
+ // Both box models exclude margin
+ if ( box === "margin" ) {
+ delta += jQuery.css( elem, box + cssExpand[ i ], true, styles );
+ }
+
+ // If we get here with a content-box, we're seeking "padding" or "border" or "margin"
+ if ( !isBorderBox ) {
+
+ // Add padding
+ delta += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+
+ // For "border" or "margin", add border
+ if ( box !== "padding" ) {
+ delta += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+
+ // But still keep track of it otherwise
+ } else {
+ extra += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+ }
+
+ // If we get here with a border-box (content + padding + border), we're seeking "content" or
+ // "padding" or "margin"
+ } else {
+
+ // For "content", subtract padding
+ if ( box === "content" ) {
+ delta -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+ }
+
+ // For "content" or "padding", subtract border
+ if ( box !== "margin" ) {
+ delta -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+ }
+ }
+ }
+
+ // Account for positive content-box scroll gutter when requested by providing computedVal
+ if ( !isBorderBox && computedVal >= 0 ) {
+
+ // offsetWidth/offsetHeight is a rounded sum of content, padding, scroll gutter, and border
+ // Assuming integer scroll gutter, subtract the rest and round down
+ delta += Math.max( 0, Math.ceil(
+ elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] -
+ computedVal -
+ delta -
+ extra -
+ 0.5
+ ) );
+ }
+
+ return delta;
+}
+
+function getWidthOrHeight( elem, dimension, extra ) {
+
+ // Start with computed style
+ var styles = getStyles( elem ),
+ val = curCSS( elem, dimension, styles ),
+ isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
+ valueIsBorderBox = isBorderBox;
+
+ // Support: Firefox <=54
+ // Return a confounding non-pixel value or feign ignorance, as appropriate.
+ if ( rnumnonpx.test( val ) ) {
+ if ( !extra ) {
+ return val;
+ }
+ val = "auto";
+ }
+
+ // Check for style in case a browser which returns unreliable values
+ // for getComputedStyle silently falls back to the reliable elem.style
+ valueIsBorderBox = valueIsBorderBox &&
+ ( support.boxSizingReliable() || val === elem.style[ dimension ] );
+
+ // Fall back to offsetWidth/offsetHeight when value is "auto"
+ // This happens for inline elements with no explicit setting (gh-3571)
+ // Support: Android <=4.1 - 4.3 only
+ // Also use offsetWidth/offsetHeight for misreported inline dimensions (gh-3602)
+ if ( val === "auto" ||
+ !parseFloat( val ) && jQuery.css( elem, "display", false, styles ) === "inline" ) {
+
+ val = elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ];
+
+ // offsetWidth/offsetHeight provide border-box values
+ valueIsBorderBox = true;
+ }
+
+ // Normalize "" and auto
+ val = parseFloat( val ) || 0;
+
+ // Adjust for the element's box model
+ return ( val +
+ boxModelAdjustment(
+ elem,
+ dimension,
+ extra || ( isBorderBox ? "border" : "content" ),
+ valueIsBorderBox,
+ styles,
+
+ // Provide the current computed size to request scroll gutter calculation (gh-3589)
+ val
+ )
+ ) + "px";
+}
+
+jQuery.extend( {
+
+ // Add in style property hooks for overriding the default
+ // behavior of getting and setting a style property
+ cssHooks: {
+ opacity: {
+ get: function( elem, computed ) {
+ if ( computed ) {
+
+ // We should always get a number back from opacity
+ var ret = curCSS( elem, "opacity" );
+ return ret === "" ? "1" : ret;
+ }
+ }
+ }
+ },
+
+ // Don't automatically add "px" to these possibly-unitless properties
+ cssNumber: {
+ "animationIterationCount": true,
+ "columnCount": true,
+ "fillOpacity": true,
+ "flexGrow": true,
+ "flexShrink": true,
+ "fontWeight": true,
+ "lineHeight": true,
+ "opacity": true,
+ "order": true,
+ "orphans": true,
+ "widows": true,
+ "zIndex": true,
+ "zoom": true
+ },
+
+ // Add in properties whose names you wish to fix before
+ // setting or getting the value
+ cssProps: {},
+
+ // Get and set the style property on a DOM Node
+ style: function( elem, name, value, extra ) {
+
+ // Don't set styles on text and comment nodes
+ if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
+ return;
+ }
+
+ // Make sure that we're working with the right name
+ var ret, type, hooks,
+ origName = camelCase( name ),
+ isCustomProp = rcustomProp.test( name ),
+ style = elem.style;
+
+ // Make sure that we're working with the right name. We don't
+ // want to query the value if it is a CSS custom property
+ // since they are user-defined.
+ if ( !isCustomProp ) {
+ name = finalPropName( origName );
+ }
+
+ // Gets hook for the prefixed version, then unprefixed version
+ hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+ // Check if we're setting a value
+ if ( value !== undefined ) {
+ type = typeof value;
+
+ // Convert "+=" or "-=" to relative numbers (#7345)
+ if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) {
+ value = adjustCSS( elem, name, ret );
+
+ // Fixes bug #9237
+ type = "number";
+ }
+
+ // Make sure that null and NaN values aren't set (#7116)
+ if ( value == null || value !== value ) {
+ return;
+ }
+
+ // If a number was passed in, add the unit (except for certain CSS properties)
+ if ( type === "number" ) {
+ value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" );
+ }
+
+ // background-* props affect original clone's values
+ if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) {
+ style[ name ] = "inherit";
+ }
+
+ // If a hook was provided, use that value, otherwise just set the specified value
+ if ( !hooks || !( "set" in hooks ) ||
+ ( value = hooks.set( elem, value, extra ) ) !== undefined ) {
+
+ if ( isCustomProp ) {
+ style.setProperty( name, value );
+ } else {
+ style[ name ] = value;
+ }
+ }
+
+ } else {
+
+ // If a hook was provided get the non-computed value from there
+ if ( hooks && "get" in hooks &&
+ ( ret = hooks.get( elem, false, extra ) ) !== undefined ) {
+
+ return ret;
+ }
+
+ // Otherwise just get the value from the style object
+ return style[ name ];
+ }
+ },
+
+ css: function( elem, name, extra, styles ) {
+ var val, num, hooks,
+ origName = camelCase( name ),
+ isCustomProp = rcustomProp.test( name );
+
+ // Make sure that we're working with the right name. We don't
+ // want to modify the value if it is a CSS custom property
+ // since they are user-defined.
+ if ( !isCustomProp ) {
+ name = finalPropName( origName );
+ }
+
+ // Try prefixed name followed by the unprefixed name
+ hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+ // If a hook was provided get the computed value from there
+ if ( hooks && "get" in hooks ) {
+ val = hooks.get( elem, true, extra );
+ }
+
+ // Otherwise, if a way to get the computed value exists, use that
+ if ( val === undefined ) {
+ val = curCSS( elem, name, styles );
+ }
+
+ // Convert "normal" to computed value
+ if ( val === "normal" && name in cssNormalTransform ) {
+ val = cssNormalTransform[ name ];
+ }
+
+ // Make numeric if forced or a qualifier was provided and val looks numeric
+ if ( extra === "" || extra ) {
+ num = parseFloat( val );
+ return extra === true || isFinite( num ) ? num || 0 : val;
+ }
+
+ return val;
+ }
+} );
+
+jQuery.each( [ "height", "width" ], function( i, dimension ) {
+ jQuery.cssHooks[ dimension ] = {
+ get: function( elem, computed, extra ) {
+ if ( computed ) {
+
+ // Certain elements can have dimension info if we invisibly show them
+ // but it must have a current display style that would benefit
+ return rdisplayswap.test( jQuery.css( elem, "display" ) ) &&
+
+ // Support: Safari 8+
+ // Table columns in Safari have non-zero offsetWidth & zero
+ // getBoundingClientRect().width unless display is changed.
+ // Support: IE <=11 only
+ // Running getBoundingClientRect on a disconnected node
+ // in IE throws an error.
+ ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ?
+ swap( elem, cssShow, function() {
+ return getWidthOrHeight( elem, dimension, extra );
+ } ) :
+ getWidthOrHeight( elem, dimension, extra );
+ }
+ },
+
+ set: function( elem, value, extra ) {
+ var matches,
+ styles = getStyles( elem ),
+ isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
+ subtract = extra && boxModelAdjustment(
+ elem,
+ dimension,
+ extra,
+ isBorderBox,
+ styles
+ );
+
+ // Account for unreliable border-box dimensions by comparing offset* to computed and
+ // faking a content-box to get border and padding (gh-3699)
+ if ( isBorderBox && support.scrollboxSize() === styles.position ) {
+ subtract -= Math.ceil(
+ elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] -
+ parseFloat( styles[ dimension ] ) -
+ boxModelAdjustment( elem, dimension, "border", false, styles ) -
+ 0.5
+ );
+ }
+
+ // Convert to pixels if value adjustment is needed
+ if ( subtract && ( matches = rcssNum.exec( value ) ) &&
+ ( matches[ 3 ] || "px" ) !== "px" ) {
+
+ elem.style[ dimension ] = value;
+ value = jQuery.css( elem, dimension );
+ }
+
+ return setPositiveNumber( elem, value, subtract );
+ }
+ };
+} );
+
+jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft,
+ function( elem, computed ) {
+ if ( computed ) {
+ return ( parseFloat( curCSS( elem, "marginLeft" ) ) ||
+ elem.getBoundingClientRect().left -
+ swap( elem, { marginLeft: 0 }, function() {
+ return elem.getBoundingClientRect().left;
+ } )
+ ) + "px";
+ }
+ }
+);
+
+// These hooks are used by animate to expand properties
+jQuery.each( {
+ margin: "",
+ padding: "",
+ border: "Width"
+}, function( prefix, suffix ) {
+ jQuery.cssHooks[ prefix + suffix ] = {
+ expand: function( value ) {
+ var i = 0,
+ expanded = {},
+
+ // Assumes a single number if not a string
+ parts = typeof value === "string" ? value.split( " " ) : [ value ];
+
+ for ( ; i < 4; i++ ) {
+ expanded[ prefix + cssExpand[ i ] + suffix ] =
+ parts[ i ] || parts[ i - 2 ] || parts[ 0 ];
+ }
+
+ return expanded;
+ }
+ };
+
+ if ( prefix !== "margin" ) {
+ jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
+ }
+} );
+
+jQuery.fn.extend( {
+ css: function( name, value ) {
+ return access( this, function( elem, name, value ) {
+ var styles, len,
+ map = {},
+ i = 0;
+
+ if ( Array.isArray( name ) ) {
+ styles = getStyles( elem );
+ len = name.length;
+
+ for ( ; i < len; i++ ) {
+ map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles );
+ }
+
+ return map;
+ }
+
+ return value !== undefined ?
+ jQuery.style( elem, name, value ) :
+ jQuery.css( elem, name );
+ }, name, value, arguments.length > 1 );
+ }
+} );
+
+
+function Tween( elem, options, prop, end, easing ) {
+ return new Tween.prototype.init( elem, options, prop, end, easing );
+}
+jQuery.Tween = Tween;
+
+Tween.prototype = {
+ constructor: Tween,
+ init: function( elem, options, prop, end, easing, unit ) {
+ this.elem = elem;
+ this.prop = prop;
+ this.easing = easing || jQuery.easing._default;
+ this.options = options;
+ this.start = this.now = this.cur();
+ this.end = end;
+ this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
+ },
+ cur: function() {
+ var hooks = Tween.propHooks[ this.prop ];
+
+ return hooks && hooks.get ?
+ hooks.get( this ) :
+ Tween.propHooks._default.get( this );
+ },
+ run: function( percent ) {
+ var eased,
+ hooks = Tween.propHooks[ this.prop ];
+
+ if ( this.options.duration ) {
+ this.pos = eased = jQuery.easing[ this.easing ](
+ percent, this.options.duration * percent, 0, 1, this.options.duration
+ );
+ } else {
+ this.pos = eased = percent;
+ }
+ this.now = ( this.end - this.start ) * eased + this.start;
+
+ if ( this.options.step ) {
+ this.options.step.call( this.elem, this.now, this );
+ }
+
+ if ( hooks && hooks.set ) {
+ hooks.set( this );
+ } else {
+ Tween.propHooks._default.set( this );
+ }
+ return this;
+ }
+};
+
+Tween.prototype.init.prototype = Tween.prototype;
+
+Tween.propHooks = {
+ _default: {
+ get: function( tween ) {
+ var result;
+
+ // Use a property on the element directly when it is not a DOM element,
+ // or when there is no matching style property that exists.
+ if ( tween.elem.nodeType !== 1 ||
+ tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) {
+ return tween.elem[ tween.prop ];
+ }
+
+ // Passing an empty string as a 3rd parameter to .css will automatically
+ // attempt a parseFloat and fallback to a string if the parse fails.
+ // Simple values such as "10px" are parsed to Float;
+ // complex values such as "rotate(1rad)" are returned as-is.
+ result = jQuery.css( tween.elem, tween.prop, "" );
+
+ // Empty strings, null, undefined and "auto" are converted to 0.
+ return !result || result === "auto" ? 0 : result;
+ },
+ set: function( tween ) {
+
+ // Use step hook for back compat.
+ // Use cssHook if its there.
+ // Use .style if available and use plain properties where available.
+ if ( jQuery.fx.step[ tween.prop ] ) {
+ jQuery.fx.step[ tween.prop ]( tween );
+ } else if ( tween.elem.nodeType === 1 &&
+ ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null ||
+ jQuery.cssHooks[ tween.prop ] ) ) {
+ jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
+ } else {
+ tween.elem[ tween.prop ] = tween.now;
+ }
+ }
+ }
+};
+
+// Support: IE <=9 only
+// Panic based approach to setting things on disconnected nodes
+Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
+ set: function( tween ) {
+ if ( tween.elem.nodeType && tween.elem.parentNode ) {
+ tween.elem[ tween.prop ] = tween.now;
+ }
+ }
+};
+
+jQuery.easing = {
+ linear: function( p ) {
+ return p;
+ },
+ swing: function( p ) {
+ return 0.5 - Math.cos( p * Math.PI ) / 2;
+ },
+ _default: "swing"
+};
+
+jQuery.fx = Tween.prototype.init;
+
+// Back compat <1.8 extension point
+jQuery.fx.step = {};
+
+
+
+
+var
+ fxNow, inProgress,
+ rfxtypes = /^(?:toggle|show|hide)$/,
+ rrun = /queueHooks$/;
+
+function schedule() {
+ if ( inProgress ) {
+ if ( document.hidden === false && window.requestAnimationFrame ) {
+ window.requestAnimationFrame( schedule );
+ } else {
+ window.setTimeout( schedule, jQuery.fx.interval );
+ }
+
+ jQuery.fx.tick();
+ }
+}
+
+// Animations created synchronously will run synchronously
+function createFxNow() {
+ window.setTimeout( function() {
+ fxNow = undefined;
+ } );
+ return ( fxNow = Date.now() );
+}
+
+// Generate parameters to create a standard animation
+function genFx( type, includeWidth ) {
+ var which,
+ i = 0,
+ attrs = { height: type };
+
+ // If we include width, step value is 1 to do all cssExpand values,
+ // otherwise step value is 2 to skip over Left and Right
+ includeWidth = includeWidth ? 1 : 0;
+ for ( ; i < 4; i += 2 - includeWidth ) {
+ which = cssExpand[ i ];
+ attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
+ }
+
+ if ( includeWidth ) {
+ attrs.opacity = attrs.width = type;
+ }
+
+ return attrs;
+}
+
+function createTween( value, prop, animation ) {
+ var tween,
+ collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ),
+ index = 0,
+ length = collection.length;
+ for ( ; index < length; index++ ) {
+ if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) {
+
+ // We're done with this property
+ return tween;
+ }
+ }
+}
+
+function defaultPrefilter( elem, props, opts ) {
+ var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display,
+ isBox = "width" in props || "height" in props,
+ anim = this,
+ orig = {},
+ style = elem.style,
+ hidden = elem.nodeType && isHiddenWithinTree( elem ),
+ dataShow = dataPriv.get( elem, "fxshow" );
+
+ // Queue-skipping animations hijack the fx hooks
+ if ( !opts.queue ) {
+ hooks = jQuery._queueHooks( elem, "fx" );
+ if ( hooks.unqueued == null ) {
+ hooks.unqueued = 0;
+ oldfire = hooks.empty.fire;
+ hooks.empty.fire = function() {
+ if ( !hooks.unqueued ) {
+ oldfire();
+ }
+ };
+ }
+ hooks.unqueued++;
+
+ anim.always( function() {
+
+ // Ensure the complete handler is called before this completes
+ anim.always( function() {
+ hooks.unqueued--;
+ if ( !jQuery.queue( elem, "fx" ).length ) {
+ hooks.empty.fire();
+ }
+ } );
+ } );
+ }
+
+ // Detect show/hide animations
+ for ( prop in props ) {
+ value = props[ prop ];
+ if ( rfxtypes.test( value ) ) {
+ delete props[ prop ];
+ toggle = toggle || value === "toggle";
+ if ( value === ( hidden ? "hide" : "show" ) ) {
+
+ // Pretend to be hidden if this is a "show" and
+ // there is still data from a stopped show/hide
+ if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) {
+ hidden = true;
+
+ // Ignore all other no-op show/hide data
+ } else {
+ continue;
+ }
+ }
+ orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop );
+ }
+ }
+
+ // Bail out if this is a no-op like .hide().hide()
+ propTween = !jQuery.isEmptyObject( props );
+ if ( !propTween && jQuery.isEmptyObject( orig ) ) {
+ return;
+ }
+
+ // Restrict "overflow" and "display" styles during box animations
+ if ( isBox && elem.nodeType === 1 ) {
+
+ // Support: IE <=9 - 11, Edge 12 - 15
+ // Record all 3 overflow attributes because IE does not infer the shorthand
+ // from identically-valued overflowX and overflowY and Edge just mirrors
+ // the overflowX value there.
+ opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
+
+ // Identify a display type, preferring old show/hide data over the CSS cascade
+ restoreDisplay = dataShow && dataShow.display;
+ if ( restoreDisplay == null ) {
+ restoreDisplay = dataPriv.get( elem, "display" );
+ }
+ display = jQuery.css( elem, "display" );
+ if ( display === "none" ) {
+ if ( restoreDisplay ) {
+ display = restoreDisplay;
+ } else {
+
+ // Get nonempty value(s) by temporarily forcing visibility
+ showHide( [ elem ], true );
+ restoreDisplay = elem.style.display || restoreDisplay;
+ display = jQuery.css( elem, "display" );
+ showHide( [ elem ] );
+ }
+ }
+
+ // Animate inline elements as inline-block
+ if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) {
+ if ( jQuery.css( elem, "float" ) === "none" ) {
+
+ // Restore the original display value at the end of pure show/hide animations
+ if ( !propTween ) {
+ anim.done( function() {
+ style.display = restoreDisplay;
+ } );
+ if ( restoreDisplay == null ) {
+ display = style.display;
+ restoreDisplay = display === "none" ? "" : display;
+ }
+ }
+ style.display = "inline-block";
+ }
+ }
+ }
+
+ if ( opts.overflow ) {
+ style.overflow = "hidden";
+ anim.always( function() {
+ style.overflow = opts.overflow[ 0 ];
+ style.overflowX = opts.overflow[ 1 ];
+ style.overflowY = opts.overflow[ 2 ];
+ } );
+ }
+
+ // Implement show/hide animations
+ propTween = false;
+ for ( prop in orig ) {
+
+ // General show/hide setup for this element animation
+ if ( !propTween ) {
+ if ( dataShow ) {
+ if ( "hidden" in dataShow ) {
+ hidden = dataShow.hidden;
+ }
+ } else {
+ dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } );
+ }
+
+ // Store hidden/visible for toggle so `.stop().toggle()` "reverses"
+ if ( toggle ) {
+ dataShow.hidden = !hidden;
+ }
+
+ // Show elements before animating them
+ if ( hidden ) {
+ showHide( [ elem ], true );
+ }
+
+ /* eslint-disable no-loop-func */
+
+ anim.done( function() {
+
+ /* eslint-enable no-loop-func */
+
+ // The final step of a "hide" animation is actually hiding the element
+ if ( !hidden ) {
+ showHide( [ elem ] );
+ }
+ dataPriv.remove( elem, "fxshow" );
+ for ( prop in orig ) {
+ jQuery.style( elem, prop, orig[ prop ] );
+ }
+ } );
+ }
+
+ // Per-property setup
+ propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
+ if ( !( prop in dataShow ) ) {
+ dataShow[ prop ] = propTween.start;
+ if ( hidden ) {
+ propTween.end = propTween.start;
+ propTween.start = 0;
+ }
+ }
+ }
+}
+
+function propFilter( props, specialEasing ) {
+ var index, name, easing, value, hooks;
+
+ // camelCase, specialEasing and expand cssHook pass
+ for ( index in props ) {
+ name = camelCase( index );
+ easing = specialEasing[ name ];
+ value = props[ index ];
+ if ( Array.isArray( value ) ) {
+ easing = value[ 1 ];
+ value = props[ index ] = value[ 0 ];
+ }
+
+ if ( index !== name ) {
+ props[ name ] = value;
+ delete props[ index ];
+ }
+
+ hooks = jQuery.cssHooks[ name ];
+ if ( hooks && "expand" in hooks ) {
+ value = hooks.expand( value );
+ delete props[ name ];
+
+ // Not quite $.extend, this won't overwrite existing keys.
+ // Reusing 'index' because we have the correct "name"
+ for ( index in value ) {
+ if ( !( index in props ) ) {
+ props[ index ] = value[ index ];
+ specialEasing[ index ] = easing;
+ }
+ }
+ } else {
+ specialEasing[ name ] = easing;
+ }
+ }
+}
+
+function Animation( elem, properties, options ) {
+ var result,
+ stopped,
+ index = 0,
+ length = Animation.prefilters.length,
+ deferred = jQuery.Deferred().always( function() {
+
+ // Don't match elem in the :animated selector
+ delete tick.elem;
+ } ),
+ tick = function() {
+ if ( stopped ) {
+ return false;
+ }
+ var currentTime = fxNow || createFxNow(),
+ remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
+
+ // Support: Android 2.3 only
+ // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497)
+ temp = remaining / animation.duration || 0,
+ percent = 1 - temp,
+ index = 0,
+ length = animation.tweens.length;
+
+ for ( ; index < length; index++ ) {
+ animation.tweens[ index ].run( percent );
+ }
+
+ deferred.notifyWith( elem, [ animation, percent, remaining ] );
+
+ // If there's more to do, yield
+ if ( percent < 1 && length ) {
+ return remaining;
+ }
+
+ // If this was an empty animation, synthesize a final progress notification
+ if ( !length ) {
+ deferred.notifyWith( elem, [ animation, 1, 0 ] );
+ }
+
+ // Resolve the animation and report its conclusion
+ deferred.resolveWith( elem, [ animation ] );
+ return false;
+ },
+ animation = deferred.promise( {
+ elem: elem,
+ props: jQuery.extend( {}, properties ),
+ opts: jQuery.extend( true, {
+ specialEasing: {},
+ easing: jQuery.easing._default
+ }, options ),
+ originalProperties: properties,
+ originalOptions: options,
+ startTime: fxNow || createFxNow(),
+ duration: options.duration,
+ tweens: [],
+ createTween: function( prop, end ) {
+ var tween = jQuery.Tween( elem, animation.opts, prop, end,
+ animation.opts.specialEasing[ prop ] || animation.opts.easing );
+ animation.tweens.push( tween );
+ return tween;
+ },
+ stop: function( gotoEnd ) {
+ var index = 0,
+
+ // If we are going to the end, we want to run all the tweens
+ // otherwise we skip this part
+ length = gotoEnd ? animation.tweens.length : 0;
+ if ( stopped ) {
+ return this;
+ }
+ stopped = true;
+ for ( ; index < length; index++ ) {
+ animation.tweens[ index ].run( 1 );
+ }
+
+ // Resolve when we played the last frame; otherwise, reject
+ if ( gotoEnd ) {
+ deferred.notifyWith( elem, [ animation, 1, 0 ] );
+ deferred.resolveWith( elem, [ animation, gotoEnd ] );
+ } else {
+ deferred.rejectWith( elem, [ animation, gotoEnd ] );
+ }
+ return this;
+ }
+ } ),
+ props = animation.props;
+
+ propFilter( props, animation.opts.specialEasing );
+
+ for ( ; index < length; index++ ) {
+ result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts );
+ if ( result ) {
+ if ( isFunction( result.stop ) ) {
+ jQuery._queueHooks( animation.elem, animation.opts.queue ).stop =
+ result.stop.bind( result );
+ }
+ return result;
+ }
+ }
+
+ jQuery.map( props, createTween, animation );
+
+ if ( isFunction( animation.opts.start ) ) {
+ animation.opts.start.call( elem, animation );
+ }
+
+ // Attach callbacks from options
+ animation
+ .progress( animation.opts.progress )
+ .done( animation.opts.done, animation.opts.complete )
+ .fail( animation.opts.fail )
+ .always( animation.opts.always );
+
+ jQuery.fx.timer(
+ jQuery.extend( tick, {
+ elem: elem,
+ anim: animation,
+ queue: animation.opts.queue
+ } )
+ );
+
+ return animation;
+}
+
+jQuery.Animation = jQuery.extend( Animation, {
+
+ tweeners: {
+ "*": [ function( prop, value ) {
+ var tween = this.createTween( prop, value );
+ adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween );
+ return tween;
+ } ]
+ },
+
+ tweener: function( props, callback ) {
+ if ( isFunction( props ) ) {
+ callback = props;
+ props = [ "*" ];
+ } else {
+ props = props.match( rnothtmlwhite );
+ }
+
+ var prop,
+ index = 0,
+ length = props.length;
+
+ for ( ; index < length; index++ ) {
+ prop = props[ index ];
+ Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || [];
+ Animation.tweeners[ prop ].unshift( callback );
+ }
+ },
+
+ prefilters: [ defaultPrefilter ],
+
+ prefilter: function( callback, prepend ) {
+ if ( prepend ) {
+ Animation.prefilters.unshift( callback );
+ } else {
+ Animation.prefilters.push( callback );
+ }
+ }
+} );
+
+jQuery.speed = function( speed, easing, fn ) {
+ var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
+ complete: fn || !fn && easing ||
+ isFunction( speed ) && speed,
+ duration: speed,
+ easing: fn && easing || easing && !isFunction( easing ) && easing
+ };
+
+ // Go to the end state if fx are off
+ if ( jQuery.fx.off ) {
+ opt.duration = 0;
+
+ } else {
+ if ( typeof opt.duration !== "number" ) {
+ if ( opt.duration in jQuery.fx.speeds ) {
+ opt.duration = jQuery.fx.speeds[ opt.duration ];
+
+ } else {
+ opt.duration = jQuery.fx.speeds._default;
+ }
+ }
+ }
+
+ // Normalize opt.queue - true/undefined/null -> "fx"
+ if ( opt.queue == null || opt.queue === true ) {
+ opt.queue = "fx";
+ }
+
+ // Queueing
+ opt.old = opt.complete;
+
+ opt.complete = function() {
+ if ( isFunction( opt.old ) ) {
+ opt.old.call( this );
+ }
+
+ if ( opt.queue ) {
+ jQuery.dequeue( this, opt.queue );
+ }
+ };
+
+ return opt;
+};
+
+jQuery.fn.extend( {
+ fadeTo: function( speed, to, easing, callback ) {
+
+ // Show any hidden elements after setting opacity to 0
+ return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show()
+
+ // Animate to the value specified
+ .end().animate( { opacity: to }, speed, easing, callback );
+ },
+ animate: function( prop, speed, easing, callback ) {
+ var empty = jQuery.isEmptyObject( prop ),
+ optall = jQuery.speed( speed, easing, callback ),
+ doAnimation = function() {
+
+ // Operate on a copy of prop so per-property easing won't be lost
+ var anim = Animation( this, jQuery.extend( {}, prop ), optall );
+
+ // Empty animations, or finishing resolves immediately
+ if ( empty || dataPriv.get( this, "finish" ) ) {
+ anim.stop( true );
+ }
+ };
+ doAnimation.finish = doAnimation;
+
+ return empty || optall.queue === false ?
+ this.each( doAnimation ) :
+ this.queue( optall.queue, doAnimation );
+ },
+ stop: function( type, clearQueue, gotoEnd ) {
+ var stopQueue = function( hooks ) {
+ var stop = hooks.stop;
+ delete hooks.stop;
+ stop( gotoEnd );
+ };
+
+ if ( typeof type !== "string" ) {
+ gotoEnd = clearQueue;
+ clearQueue = type;
+ type = undefined;
+ }
+ if ( clearQueue && type !== false ) {
+ this.queue( type || "fx", [] );
+ }
+
+ return this.each( function() {
+ var dequeue = true,
+ index = type != null && type + "queueHooks",
+ timers = jQuery.timers,
+ data = dataPriv.get( this );
+
+ if ( index ) {
+ if ( data[ index ] && data[ index ].stop ) {
+ stopQueue( data[ index ] );
+ }
+ } else {
+ for ( index in data ) {
+ if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
+ stopQueue( data[ index ] );
+ }
+ }
+ }
+
+ for ( index = timers.length; index--; ) {
+ if ( timers[ index ].elem === this &&
+ ( type == null || timers[ index ].queue === type ) ) {
+
+ timers[ index ].anim.stop( gotoEnd );
+ dequeue = false;
+ timers.splice( index, 1 );
+ }
+ }
+
+ // Start the next in the queue if the last step wasn't forced.
+ // Timers currently will call their complete callbacks, which
+ // will dequeue but only if they were gotoEnd.
+ if ( dequeue || !gotoEnd ) {
+ jQuery.dequeue( this, type );
+ }
+ } );
+ },
+ finish: function( type ) {
+ if ( type !== false ) {
+ type = type || "fx";
+ }
+ return this.each( function() {
+ var index,
+ data = dataPriv.get( this ),
+ queue = data[ type + "queue" ],
+ hooks = data[ type + "queueHooks" ],
+ timers = jQuery.timers,
+ length = queue ? queue.length : 0;
+
+ // Enable finishing flag on private data
+ data.finish = true;
+
+ // Empty the queue first
+ jQuery.queue( this, type, [] );
+
+ if ( hooks && hooks.stop ) {
+ hooks.stop.call( this, true );
+ }
+
+ // Look for any active animations, and finish them
+ for ( index = timers.length; index--; ) {
+ if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
+ timers[ index ].anim.stop( true );
+ timers.splice( index, 1 );
+ }
+ }
+
+ // Look for any animations in the old queue and finish them
+ for ( index = 0; index < length; index++ ) {
+ if ( queue[ index ] && queue[ index ].finish ) {
+ queue[ index ].finish.call( this );
+ }
+ }
+
+ // Turn off finishing flag
+ delete data.finish;
+ } );
+ }
+} );
+
+jQuery.each( [ "toggle", "show", "hide" ], function( i, name ) {
+ var cssFn = jQuery.fn[ name ];
+ jQuery.fn[ name ] = function( speed, easing, callback ) {
+ return speed == null || typeof speed === "boolean" ?
+ cssFn.apply( this, arguments ) :
+ this.animate( genFx( name, true ), speed, easing, callback );
+ };
+} );
+
+// Generate shortcuts for custom animations
+jQuery.each( {
+ slideDown: genFx( "show" ),
+ slideUp: genFx( "hide" ),
+ slideToggle: genFx( "toggle" ),
+ fadeIn: { opacity: "show" },
+ fadeOut: { opacity: "hide" },
+ fadeToggle: { opacity: "toggle" }
+}, function( name, props ) {
+ jQuery.fn[ name ] = function( speed, easing, callback ) {
+ return this.animate( props, speed, easing, callback );
+ };
+} );
+
+jQuery.timers = [];
+jQuery.fx.tick = function() {
+ var timer,
+ i = 0,
+ timers = jQuery.timers;
+
+ fxNow = Date.now();
+
+ for ( ; i < timers.length; i++ ) {
+ timer = timers[ i ];
+
+ // Run the timer and safely remove it when done (allowing for external removal)
+ if ( !timer() && timers[ i ] === timer ) {
+ timers.splice( i--, 1 );
+ }
+ }
+
+ if ( !timers.length ) {
+ jQuery.fx.stop();
+ }
+ fxNow = undefined;
+};
+
+jQuery.fx.timer = function( timer ) {
+ jQuery.timers.push( timer );
+ jQuery.fx.start();
+};
+
+jQuery.fx.interval = 13;
+jQuery.fx.start = function() {
+ if ( inProgress ) {
+ return;
+ }
+
+ inProgress = true;
+ schedule();
+};
+
+jQuery.fx.stop = function() {
+ inProgress = null;
+};
+
+jQuery.fx.speeds = {
+ slow: 600,
+ fast: 200,
+
+ // Default speed
+ _default: 400
+};
+
+
+// Based off of the plugin by Clint Helfers, with permission.
+// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/
+jQuery.fn.delay = function( time, type ) {
+ time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
+ type = type || "fx";
+
+ return this.queue( type, function( next, hooks ) {
+ var timeout = window.setTimeout( next, time );
+ hooks.stop = function() {
+ window.clearTimeout( timeout );
+ };
+ } );
+};
+
+
+( function() {
+ var input = document.createElement( "input" ),
+ select = document.createElement( "select" ),
+ opt = select.appendChild( document.createElement( "option" ) );
+
+ input.type = "checkbox";
+
+ // Support: Android <=4.3 only
+ // Default value for a checkbox should be "on"
+ support.checkOn = input.value !== "";
+
+ // Support: IE <=11 only
+ // Must access selectedIndex to make default options select
+ support.optSelected = opt.selected;
+
+ // Support: IE <=11 only
+ // An input loses its value after becoming a radio
+ input = document.createElement( "input" );
+ input.value = "t";
+ input.type = "radio";
+ support.radioValue = input.value === "t";
+} )();
+
+
+var boolHook,
+ attrHandle = jQuery.expr.attrHandle;
+
+jQuery.fn.extend( {
+ attr: function( name, value ) {
+ return access( this, jQuery.attr, name, value, arguments.length > 1 );
+ },
+
+ removeAttr: function( name ) {
+ return this.each( function() {
+ jQuery.removeAttr( this, name );
+ } );
+ }
+} );
+
+jQuery.extend( {
+ attr: function( elem, name, value ) {
+ var ret, hooks,
+ nType = elem.nodeType;
+
+ // Don't get/set attributes on text, comment and attribute nodes
+ if ( nType === 3 || nType === 8 || nType === 2 ) {
+ return;
+ }
+
+ // Fallback to prop when attributes are not supported
+ if ( typeof elem.getAttribute === "undefined" ) {
+ return jQuery.prop( elem, name, value );
+ }
+
+ // Attribute hooks are determined by the lowercase version
+ // Grab necessary hook if one is defined
+ if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
+ hooks = jQuery.attrHooks[ name.toLowerCase() ] ||
+ ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined );
+ }
+
+ if ( value !== undefined ) {
+ if ( value === null ) {
+ jQuery.removeAttr( elem, name );
+ return;
+ }
+
+ if ( hooks && "set" in hooks &&
+ ( ret = hooks.set( elem, value, name ) ) !== undefined ) {
+ return ret;
+ }
+
+ elem.setAttribute( name, value + "" );
+ return value;
+ }
+
+ if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
+ return ret;
+ }
+
+ ret = jQuery.find.attr( elem, name );
+
+ // Non-existent attributes return null, we normalize to undefined
+ return ret == null ? undefined : ret;
+ },
+
+ attrHooks: {
+ type: {
+ set: function( elem, value ) {
+ if ( !support.radioValue && value === "radio" &&
+ nodeName( elem, "input" ) ) {
+ var val = elem.value;
+ elem.setAttribute( "type", value );
+ if ( val ) {
+ elem.value = val;
+ }
+ return value;
+ }
+ }
+ }
+ },
+
+ removeAttr: function( elem, value ) {
+ var name,
+ i = 0,
+
+ // Attribute names can contain non-HTML whitespace characters
+ // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2
+ attrNames = value && value.match( rnothtmlwhite );
+
+ if ( attrNames && elem.nodeType === 1 ) {
+ while ( ( name = attrNames[ i++ ] ) ) {
+ elem.removeAttribute( name );
+ }
+ }
+ }
+} );
+
+// Hooks for boolean attributes
+boolHook = {
+ set: function( elem, value, name ) {
+ if ( value === false ) {
+
+ // Remove boolean attributes when set to false
+ jQuery.removeAttr( elem, name );
+ } else {
+ elem.setAttribute( name, name );
+ }
+ return name;
+ }
+};
+
+jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) {
+ var getter = attrHandle[ name ] || jQuery.find.attr;
+
+ attrHandle[ name ] = function( elem, name, isXML ) {
+ var ret, handle,
+ lowercaseName = name.toLowerCase();
+
+ if ( !isXML ) {
+
+ // Avoid an infinite loop by temporarily removing this function from the getter
+ handle = attrHandle[ lowercaseName ];
+ attrHandle[ lowercaseName ] = ret;
+ ret = getter( elem, name, isXML ) != null ?
+ lowercaseName :
+ null;
+ attrHandle[ lowercaseName ] = handle;
+ }
+ return ret;
+ };
+} );
+
+
+
+
+var rfocusable = /^(?:input|select|textarea|button)$/i,
+ rclickable = /^(?:a|area)$/i;
+
+jQuery.fn.extend( {
+ prop: function( name, value ) {
+ return access( this, jQuery.prop, name, value, arguments.length > 1 );
+ },
+
+ removeProp: function( name ) {
+ return this.each( function() {
+ delete this[ jQuery.propFix[ name ] || name ];
+ } );
+ }
+} );
+
+jQuery.extend( {
+ prop: function( elem, name, value ) {
+ var ret, hooks,
+ nType = elem.nodeType;
+
+ // Don't get/set properties on text, comment and attribute nodes
+ if ( nType === 3 || nType === 8 || nType === 2 ) {
+ return;
+ }
+
+ if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
+
+ // Fix name and attach hooks
+ name = jQuery.propFix[ name ] || name;
+ hooks = jQuery.propHooks[ name ];
+ }
+
+ if ( value !== undefined ) {
+ if ( hooks && "set" in hooks &&
+ ( ret = hooks.set( elem, value, name ) ) !== undefined ) {
+ return ret;
+ }
+
+ return ( elem[ name ] = value );
+ }
+
+ if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
+ return ret;
+ }
+
+ return elem[ name ];
+ },
+
+ propHooks: {
+ tabIndex: {
+ get: function( elem ) {
+
+ // Support: IE <=9 - 11 only
+ // elem.tabIndex doesn't always return the
+ // correct value when it hasn't been explicitly set
+ // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
+ // Use proper attribute retrieval(#12072)
+ var tabindex = jQuery.find.attr( elem, "tabindex" );
+
+ if ( tabindex ) {
+ return parseInt( tabindex, 10 );
+ }
+
+ if (
+ rfocusable.test( elem.nodeName ) ||
+ rclickable.test( elem.nodeName ) &&
+ elem.href
+ ) {
+ return 0;
+ }
+
+ return -1;
+ }
+ }
+ },
+
+ propFix: {
+ "for": "htmlFor",
+ "class": "className"
+ }
+} );
+
+// Support: IE <=11 only
+// Accessing the selectedIndex property
+// forces the browser to respect setting selected
+// on the option
+// The getter ensures a default option is selected
+// when in an optgroup
+// eslint rule "no-unused-expressions" is disabled for this code
+// since it considers such accessions noop
+if ( !support.optSelected ) {
+ jQuery.propHooks.selected = {
+ get: function( elem ) {
+
+ /* eslint no-unused-expressions: "off" */
+
+ var parent = elem.parentNode;
+ if ( parent && parent.parentNode ) {
+ parent.parentNode.selectedIndex;
+ }
+ return null;
+ },
+ set: function( elem ) {
+
+ /* eslint no-unused-expressions: "off" */
+
+ var parent = elem.parentNode;
+ if ( parent ) {
+ parent.selectedIndex;
+
+ if ( parent.parentNode ) {
+ parent.parentNode.selectedIndex;
+ }
+ }
+ }
+ };
+}
+
+jQuery.each( [
+ "tabIndex",
+ "readOnly",
+ "maxLength",
+ "cellSpacing",
+ "cellPadding",
+ "rowSpan",
+ "colSpan",
+ "useMap",
+ "frameBorder",
+ "contentEditable"
+], function() {
+ jQuery.propFix[ this.toLowerCase() ] = this;
+} );
+
+
+
+
+ // Strip and collapse whitespace according to HTML spec
+ // https://infra.spec.whatwg.org/#strip-and-collapse-ascii-whitespace
+ function stripAndCollapse( value ) {
+ var tokens = value.match( rnothtmlwhite ) || [];
+ return tokens.join( " " );
+ }
+
+
+function getClass( elem ) {
+ return elem.getAttribute && elem.getAttribute( "class" ) || "";
+}
+
+function classesToArray( value ) {
+ if ( Array.isArray( value ) ) {
+ return value;
+ }
+ if ( typeof value === "string" ) {
+ return value.match( rnothtmlwhite ) || [];
+ }
+ return [];
+}
+
+jQuery.fn.extend( {
+ addClass: function( value ) {
+ var classes, elem, cur, curValue, clazz, j, finalValue,
+ i = 0;
+
+ if ( isFunction( value ) ) {
+ return this.each( function( j ) {
+ jQuery( this ).addClass( value.call( this, j, getClass( this ) ) );
+ } );
+ }
+
+ classes = classesToArray( value );
+
+ if ( classes.length ) {
+ while ( ( elem = this[ i++ ] ) ) {
+ curValue = getClass( elem );
+ cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
+
+ if ( cur ) {
+ j = 0;
+ while ( ( clazz = classes[ j++ ] ) ) {
+ if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
+ cur += clazz + " ";
+ }
+ }
+
+ // Only assign if different to avoid unneeded rendering.
+ finalValue = stripAndCollapse( cur );
+ if ( curValue !== finalValue ) {
+ elem.setAttribute( "class", finalValue );
+ }
+ }
+ }
+ }
+
+ return this;
+ },
+
+ removeClass: function( value ) {
+ var classes, elem, cur, curValue, clazz, j, finalValue,
+ i = 0;
+
+ if ( isFunction( value ) ) {
+ return this.each( function( j ) {
+ jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) );
+ } );
+ }
+
+ if ( !arguments.length ) {
+ return this.attr( "class", "" );
+ }
+
+ classes = classesToArray( value );
+
+ if ( classes.length ) {
+ while ( ( elem = this[ i++ ] ) ) {
+ curValue = getClass( elem );
+
+ // This expression is here for better compressibility (see addClass)
+ cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
+
+ if ( cur ) {
+ j = 0;
+ while ( ( clazz = classes[ j++ ] ) ) {
+
+ // Remove *all* instances
+ while ( cur.indexOf( " " + clazz + " " ) > -1 ) {
+ cur = cur.replace( " " + clazz + " ", " " );
+ }
+ }
+
+ // Only assign if different to avoid unneeded rendering.
+ finalValue = stripAndCollapse( cur );
+ if ( curValue !== finalValue ) {
+ elem.setAttribute( "class", finalValue );
+ }
+ }
+ }
+ }
+
+ return this;
+ },
+
+ toggleClass: function( value, stateVal ) {
+ var type = typeof value,
+ isValidValue = type === "string" || Array.isArray( value );
+
+ if ( typeof stateVal === "boolean" && isValidValue ) {
+ return stateVal ? this.addClass( value ) : this.removeClass( value );
+ }
+
+ if ( isFunction( value ) ) {
+ return this.each( function( i ) {
+ jQuery( this ).toggleClass(
+ value.call( this, i, getClass( this ), stateVal ),
+ stateVal
+ );
+ } );
+ }
+
+ return this.each( function() {
+ var className, i, self, classNames;
+
+ if ( isValidValue ) {
+
+ // Toggle individual class names
+ i = 0;
+ self = jQuery( this );
+ classNames = classesToArray( value );
+
+ while ( ( className = classNames[ i++ ] ) ) {
+
+ // Check each className given, space separated list
+ if ( self.hasClass( className ) ) {
+ self.removeClass( className );
+ } else {
+ self.addClass( className );
+ }
+ }
+
+ // Toggle whole class name
+ } else if ( value === undefined || type === "boolean" ) {
+ className = getClass( this );
+ if ( className ) {
+
+ // Store className if set
+ dataPriv.set( this, "__className__", className );
+ }
+
+ // If the element has a class name or if we're passed `false`,
+ // then remove the whole classname (if there was one, the above saved it).
+ // Otherwise bring back whatever was previously saved (if anything),
+ // falling back to the empty string if nothing was stored.
+ if ( this.setAttribute ) {
+ this.setAttribute( "class",
+ className || value === false ?
+ "" :
+ dataPriv.get( this, "__className__" ) || ""
+ );
+ }
+ }
+ } );
+ },
+
+ hasClass: function( selector ) {
+ var className, elem,
+ i = 0;
+
+ className = " " + selector + " ";
+ while ( ( elem = this[ i++ ] ) ) {
+ if ( elem.nodeType === 1 &&
+ ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) {
+ return true;
+ }
+ }
+
+ return false;
+ }
+} );
+
+
+
+
+var rreturn = /\r/g;
+
+jQuery.fn.extend( {
+ val: function( value ) {
+ var hooks, ret, valueIsFunction,
+ elem = this[ 0 ];
+
+ if ( !arguments.length ) {
+ if ( elem ) {
+ hooks = jQuery.valHooks[ elem.type ] ||
+ jQuery.valHooks[ elem.nodeName.toLowerCase() ];
+
+ if ( hooks &&
+ "get" in hooks &&
+ ( ret = hooks.get( elem, "value" ) ) !== undefined
+ ) {
+ return ret;
+ }
+
+ ret = elem.value;
+
+ // Handle most common string cases
+ if ( typeof ret === "string" ) {
+ return ret.replace( rreturn, "" );
+ }
+
+ // Handle cases where value is null/undef or number
+ return ret == null ? "" : ret;
+ }
+
+ return;
+ }
+
+ valueIsFunction = isFunction( value );
+
+ return this.each( function( i ) {
+ var val;
+
+ if ( this.nodeType !== 1 ) {
+ return;
+ }
+
+ if ( valueIsFunction ) {
+ val = value.call( this, i, jQuery( this ).val() );
+ } else {
+ val = value;
+ }
+
+ // Treat null/undefined as ""; convert numbers to string
+ if ( val == null ) {
+ val = "";
+
+ } else if ( typeof val === "number" ) {
+ val += "";
+
+ } else if ( Array.isArray( val ) ) {
+ val = jQuery.map( val, function( value ) {
+ return value == null ? "" : value + "";
+ } );
+ }
+
+ hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
+
+ // If set returns undefined, fall back to normal setting
+ if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) {
+ this.value = val;
+ }
+ } );
+ }
+} );
+
+jQuery.extend( {
+ valHooks: {
+ option: {
+ get: function( elem ) {
+
+ var val = jQuery.find.attr( elem, "value" );
+ return val != null ?
+ val :
+
+ // Support: IE <=10 - 11 only
+ // option.text throws exceptions (#14686, #14858)
+ // Strip and collapse whitespace
+ // https://html.spec.whatwg.org/#strip-and-collapse-whitespace
+ stripAndCollapse( jQuery.text( elem ) );
+ }
+ },
+ select: {
+ get: function( elem ) {
+ var value, option, i,
+ options = elem.options,
+ index = elem.selectedIndex,
+ one = elem.type === "select-one",
+ values = one ? null : [],
+ max = one ? index + 1 : options.length;
+
+ if ( index < 0 ) {
+ i = max;
+
+ } else {
+ i = one ? index : 0;
+ }
+
+ // Loop through all the selected options
+ for ( ; i < max; i++ ) {
+ option = options[ i ];
+
+ // Support: IE <=9 only
+ // IE8-9 doesn't update selected after form reset (#2551)
+ if ( ( option.selected || i === index ) &&
+
+ // Don't return options that are disabled or in a disabled optgroup
+ !option.disabled &&
+ ( !option.parentNode.disabled ||
+ !nodeName( option.parentNode, "optgroup" ) ) ) {
+
+ // Get the specific value for the option
+ value = jQuery( option ).val();
+
+ // We don't need an array for one selects
+ if ( one ) {
+ return value;
+ }
+
+ // Multi-Selects return an array
+ values.push( value );
+ }
+ }
+
+ return values;
+ },
+
+ set: function( elem, value ) {
+ var optionSet, option,
+ options = elem.options,
+ values = jQuery.makeArray( value ),
+ i = options.length;
+
+ while ( i-- ) {
+ option = options[ i ];
+
+ /* eslint-disable no-cond-assign */
+
+ if ( option.selected =
+ jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1
+ ) {
+ optionSet = true;
+ }
+
+ /* eslint-enable no-cond-assign */
+ }
+
+ // Force browsers to behave consistently when non-matching value is set
+ if ( !optionSet ) {
+ elem.selectedIndex = -1;
+ }
+ return values;
+ }
+ }
+ }
+} );
+
+// Radios and checkboxes getter/setter
+jQuery.each( [ "radio", "checkbox" ], function() {
+ jQuery.valHooks[ this ] = {
+ set: function( elem, value ) {
+ if ( Array.isArray( value ) ) {
+ return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 );
+ }
+ }
+ };
+ if ( !support.checkOn ) {
+ jQuery.valHooks[ this ].get = function( elem ) {
+ return elem.getAttribute( "value" ) === null ? "on" : elem.value;
+ };
+ }
+} );
+
+
+
+
+// Return jQuery for attributes-only inclusion
+
+
+support.focusin = "onfocusin" in window;
+
+
+var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
+ stopPropagationCallback = function( e ) {
+ e.stopPropagation();
+ };
+
+jQuery.extend( jQuery.event, {
+
+ trigger: function( event, data, elem, onlyHandlers ) {
+
+ var i, cur, tmp, bubbleType, ontype, handle, special, lastElement,
+ eventPath = [ elem || document ],
+ type = hasOwn.call( event, "type" ) ? event.type : event,
+ namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : [];
+
+ cur = lastElement = tmp = elem = elem || document;
+
+ // Don't do events on text and comment nodes
+ if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
+ return;
+ }
+
+ // focus/blur morphs to focusin/out; ensure we're not firing them right now
+ if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
+ return;
+ }
+
+ if ( type.indexOf( "." ) > -1 ) {
+
+ // Namespaced trigger; create a regexp to match event type in handle()
+ namespaces = type.split( "." );
+ type = namespaces.shift();
+ namespaces.sort();
+ }
+ ontype = type.indexOf( ":" ) < 0 && "on" + type;
+
+ // Caller can pass in a jQuery.Event object, Object, or just an event type string
+ event = event[ jQuery.expando ] ?
+ event :
+ new jQuery.Event( type, typeof event === "object" && event );
+
+ // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
+ event.isTrigger = onlyHandlers ? 2 : 3;
+ event.namespace = namespaces.join( "." );
+ event.rnamespace = event.namespace ?
+ new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) :
+ null;
+
+ // Clean up the event in case it is being reused
+ event.result = undefined;
+ if ( !event.target ) {
+ event.target = elem;
+ }
+
+ // Clone any incoming data and prepend the event, creating the handler arg list
+ data = data == null ?
+ [ event ] :
+ jQuery.makeArray( data, [ event ] );
+
+ // Allow special events to draw outside the lines
+ special = jQuery.event.special[ type ] || {};
+ if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
+ return;
+ }
+
+ // Determine event propagation path in advance, per W3C events spec (#9951)
+ // Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
+ if ( !onlyHandlers && !special.noBubble && !isWindow( elem ) ) {
+
+ bubbleType = special.delegateType || type;
+ if ( !rfocusMorph.test( bubbleType + type ) ) {
+ cur = cur.parentNode;
+ }
+ for ( ; cur; cur = cur.parentNode ) {
+ eventPath.push( cur );
+ tmp = cur;
+ }
+
+ // Only add window if we got to document (e.g., not plain obj or detached DOM)
+ if ( tmp === ( elem.ownerDocument || document ) ) {
+ eventPath.push( tmp.defaultView || tmp.parentWindow || window );
+ }
+ }
+
+ // Fire handlers on the event path
+ i = 0;
+ while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) {
+ lastElement = cur;
+ event.type = i > 1 ?
+ bubbleType :
+ special.bindType || type;
+
+ // jQuery handler
+ handle = ( dataPriv.get( cur, "events" ) || {} )[ event.type ] &&
+ dataPriv.get( cur, "handle" );
+ if ( handle ) {
+ handle.apply( cur, data );
+ }
+
+ // Native handler
+ handle = ontype && cur[ ontype ];
+ if ( handle && handle.apply && acceptData( cur ) ) {
+ event.result = handle.apply( cur, data );
+ if ( event.result === false ) {
+ event.preventDefault();
+ }
+ }
+ }
+ event.type = type;
+
+ // If nobody prevented the default action, do it now
+ if ( !onlyHandlers && !event.isDefaultPrevented() ) {
+
+ if ( ( !special._default ||
+ special._default.apply( eventPath.pop(), data ) === false ) &&
+ acceptData( elem ) ) {
+
+ // Call a native DOM method on the target with the same name as the event.
+ // Don't do default actions on window, that's where global variables be (#6170)
+ if ( ontype && isFunction( elem[ type ] ) && !isWindow( elem ) ) {
+
+ // Don't re-trigger an onFOO event when we call its FOO() method
+ tmp = elem[ ontype ];
+
+ if ( tmp ) {
+ elem[ ontype ] = null;
+ }
+
+ // Prevent re-triggering of the same event, since we already bubbled it above
+ jQuery.event.triggered = type;
+
+ if ( event.isPropagationStopped() ) {
+ lastElement.addEventListener( type, stopPropagationCallback );
+ }
+
+ elem[ type ]();
+
+ if ( event.isPropagationStopped() ) {
+ lastElement.removeEventListener( type, stopPropagationCallback );
+ }
+
+ jQuery.event.triggered = undefined;
+
+ if ( tmp ) {
+ elem[ ontype ] = tmp;
+ }
+ }
+ }
+ }
+
+ return event.result;
+ },
+
+ // Piggyback on a donor event to simulate a different one
+ // Used only for `focus(in | out)` events
+ simulate: function( type, elem, event ) {
+ var e = jQuery.extend(
+ new jQuery.Event(),
+ event,
+ {
+ type: type,
+ isSimulated: true
+ }
+ );
+
+ jQuery.event.trigger( e, null, elem );
+ }
+
+} );
+
+jQuery.fn.extend( {
+
+ trigger: function( type, data ) {
+ return this.each( function() {
+ jQuery.event.trigger( type, data, this );
+ } );
+ },
+ triggerHandler: function( type, data ) {
+ var elem = this[ 0 ];
+ if ( elem ) {
+ return jQuery.event.trigger( type, data, elem, true );
+ }
+ }
+} );
+
+
+// Support: Firefox <=44
+// Firefox doesn't have focus(in | out) events
+// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787
+//
+// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1
+// focus(in | out) events fire after focus & blur events,
+// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order
+// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857
+if ( !support.focusin ) {
+ jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) {
+
+ // Attach a single capturing handler on the document while someone wants focusin/focusout
+ var handler = function( event ) {
+ jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) );
+ };
+
+ jQuery.event.special[ fix ] = {
+ setup: function() {
+ var doc = this.ownerDocument || this,
+ attaches = dataPriv.access( doc, fix );
+
+ if ( !attaches ) {
+ doc.addEventListener( orig, handler, true );
+ }
+ dataPriv.access( doc, fix, ( attaches || 0 ) + 1 );
+ },
+ teardown: function() {
+ var doc = this.ownerDocument || this,
+ attaches = dataPriv.access( doc, fix ) - 1;
+
+ if ( !attaches ) {
+ doc.removeEventListener( orig, handler, true );
+ dataPriv.remove( doc, fix );
+
+ } else {
+ dataPriv.access( doc, fix, attaches );
+ }
+ }
+ };
+ } );
+}
+var location = window.location;
+
+var nonce = Date.now();
+
+var rquery = ( /\?/ );
+
+
+
+// Cross-browser xml parsing
+jQuery.parseXML = function( data ) {
+ var xml;
+ if ( !data || typeof data !== "string" ) {
+ return null;
+ }
+
+ // Support: IE 9 - 11 only
+ // IE throws on parseFromString with invalid input.
+ try {
+ xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" );
+ } catch ( e ) {
+ xml = undefined;
+ }
+
+ if ( !xml || xml.getElementsByTagName( "parsererror" ).length ) {
+ jQuery.error( "Invalid XML: " + data );
+ }
+ return xml;
+};
+
+
+var
+ rbracket = /\[\]$/,
+ rCRLF = /\r?\n/g,
+ rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
+ rsubmittable = /^(?:input|select|textarea|keygen)/i;
+
+function buildParams( prefix, obj, traditional, add ) {
+ var name;
+
+ if ( Array.isArray( obj ) ) {
+
+ // Serialize array item.
+ jQuery.each( obj, function( i, v ) {
+ if ( traditional || rbracket.test( prefix ) ) {
+
+ // Treat each array item as a scalar.
+ add( prefix, v );
+
+ } else {
+
+ // Item is non-scalar (array or object), encode its numeric index.
+ buildParams(
+ prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]",
+ v,
+ traditional,
+ add
+ );
+ }
+ } );
+
+ } else if ( !traditional && toType( obj ) === "object" ) {
+
+ // Serialize object item.
+ for ( name in obj ) {
+ buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
+ }
+
+ } else {
+
+ // Serialize scalar item.
+ add( prefix, obj );
+ }
+}
+
+// Serialize an array of form elements or a set of
+// key/values into a query string
+jQuery.param = function( a, traditional ) {
+ var prefix,
+ s = [],
+ add = function( key, valueOrFunction ) {
+
+ // If value is a function, invoke it and use its return value
+ var value = isFunction( valueOrFunction ) ?
+ valueOrFunction() :
+ valueOrFunction;
+
+ s[ s.length ] = encodeURIComponent( key ) + "=" +
+ encodeURIComponent( value == null ? "" : value );
+ };
+
+ // If an array was passed in, assume that it is an array of form elements.
+ if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
+
+ // Serialize the form elements
+ jQuery.each( a, function() {
+ add( this.name, this.value );
+ } );
+
+ } else {
+
+ // If traditional, encode the "old" way (the way 1.3.2 or older
+ // did it), otherwise encode params recursively.
+ for ( prefix in a ) {
+ buildParams( prefix, a[ prefix ], traditional, add );
+ }
+ }
+
+ // Return the resulting serialization
+ return s.join( "&" );
+};
+
+jQuery.fn.extend( {
+ serialize: function() {
+ return jQuery.param( this.serializeArray() );
+ },
+ serializeArray: function() {
+ return this.map( function() {
+
+ // Can add propHook for "elements" to filter or add form elements
+ var elements = jQuery.prop( this, "elements" );
+ return elements ? jQuery.makeArray( elements ) : this;
+ } )
+ .filter( function() {
+ var type = this.type;
+
+ // Use .is( ":disabled" ) so that fieldset[disabled] works
+ return this.name && !jQuery( this ).is( ":disabled" ) &&
+ rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
+ ( this.checked || !rcheckableType.test( type ) );
+ } )
+ .map( function( i, elem ) {
+ var val = jQuery( this ).val();
+
+ if ( val == null ) {
+ return null;
+ }
+
+ if ( Array.isArray( val ) ) {
+ return jQuery.map( val, function( val ) {
+ return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+ } );
+ }
+
+ return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+ } ).get();
+ }
+} );
+
+
+var
+ r20 = /%20/g,
+ rhash = /#.*$/,
+ rantiCache = /([?&])_=[^&]*/,
+ rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg,
+
+ // #7653, #8125, #8152: local protocol detection
+ rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
+ rnoContent = /^(?:GET|HEAD)$/,
+ rprotocol = /^\/\//,
+
+ /* Prefilters
+ * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
+ * 2) These are called:
+ * - BEFORE asking for a transport
+ * - AFTER param serialization (s.data is a string if s.processData is true)
+ * 3) key is the dataType
+ * 4) the catchall symbol "*" can be used
+ * 5) execution will start with transport dataType and THEN continue down to "*" if needed
+ */
+ prefilters = {},
+
+ /* Transports bindings
+ * 1) key is the dataType
+ * 2) the catchall symbol "*" can be used
+ * 3) selection will start with transport dataType and THEN go to "*" if needed
+ */
+ transports = {},
+
+ // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
+ allTypes = "*/".concat( "*" ),
+
+ // Anchor tag for parsing the document origin
+ originAnchor = document.createElement( "a" );
+ originAnchor.href = location.href;
+
+// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
+function addToPrefiltersOrTransports( structure ) {
+
+ // dataTypeExpression is optional and defaults to "*"
+ return function( dataTypeExpression, func ) {
+
+ if ( typeof dataTypeExpression !== "string" ) {
+ func = dataTypeExpression;
+ dataTypeExpression = "*";
+ }
+
+ var dataType,
+ i = 0,
+ dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || [];
+
+ if ( isFunction( func ) ) {
+
+ // For each dataType in the dataTypeExpression
+ while ( ( dataType = dataTypes[ i++ ] ) ) {
+
+ // Prepend if requested
+ if ( dataType[ 0 ] === "+" ) {
+ dataType = dataType.slice( 1 ) || "*";
+ ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func );
+
+ // Otherwise append
+ } else {
+ ( structure[ dataType ] = structure[ dataType ] || [] ).push( func );
+ }
+ }
+ }
+ };
+}
+
+// Base inspection function for prefilters and transports
+function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) {
+
+ var inspected = {},
+ seekingTransport = ( structure === transports );
+
+ function inspect( dataType ) {
+ var selected;
+ inspected[ dataType ] = true;
+ jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
+ var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
+ if ( typeof dataTypeOrTransport === "string" &&
+ !seekingTransport && !inspected[ dataTypeOrTransport ] ) {
+
+ options.dataTypes.unshift( dataTypeOrTransport );
+ inspect( dataTypeOrTransport );
+ return false;
+ } else if ( seekingTransport ) {
+ return !( selected = dataTypeOrTransport );
+ }
+ } );
+ return selected;
+ }
+
+ return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" );
+}
+
+// A special extend for ajax options
+// that takes "flat" options (not to be deep extended)
+// Fixes #9887
+function ajaxExtend( target, src ) {
+ var key, deep,
+ flatOptions = jQuery.ajaxSettings.flatOptions || {};
+
+ for ( key in src ) {
+ if ( src[ key ] !== undefined ) {
+ ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ];
+ }
+ }
+ if ( deep ) {
+ jQuery.extend( true, target, deep );
+ }
+
+ return target;
+}
+
+/* Handles responses to an ajax request:
+ * - finds the right dataType (mediates between content-type and expected dataType)
+ * - returns the corresponding response
+ */
+function ajaxHandleResponses( s, jqXHR, responses ) {
+
+ var ct, type, finalDataType, firstDataType,
+ contents = s.contents,
+ dataTypes = s.dataTypes;
+
+ // Remove auto dataType and get content-type in the process
+ while ( dataTypes[ 0 ] === "*" ) {
+ dataTypes.shift();
+ if ( ct === undefined ) {
+ ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" );
+ }
+ }
+
+ // Check if we're dealing with a known content-type
+ if ( ct ) {
+ for ( type in contents ) {
+ if ( contents[ type ] && contents[ type ].test( ct ) ) {
+ dataTypes.unshift( type );
+ break;
+ }
+ }
+ }
+
+ // Check to see if we have a response for the expected dataType
+ if ( dataTypes[ 0 ] in responses ) {
+ finalDataType = dataTypes[ 0 ];
+ } else {
+
+ // Try convertible dataTypes
+ for ( type in responses ) {
+ if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) {
+ finalDataType = type;
+ break;
+ }
+ if ( !firstDataType ) {
+ firstDataType = type;
+ }
+ }
+
+ // Or just use first one
+ finalDataType = finalDataType || firstDataType;
+ }
+
+ // If we found a dataType
+ // We add the dataType to the list if needed
+ // and return the corresponding response
+ if ( finalDataType ) {
+ if ( finalDataType !== dataTypes[ 0 ] ) {
+ dataTypes.unshift( finalDataType );
+ }
+ return responses[ finalDataType ];
+ }
+}
+
+/* Chain conversions given the request and the original response
+ * Also sets the responseXXX fields on the jqXHR instance
+ */
+function ajaxConvert( s, response, jqXHR, isSuccess ) {
+ var conv2, current, conv, tmp, prev,
+ converters = {},
+
+ // Work with a copy of dataTypes in case we need to modify it for conversion
+ dataTypes = s.dataTypes.slice();
+
+ // Create converters map with lowercased keys
+ if ( dataTypes[ 1 ] ) {
+ for ( conv in s.converters ) {
+ converters[ conv.toLowerCase() ] = s.converters[ conv ];
+ }
+ }
+
+ current = dataTypes.shift();
+
+ // Convert to each sequential dataType
+ while ( current ) {
+
+ if ( s.responseFields[ current ] ) {
+ jqXHR[ s.responseFields[ current ] ] = response;
+ }
+
+ // Apply the dataFilter if provided
+ if ( !prev && isSuccess && s.dataFilter ) {
+ response = s.dataFilter( response, s.dataType );
+ }
+
+ prev = current;
+ current = dataTypes.shift();
+
+ if ( current ) {
+
+ // There's only work to do if current dataType is non-auto
+ if ( current === "*" ) {
+
+ current = prev;
+
+ // Convert response if prev dataType is non-auto and differs from current
+ } else if ( prev !== "*" && prev !== current ) {
+
+ // Seek a direct converter
+ conv = converters[ prev + " " + current ] || converters[ "* " + current ];
+
+ // If none found, seek a pair
+ if ( !conv ) {
+ for ( conv2 in converters ) {
+
+ // If conv2 outputs current
+ tmp = conv2.split( " " );
+ if ( tmp[ 1 ] === current ) {
+
+ // If prev can be converted to accepted input
+ conv = converters[ prev + " " + tmp[ 0 ] ] ||
+ converters[ "* " + tmp[ 0 ] ];
+ if ( conv ) {
+
+ // Condense equivalence converters
+ if ( conv === true ) {
+ conv = converters[ conv2 ];
+
+ // Otherwise, insert the intermediate dataType
+ } else if ( converters[ conv2 ] !== true ) {
+ current = tmp[ 0 ];
+ dataTypes.unshift( tmp[ 1 ] );
+ }
+ break;
+ }
+ }
+ }
+ }
+
+ // Apply converter (if not an equivalence)
+ if ( conv !== true ) {
+
+ // Unless errors are allowed to bubble, catch and return them
+ if ( conv && s.throws ) {
+ response = conv( response );
+ } else {
+ try {
+ response = conv( response );
+ } catch ( e ) {
+ return {
+ state: "parsererror",
+ error: conv ? e : "No conversion from " + prev + " to " + current
+ };
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return { state: "success", data: response };
+}
+
+jQuery.extend( {
+
+ // Counter for holding the number of active queries
+ active: 0,
+
+ // Last-Modified header cache for next request
+ lastModified: {},
+ etag: {},
+
+ ajaxSettings: {
+ url: location.href,
+ type: "GET",
+ isLocal: rlocalProtocol.test( location.protocol ),
+ global: true,
+ processData: true,
+ async: true,
+ contentType: "application/x-www-form-urlencoded; charset=UTF-8",
+
+ /*
+ timeout: 0,
+ data: null,
+ dataType: null,
+ username: null,
+ password: null,
+ cache: null,
+ throws: false,
+ traditional: false,
+ headers: {},
+ */
+
+ accepts: {
+ "*": allTypes,
+ text: "text/plain",
+ html: "text/html",
+ xml: "application/xml, text/xml",
+ json: "application/json, text/javascript"
+ },
+
+ contents: {
+ xml: /\bxml\b/,
+ html: /\bhtml/,
+ json: /\bjson\b/
+ },
+
+ responseFields: {
+ xml: "responseXML",
+ text: "responseText",
+ json: "responseJSON"
+ },
+
+ // Data converters
+ // Keys separate source (or catchall "*") and destination types with a single space
+ converters: {
+
+ // Convert anything to text
+ "* text": String,
+
+ // Text to html (true = no transformation)
+ "text html": true,
+
+ // Evaluate text as a json expression
+ "text json": JSON.parse,
+
+ // Parse text as xml
+ "text xml": jQuery.parseXML
+ },
+
+ // For options that shouldn't be deep extended:
+ // you can add your own custom options here if
+ // and when you create one that shouldn't be
+ // deep extended (see ajaxExtend)
+ flatOptions: {
+ url: true,
+ context: true
+ }
+ },
+
+ // Creates a full fledged settings object into target
+ // with both ajaxSettings and settings fields.
+ // If target is omitted, writes into ajaxSettings.
+ ajaxSetup: function( target, settings ) {
+ return settings ?
+
+ // Building a settings object
+ ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) :
+
+ // Extending ajaxSettings
+ ajaxExtend( jQuery.ajaxSettings, target );
+ },
+
+ ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
+ ajaxTransport: addToPrefiltersOrTransports( transports ),
+
+ // Main method
+ ajax: function( url, options ) {
+
+ // If url is an object, simulate pre-1.5 signature
+ if ( typeof url === "object" ) {
+ options = url;
+ url = undefined;
+ }
+
+ // Force options to be an object
+ options = options || {};
+
+ var transport,
+
+ // URL without anti-cache param
+ cacheURL,
+
+ // Response headers
+ responseHeadersString,
+ responseHeaders,
+
+ // timeout handle
+ timeoutTimer,
+
+ // Url cleanup var
+ urlAnchor,
+
+ // Request state (becomes false upon send and true upon completion)
+ completed,
+
+ // To know if global events are to be dispatched
+ fireGlobals,
+
+ // Loop variable
+ i,
+
+ // uncached part of the url
+ uncached,
+
+ // Create the final options object
+ s = jQuery.ajaxSetup( {}, options ),
+
+ // Callbacks context
+ callbackContext = s.context || s,
+
+ // Context for global events is callbackContext if it is a DOM node or jQuery collection
+ globalEventContext = s.context &&
+ ( callbackContext.nodeType || callbackContext.jquery ) ?
+ jQuery( callbackContext ) :
+ jQuery.event,
+
+ // Deferreds
+ deferred = jQuery.Deferred(),
+ completeDeferred = jQuery.Callbacks( "once memory" ),
+
+ // Status-dependent callbacks
+ statusCode = s.statusCode || {},
+
+ // Headers (they are sent all at once)
+ requestHeaders = {},
+ requestHeadersNames = {},
+
+ // Default abort message
+ strAbort = "canceled",
+
+ // Fake xhr
+ jqXHR = {
+ readyState: 0,
+
+ // Builds headers hashtable if needed
+ getResponseHeader: function( key ) {
+ var match;
+ if ( completed ) {
+ if ( !responseHeaders ) {
+ responseHeaders = {};
+ while ( ( match = rheaders.exec( responseHeadersString ) ) ) {
+ responseHeaders[ match[ 1 ].toLowerCase() ] = match[ 2 ];
+ }
+ }
+ match = responseHeaders[ key.toLowerCase() ];
+ }
+ return match == null ? null : match;
+ },
+
+ // Raw string
+ getAllResponseHeaders: function() {
+ return completed ? responseHeadersString : null;
+ },
+
+ // Caches the header
+ setRequestHeader: function( name, value ) {
+ if ( completed == null ) {
+ name = requestHeadersNames[ name.toLowerCase() ] =
+ requestHeadersNames[ name.toLowerCase() ] || name;
+ requestHeaders[ name ] = value;
+ }
+ return this;
+ },
+
+ // Overrides response content-type header
+ overrideMimeType: function( type ) {
+ if ( completed == null ) {
+ s.mimeType = type;
+ }
+ return this;
+ },
+
+ // Status-dependent callbacks
+ statusCode: function( map ) {
+ var code;
+ if ( map ) {
+ if ( completed ) {
+
+ // Execute the appropriate callbacks
+ jqXHR.always( map[ jqXHR.status ] );
+ } else {
+
+ // Lazy-add the new callbacks in a way that preserves old ones
+ for ( code in map ) {
+ statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
+ }
+ }
+ }
+ return this;
+ },
+
+ // Cancel the request
+ abort: function( statusText ) {
+ var finalText = statusText || strAbort;
+ if ( transport ) {
+ transport.abort( finalText );
+ }
+ done( 0, finalText );
+ return this;
+ }
+ };
+
+ // Attach deferreds
+ deferred.promise( jqXHR );
+
+ // Add protocol if not provided (prefilters might expect it)
+ // Handle falsy url in the settings object (#10093: consistency with old signature)
+ // We also use the url parameter if available
+ s.url = ( ( url || s.url || location.href ) + "" )
+ .replace( rprotocol, location.protocol + "//" );
+
+ // Alias method option to type as per ticket #12004
+ s.type = options.method || options.type || s.method || s.type;
+
+ // Extract dataTypes list
+ s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ];
+
+ // A cross-domain request is in order when the origin doesn't match the current origin.
+ if ( s.crossDomain == null ) {
+ urlAnchor = document.createElement( "a" );
+
+ // Support: IE <=8 - 11, Edge 12 - 15
+ // IE throws exception on accessing the href property if url is malformed,
+ // e.g. http://example.com:80x/
+ try {
+ urlAnchor.href = s.url;
+
+ // Support: IE <=8 - 11 only
+ // Anchor's host property isn't correctly set when s.url is relative
+ urlAnchor.href = urlAnchor.href;
+ s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !==
+ urlAnchor.protocol + "//" + urlAnchor.host;
+ } catch ( e ) {
+
+ // If there is an error parsing the URL, assume it is crossDomain,
+ // it can be rejected by the transport if it is invalid
+ s.crossDomain = true;
+ }
+ }
+
+ // Convert data if not already a string
+ if ( s.data && s.processData && typeof s.data !== "string" ) {
+ s.data = jQuery.param( s.data, s.traditional );
+ }
+
+ // Apply prefilters
+ inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
+
+ // If request was aborted inside a prefilter, stop there
+ if ( completed ) {
+ return jqXHR;
+ }
+
+ // We can fire global events as of now if asked to
+ // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118)
+ fireGlobals = jQuery.event && s.global;
+
+ // Watch for a new set of requests
+ if ( fireGlobals && jQuery.active++ === 0 ) {
+ jQuery.event.trigger( "ajaxStart" );
+ }
+
+ // Uppercase the type
+ s.type = s.type.toUpperCase();
+
+ // Determine if request has content
+ s.hasContent = !rnoContent.test( s.type );
+
+ // Save the URL in case we're toying with the If-Modified-Since
+ // and/or If-None-Match header later on
+ // Remove hash to simplify url manipulation
+ cacheURL = s.url.replace( rhash, "" );
+
+ // More options handling for requests with no content
+ if ( !s.hasContent ) {
+
+ // Remember the hash so we can put it back
+ uncached = s.url.slice( cacheURL.length );
+
+ // If data is available and should be processed, append data to url
+ if ( s.data && ( s.processData || typeof s.data === "string" ) ) {
+ cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data;
+
+ // #9682: remove data so that it's not used in an eventual retry
+ delete s.data;
+ }
+
+ // Add or update anti-cache param if needed
+ if ( s.cache === false ) {
+ cacheURL = cacheURL.replace( rantiCache, "$1" );
+ uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce++ ) + uncached;
+ }
+
+ // Put hash and anti-cache on the URL that will be requested (gh-1732)
+ s.url = cacheURL + uncached;
+
+ // Change '%20' to '+' if this is encoded form body content (gh-2658)
+ } else if ( s.data && s.processData &&
+ ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) {
+ s.data = s.data.replace( r20, "+" );
+ }
+
+ // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+ if ( s.ifModified ) {
+ if ( jQuery.lastModified[ cacheURL ] ) {
+ jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] );
+ }
+ if ( jQuery.etag[ cacheURL ] ) {
+ jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] );
+ }
+ }
+
+ // Set the correct header, if data is being sent
+ if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
+ jqXHR.setRequestHeader( "Content-Type", s.contentType );
+ }
+
+ // Set the Accepts header for the server, depending on the dataType
+ jqXHR.setRequestHeader(
+ "Accept",
+ s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ?
+ s.accepts[ s.dataTypes[ 0 ] ] +
+ ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
+ s.accepts[ "*" ]
+ );
+
+ // Check for headers option
+ for ( i in s.headers ) {
+ jqXHR.setRequestHeader( i, s.headers[ i ] );
+ }
+
+ // Allow custom headers/mimetypes and early abort
+ if ( s.beforeSend &&
+ ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) {
+
+ // Abort if not done already and return
+ return jqXHR.abort();
+ }
+
+ // Aborting is no longer a cancellation
+ strAbort = "abort";
+
+ // Install callbacks on deferreds
+ completeDeferred.add( s.complete );
+ jqXHR.done( s.success );
+ jqXHR.fail( s.error );
+
+ // Get transport
+ transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
+
+ // If no transport, we auto-abort
+ if ( !transport ) {
+ done( -1, "No Transport" );
+ } else {
+ jqXHR.readyState = 1;
+
+ // Send global event
+ if ( fireGlobals ) {
+ globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
+ }
+
+ // If request was aborted inside ajaxSend, stop there
+ if ( completed ) {
+ return jqXHR;
+ }
+
+ // Timeout
+ if ( s.async && s.timeout > 0 ) {
+ timeoutTimer = window.setTimeout( function() {
+ jqXHR.abort( "timeout" );
+ }, s.timeout );
+ }
+
+ try {
+ completed = false;
+ transport.send( requestHeaders, done );
+ } catch ( e ) {
+
+ // Rethrow post-completion exceptions
+ if ( completed ) {
+ throw e;
+ }
+
+ // Propagate others as results
+ done( -1, e );
+ }
+ }
+
+ // Callback for when everything is done
+ function done( status, nativeStatusText, responses, headers ) {
+ var isSuccess, success, error, response, modified,
+ statusText = nativeStatusText;
+
+ // Ignore repeat invocations
+ if ( completed ) {
+ return;
+ }
+
+ completed = true;
+
+ // Clear timeout if it exists
+ if ( timeoutTimer ) {
+ window.clearTimeout( timeoutTimer );
+ }
+
+ // Dereference transport for early garbage collection
+ // (no matter how long the jqXHR object will be used)
+ transport = undefined;
+
+ // Cache response headers
+ responseHeadersString = headers || "";
+
+ // Set readyState
+ jqXHR.readyState = status > 0 ? 4 : 0;
+
+ // Determine if successful
+ isSuccess = status >= 200 && status < 300 || status === 304;
+
+ // Get response data
+ if ( responses ) {
+ response = ajaxHandleResponses( s, jqXHR, responses );
+ }
+
+ // Convert no matter what (that way responseXXX fields are always set)
+ response = ajaxConvert( s, response, jqXHR, isSuccess );
+
+ // If successful, handle type chaining
+ if ( isSuccess ) {
+
+ // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+ if ( s.ifModified ) {
+ modified = jqXHR.getResponseHeader( "Last-Modified" );
+ if ( modified ) {
+ jQuery.lastModified[ cacheURL ] = modified;
+ }
+ modified = jqXHR.getResponseHeader( "etag" );
+ if ( modified ) {
+ jQuery.etag[ cacheURL ] = modified;
+ }
+ }
+
+ // if no content
+ if ( status === 204 || s.type === "HEAD" ) {
+ statusText = "nocontent";
+
+ // if not modified
+ } else if ( status === 304 ) {
+ statusText = "notmodified";
+
+ // If we have data, let's convert it
+ } else {
+ statusText = response.state;
+ success = response.data;
+ error = response.error;
+ isSuccess = !error;
+ }
+ } else {
+
+ // Extract error from statusText and normalize for non-aborts
+ error = statusText;
+ if ( status || !statusText ) {
+ statusText = "error";
+ if ( status < 0 ) {
+ status = 0;
+ }
+ }
+ }
+
+ // Set data for the fake xhr object
+ jqXHR.status = status;
+ jqXHR.statusText = ( nativeStatusText || statusText ) + "";
+
+ // Success/Error
+ if ( isSuccess ) {
+ deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
+ } else {
+ deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
+ }
+
+ // Status-dependent callbacks
+ jqXHR.statusCode( statusCode );
+ statusCode = undefined;
+
+ if ( fireGlobals ) {
+ globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError",
+ [ jqXHR, s, isSuccess ? success : error ] );
+ }
+
+ // Complete
+ completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
+
+ if ( fireGlobals ) {
+ globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
+
+ // Handle the global AJAX counter
+ if ( !( --jQuery.active ) ) {
+ jQuery.event.trigger( "ajaxStop" );
+ }
+ }
+ }
+
+ return jqXHR;
+ },
+
+ getJSON: function( url, data, callback ) {
+ return jQuery.get( url, data, callback, "json" );
+ },
+
+ getScript: function( url, callback ) {
+ return jQuery.get( url, undefined, callback, "script" );
+ }
+} );
+
+jQuery.each( [ "get", "post" ], function( i, method ) {
+ jQuery[ method ] = function( url, data, callback, type ) {
+
+ // Shift arguments if data argument was omitted
+ if ( isFunction( data ) ) {
+ type = type || callback;
+ callback = data;
+ data = undefined;
+ }
+
+ // The url can be an options object (which then must have .url)
+ return jQuery.ajax( jQuery.extend( {
+ url: url,
+ type: method,
+ dataType: type,
+ data: data,
+ success: callback
+ }, jQuery.isPlainObject( url ) && url ) );
+ };
+} );
+
+
+jQuery._evalUrl = function( url ) {
+ return jQuery.ajax( {
+ url: url,
+
+ // Make this explicit, since user can override this through ajaxSetup (#11264)
+ type: "GET",
+ dataType: "script",
+ cache: true,
+ async: false,
+ global: false,
+ "throws": true
+ } );
+};
+
+
+jQuery.fn.extend( {
+ wrapAll: function( html ) {
+ var wrap;
+
+ if ( this[ 0 ] ) {
+ if ( isFunction( html ) ) {
+ html = html.call( this[ 0 ] );
+ }
+
+ // The elements to wrap the target around
+ wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true );
+
+ if ( this[ 0 ].parentNode ) {
+ wrap.insertBefore( this[ 0 ] );
+ }
+
+ wrap.map( function() {
+ var elem = this;
+
+ while ( elem.firstElementChild ) {
+ elem = elem.firstElementChild;
+ }
+
+ return elem;
+ } ).append( this );
+ }
+
+ return this;
+ },
+
+ wrapInner: function( html ) {
+ if ( isFunction( html ) ) {
+ return this.each( function( i ) {
+ jQuery( this ).wrapInner( html.call( this, i ) );
+ } );
+ }
+
+ return this.each( function() {
+ var self = jQuery( this ),
+ contents = self.contents();
+
+ if ( contents.length ) {
+ contents.wrapAll( html );
+
+ } else {
+ self.append( html );
+ }
+ } );
+ },
+
+ wrap: function( html ) {
+ var htmlIsFunction = isFunction( html );
+
+ return this.each( function( i ) {
+ jQuery( this ).wrapAll( htmlIsFunction ? html.call( this, i ) : html );
+ } );
+ },
+
+ unwrap: function( selector ) {
+ this.parent( selector ).not( "body" ).each( function() {
+ jQuery( this ).replaceWith( this.childNodes );
+ } );
+ return this;
+ }
+} );
+
+
+jQuery.expr.pseudos.hidden = function( elem ) {
+ return !jQuery.expr.pseudos.visible( elem );
+};
+jQuery.expr.pseudos.visible = function( elem ) {
+ return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length );
+};
+
+
+
+
+jQuery.ajaxSettings.xhr = function() {
+ try {
+ return new window.XMLHttpRequest();
+ } catch ( e ) {}
+};
+
+var xhrSuccessStatus = {
+
+ // File protocol always yields status code 0, assume 200
+ 0: 200,
+
+ // Support: IE <=9 only
+ // #1450: sometimes IE returns 1223 when it should be 204
+ 1223: 204
+ },
+ xhrSupported = jQuery.ajaxSettings.xhr();
+
+support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
+support.ajax = xhrSupported = !!xhrSupported;
+
+jQuery.ajaxTransport( function( options ) {
+ var callback, errorCallback;
+
+ // Cross domain only allowed if supported through XMLHttpRequest
+ if ( support.cors || xhrSupported && !options.crossDomain ) {
+ return {
+ send: function( headers, complete ) {
+ var i,
+ xhr = options.xhr();
+
+ xhr.open(
+ options.type,
+ options.url,
+ options.async,
+ options.username,
+ options.password
+ );
+
+ // Apply custom fields if provided
+ if ( options.xhrFields ) {
+ for ( i in options.xhrFields ) {
+ xhr[ i ] = options.xhrFields[ i ];
+ }
+ }
+
+ // Override mime type if needed
+ if ( options.mimeType && xhr.overrideMimeType ) {
+ xhr.overrideMimeType( options.mimeType );
+ }
+
+ // X-Requested-With header
+ // For cross-domain requests, seeing as conditions for a preflight are
+ // akin to a jigsaw puzzle, we simply never set it to be sure.
+ // (it can always be set on a per-request basis or even using ajaxSetup)
+ // For same-domain requests, won't change header if already provided.
+ if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) {
+ headers[ "X-Requested-With" ] = "XMLHttpRequest";
+ }
+
+ // Set headers
+ for ( i in headers ) {
+ xhr.setRequestHeader( i, headers[ i ] );
+ }
+
+ // Callback
+ callback = function( type ) {
+ return function() {
+ if ( callback ) {
+ callback = errorCallback = xhr.onload =
+ xhr.onerror = xhr.onabort = xhr.ontimeout =
+ xhr.onreadystatechange = null;
+
+ if ( type === "abort" ) {
+ xhr.abort();
+ } else if ( type === "error" ) {
+
+ // Support: IE <=9 only
+ // On a manual native abort, IE9 throws
+ // errors on any property access that is not readyState
+ if ( typeof xhr.status !== "number" ) {
+ complete( 0, "error" );
+ } else {
+ complete(
+
+ // File: protocol always yields status 0; see #8605, #14207
+ xhr.status,
+ xhr.statusText
+ );
+ }
+ } else {
+ complete(
+ xhrSuccessStatus[ xhr.status ] || xhr.status,
+ xhr.statusText,
+
+ // Support: IE <=9 only
+ // IE9 has no XHR2 but throws on binary (trac-11426)
+ // For XHR2 non-text, let the caller handle it (gh-2498)
+ ( xhr.responseType || "text" ) !== "text" ||
+ typeof xhr.responseText !== "string" ?
+ { binary: xhr.response } :
+ { text: xhr.responseText },
+ xhr.getAllResponseHeaders()
+ );
+ }
+ }
+ };
+ };
+
+ // Listen to events
+ xhr.onload = callback();
+ errorCallback = xhr.onerror = xhr.ontimeout = callback( "error" );
+
+ // Support: IE 9 only
+ // Use onreadystatechange to replace onabort
+ // to handle uncaught aborts
+ if ( xhr.onabort !== undefined ) {
+ xhr.onabort = errorCallback;
+ } else {
+ xhr.onreadystatechange = function() {
+
+ // Check readyState before timeout as it changes
+ if ( xhr.readyState === 4 ) {
+
+ // Allow onerror to be called first,
+ // but that will not handle a native abort
+ // Also, save errorCallback to a variable
+ // as xhr.onerror cannot be accessed
+ window.setTimeout( function() {
+ if ( callback ) {
+ errorCallback();
+ }
+ } );
+ }
+ };
+ }
+
+ // Create the abort callback
+ callback = callback( "abort" );
+
+ try {
+
+ // Do send the request (this may raise an exception)
+ xhr.send( options.hasContent && options.data || null );
+ } catch ( e ) {
+
+ // #14683: Only rethrow if this hasn't been notified as an error yet
+ if ( callback ) {
+ throw e;
+ }
+ }
+ },
+
+ abort: function() {
+ if ( callback ) {
+ callback();
+ }
+ }
+ };
+ }
+} );
+
+
+
+
+// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432)
+jQuery.ajaxPrefilter( function( s ) {
+ if ( s.crossDomain ) {
+ s.contents.script = false;
+ }
+} );
+
+// Install script dataType
+jQuery.ajaxSetup( {
+ accepts: {
+ script: "text/javascript, application/javascript, " +
+ "application/ecmascript, application/x-ecmascript"
+ },
+ contents: {
+ script: /\b(?:java|ecma)script\b/
+ },
+ converters: {
+ "text script": function( text ) {
+ jQuery.globalEval( text );
+ return text;
+ }
+ }
+} );
+
+// Handle cache's special case and crossDomain
+jQuery.ajaxPrefilter( "script", function( s ) {
+ if ( s.cache === undefined ) {
+ s.cache = false;
+ }
+ if ( s.crossDomain ) {
+ s.type = "GET";
+ }
+} );
+
+// Bind script tag hack transport
+jQuery.ajaxTransport( "script", function( s ) {
+
+ // This transport only deals with cross domain requests
+ if ( s.crossDomain ) {
+ var script, callback;
+ return {
+ send: function( _, complete ) {
+ script = jQuery( "<script>" ).prop( {
+ charset: s.scriptCharset,
+ src: s.url
+ } ).on(
+ "load error",
+ callback = function( evt ) {
+ script.remove();
+ callback = null;
+ if ( evt ) {
+ complete( evt.type === "error" ? 404 : 200, evt.type );
+ }
+ }
+ );
+
+ // Use native DOM manipulation to avoid our domManip AJAX trickery
+ document.head.appendChild( script[ 0 ] );
+ },
+ abort: function() {
+ if ( callback ) {
+ callback();
+ }
+ }
+ };
+ }
+} );
+
+
+
+
+var oldCallbacks = [],
+ rjsonp = /(=)\?(?=&|$)|\?\?/;
+
+// Default jsonp settings
+jQuery.ajaxSetup( {
+ jsonp: "callback",
+ jsonpCallback: function() {
+ var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce++ ) );
+ this[ callback ] = true;
+ return callback;
+ }
+} );
+
+// Detect, normalize options and install callbacks for jsonp requests
+jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
+
+ var callbackName, overwritten, responseContainer,
+ jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ?
+ "url" :
+ typeof s.data === "string" &&
+ ( s.contentType || "" )
+ .indexOf( "application/x-www-form-urlencoded" ) === 0 &&
+ rjsonp.test( s.data ) && "data"
+ );
+
+ // Handle iff the expected data type is "jsonp" or we have a parameter to set
+ if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) {
+
+ // Get callback name, remembering preexisting value associated with it
+ callbackName = s.jsonpCallback = isFunction( s.jsonpCallback ) ?
+ s.jsonpCallback() :
+ s.jsonpCallback;
+
+ // Insert callback into url or form data
+ if ( jsonProp ) {
+ s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName );
+ } else if ( s.jsonp !== false ) {
+ s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName;
+ }
+
+ // Use data converter to retrieve json after script execution
+ s.converters[ "script json" ] = function() {
+ if ( !responseContainer ) {
+ jQuery.error( callbackName + " was not called" );
+ }
+ return responseContainer[ 0 ];
+ };
+
+ // Force json dataType
+ s.dataTypes[ 0 ] = "json";
+
+ // Install callback
+ overwritten = window[ callbackName ];
+ window[ callbackName ] = function() {
+ responseContainer = arguments;
+ };
+
+ // Clean-up function (fires after converters)
+ jqXHR.always( function() {
+
+ // If previous value didn't exist - remove it
+ if ( overwritten === undefined ) {
+ jQuery( window ).removeProp( callbackName );
+
+ // Otherwise restore preexisting value
+ } else {
+ window[ callbackName ] = overwritten;
+ }
+
+ // Save back as free
+ if ( s[ callbackName ] ) {
+
+ // Make sure that re-using the options doesn't screw things around
+ s.jsonpCallback = originalSettings.jsonpCallback;
+
+ // Save the callback name for future use
+ oldCallbacks.push( callbackName );
+ }
+
+ // Call if it was a function and we have a response
+ if ( responseContainer && isFunction( overwritten ) ) {
+ overwritten( responseContainer[ 0 ] );
+ }
+
+ responseContainer = overwritten = undefined;
+ } );
+
+ // Delegate to script
+ return "script";
+ }
+} );
+
+
+
+
+// Support: Safari 8 only
+// In Safari 8 documents created via document.implementation.createHTMLDocument
+// collapse sibling forms: the second one becomes a child of the first one.
+// Because of that, this security measure has to be disabled in Safari 8.
+// https://bugs.webkit.org/show_bug.cgi?id=137337
+support.createHTMLDocument = ( function() {
+ var body = document.implementation.createHTMLDocument( "" ).body;
+ body.innerHTML = "<form></form><form></form>";
+ return body.childNodes.length === 2;
+} )();
+
+
+// Argument "data" should be string of html
+// context (optional): If specified, the fragment will be created in this context,
+// defaults to document
+// keepScripts (optional): If true, will include scripts passed in the html string
+jQuery.parseHTML = function( data, context, keepScripts ) {
+ if ( typeof data !== "string" ) {
+ return [];
+ }
+ if ( typeof context === "boolean" ) {
+ keepScripts = context;
+ context = false;
+ }
+
+ var base, parsed, scripts;
+
+ if ( !context ) {
+
+ // Stop scripts or inline event handlers from being executed immediately
+ // by using document.implementation
+ if ( support.createHTMLDocument ) {
+ context = document.implementation.createHTMLDocument( "" );
+
+ // Set the base href for the created document
+ // so any parsed elements with URLs
+ // are based on the document's URL (gh-2965)
+ base = context.createElement( "base" );
+ base.href = document.location.href;
+ context.head.appendChild( base );
+ } else {
+ context = document;
+ }
+ }
+
+ parsed = rsingleTag.exec( data );
+ scripts = !keepScripts && [];
+
+ // Single tag
+ if ( parsed ) {
+ return [ context.createElement( parsed[ 1 ] ) ];
+ }
+
+ parsed = buildFragment( [ data ], context, scripts );
+
+ if ( scripts && scripts.length ) {
+ jQuery( scripts ).remove();
+ }
+
+ return jQuery.merge( [], parsed.childNodes );
+};
+
+
+/**
+ * Load a url into a page
+ */
+jQuery.fn.load = function( url, params, callback ) {
+ var selector, type, response,
+ self = this,
+ off = url.indexOf( " " );
+
+ if ( off > -1 ) {
+ selector = stripAndCollapse( url.slice( off ) );
+ url = url.slice( 0, off );
+ }
+
+ // If it's a function
+ if ( isFunction( params ) ) {
+
+ // We assume that it's the callback
+ callback = params;
+ params = undefined;
+
+ // Otherwise, build a param string
+ } else if ( params && typeof params === "object" ) {
+ type = "POST";
+ }
+
+ // If we have elements to modify, make the request
+ if ( self.length > 0 ) {
+ jQuery.ajax( {
+ url: url,
+
+ // If "type" variable is undefined, then "GET" method will be used.
+ // Make value of this field explicit since
+ // user can override it through ajaxSetup method
+ type: type || "GET",
+ dataType: "html",
+ data: params
+ } ).done( function( responseText ) {
+
+ // Save response for use in complete callback
+ response = arguments;
+
+ self.html( selector ?
+
+ // If a selector was specified, locate the right elements in a dummy div
+ // Exclude scripts to avoid IE 'Permission Denied' errors
+ jQuery( "<div>" ).append( jQuery.parseHTML( responseText ) ).find( selector ) :
+
+ // Otherwise use the full result
+ responseText );
+
+ // If the request succeeds, this function gets "data", "status", "jqXHR"
+ // but they are ignored because response was set above.
+ // If it fails, this function gets "jqXHR", "status", "error"
+ } ).always( callback && function( jqXHR, status ) {
+ self.each( function() {
+ callback.apply( this, response || [ jqXHR.responseText, status, jqXHR ] );
+ } );
+ } );
+ }
+
+ return this;
+};
+
+
+
+
+// Attach a bunch of functions for handling common AJAX events
+jQuery.each( [
+ "ajaxStart",
+ "ajaxStop",
+ "ajaxComplete",
+ "ajaxError",
+ "ajaxSuccess",
+ "ajaxSend"
+], function( i, type ) {
+ jQuery.fn[ type ] = function( fn ) {
+ return this.on( type, fn );
+ };
+} );
+
+
+
+
+jQuery.expr.pseudos.animated = function( elem ) {
+ return jQuery.grep( jQuery.timers, function( fn ) {
+ return elem === fn.elem;
+ } ).length;
+};
+
+
+
+
+jQuery.offset = {
+ setOffset: function( elem, options, i ) {
+ var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition,
+ position = jQuery.css( elem, "position" ),
+ curElem = jQuery( elem ),
+ props = {};
+
+ // Set position first, in-case top/left are set even on static elem
+ if ( position === "static" ) {
+ elem.style.position = "relative";
+ }
+
+ curOffset = curElem.offset();
+ curCSSTop = jQuery.css( elem, "top" );
+ curCSSLeft = jQuery.css( elem, "left" );
+ calculatePosition = ( position === "absolute" || position === "fixed" ) &&
+ ( curCSSTop + curCSSLeft ).indexOf( "auto" ) > -1;
+
+ // Need to be able to calculate position if either
+ // top or left is auto and position is either absolute or fixed
+ if ( calculatePosition ) {
+ curPosition = curElem.position();
+ curTop = curPosition.top;
+ curLeft = curPosition.left;
+
+ } else {
+ curTop = parseFloat( curCSSTop ) || 0;
+ curLeft = parseFloat( curCSSLeft ) || 0;
+ }
+
+ if ( isFunction( options ) ) {
+
+ // Use jQuery.extend here to allow modification of coordinates argument (gh-1848)
+ options = options.call( elem, i, jQuery.extend( {}, curOffset ) );
+ }
+
+ if ( options.top != null ) {
+ props.top = ( options.top - curOffset.top ) + curTop;
+ }
+ if ( options.left != null ) {
+ props.left = ( options.left - curOffset.left ) + curLeft;
+ }
+
+ if ( "using" in options ) {
+ options.using.call( elem, props );
+
+ } else {
+ curElem.css( props );
+ }
+ }
+};
+
+jQuery.fn.extend( {
+
+ // offset() relates an element's border box to the document origin
+ offset: function( options ) {
+
+ // Preserve chaining for setter
+ if ( arguments.length ) {
+ return options === undefined ?
+ this :
+ this.each( function( i ) {
+ jQuery.offset.setOffset( this, options, i );
+ } );
+ }
+
+ var rect, win,
+ elem = this[ 0 ];
+
+ if ( !elem ) {
+ return;
+ }
+
+ // Return zeros for disconnected and hidden (display: none) elements (gh-2310)
+ // Support: IE <=11 only
+ // Running getBoundingClientRect on a
+ // disconnected node in IE throws an error
+ if ( !elem.getClientRects().length ) {
+ return { top: 0, left: 0 };
+ }
+
+ // Get document-relative position by adding viewport scroll to viewport-relative gBCR
+ rect = elem.getBoundingClientRect();
+ win = elem.ownerDocument.defaultView;
+ return {
+ top: rect.top + win.pageYOffset,
+ left: rect.left + win.pageXOffset
+ };
+ },
+
+ // position() relates an element's margin box to its offset parent's padding box
+ // This corresponds to the behavior of CSS absolute positioning
+ position: function() {
+ if ( !this[ 0 ] ) {
+ return;
+ }
+
+ var offsetParent, offset, doc,
+ elem = this[ 0 ],
+ parentOffset = { top: 0, left: 0 };
+
+ // position:fixed elements are offset from the viewport, which itself always has zero offset
+ if ( jQuery.css( elem, "position" ) === "fixed" ) {
+
+ // Assume position:fixed implies availability of getBoundingClientRect
+ offset = elem.getBoundingClientRect();
+
+ } else {
+ offset = this.offset();
+
+ // Account for the *real* offset parent, which can be the document or its root element
+ // when a statically positioned element is identified
+ doc = elem.ownerDocument;
+ offsetParent = elem.offsetParent || doc.documentElement;
+ while ( offsetParent &&
+ ( offsetParent === doc.body || offsetParent === doc.documentElement ) &&
+ jQuery.css( offsetParent, "position" ) === "static" ) {
+
+ offsetParent = offsetParent.parentNode;
+ }
+ if ( offsetParent && offsetParent !== elem && offsetParent.nodeType === 1 ) {
+
+ // Incorporate borders into its offset, since they are outside its content origin
+ parentOffset = jQuery( offsetParent ).offset();
+ parentOffset.top += jQuery.css( offsetParent, "borderTopWidth", true );
+ parentOffset.left += jQuery.css( offsetParent, "borderLeftWidth", true );
+ }
+ }
+
+ // Subtract parent offsets and element margins
+ return {
+ top: offset.top - parentOffset.top - jQuery.css( elem, "marginTop", true ),
+ left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true )
+ };
+ },
+
+ // This method will return documentElement in the following cases:
+ // 1) For the element inside the iframe without offsetParent, this method will return
+ // documentElement of the parent window
+ // 2) For the hidden or detached element
+ // 3) For body or html element, i.e. in case of the html node - it will return itself
+ //
+ // but those exceptions were never presented as a real life use-cases
+ // and might be considered as more preferable results.
+ //
+ // This logic, however, is not guaranteed and can change at any point in the future
+ offsetParent: function() {
+ return this.map( function() {
+ var offsetParent = this.offsetParent;
+
+ while ( offsetParent && jQuery.css( offsetParent, "position" ) === "static" ) {
+ offsetParent = offsetParent.offsetParent;
+ }
+
+ return offsetParent || documentElement;
+ } );
+ }
+} );
+
+// Create scrollLeft and scrollTop methods
+jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) {
+ var top = "pageYOffset" === prop;
+
+ jQuery.fn[ method ] = function( val ) {
+ return access( this, function( elem, method, val ) {
+
+ // Coalesce documents and windows
+ var win;
+ if ( isWindow( elem ) ) {
+ win = elem;
+ } else if ( elem.nodeType === 9 ) {
+ win = elem.defaultView;
+ }
+
+ if ( val === undefined ) {
+ return win ? win[ prop ] : elem[ method ];
+ }
+
+ if ( win ) {
+ win.scrollTo(
+ !top ? val : win.pageXOffset,
+ top ? val : win.pageYOffset
+ );
+
+ } else {
+ elem[ method ] = val;
+ }
+ }, method, val, arguments.length );
+ };
+} );
+
+// Support: Safari <=7 - 9.1, Chrome <=37 - 49
+// Add the top/left cssHooks using jQuery.fn.position
+// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084
+// Blink bug: https://bugs.chromium.org/p/chromium/issues/detail?id=589347
+// getComputedStyle returns percent when specified for top/left/bottom/right;
+// rather than make the css module depend on the offset module, just check for it here
+jQuery.each( [ "top", "left" ], function( i, prop ) {
+ jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition,
+ function( elem, computed ) {
+ if ( computed ) {
+ computed = curCSS( elem, prop );
+
+ // If curCSS returns percentage, fallback to offset
+ return rnumnonpx.test( computed ) ?
+ jQuery( elem ).position()[ prop ] + "px" :
+ computed;
+ }
+ }
+ );
+} );
+
+
+// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
+jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
+ jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name },
+ function( defaultExtra, funcName ) {
+
+ // Margin is only for outerHeight, outerWidth
+ jQuery.fn[ funcName ] = function( margin, value ) {
+ var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),
+ extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );
+
+ return access( this, function( elem, type, value ) {
+ var doc;
+
+ if ( isWindow( elem ) ) {
+
+ // $( window ).outerWidth/Height return w/h including scrollbars (gh-1729)
+ return funcName.indexOf( "outer" ) === 0 ?
+ elem[ "inner" + name ] :
+ elem.document.documentElement[ "client" + name ];
+ }
+
+ // Get document width or height
+ if ( elem.nodeType === 9 ) {
+ doc = elem.documentElement;
+
+ // Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height],
+ // whichever is greatest
+ return Math.max(
+ elem.body[ "scroll" + name ], doc[ "scroll" + name ],
+ elem.body[ "offset" + name ], doc[ "offset" + name ],
+ doc[ "client" + name ]
+ );
+ }
+
+ return value === undefined ?
+
+ // Get width or height on the element, requesting but not forcing parseFloat
+ jQuery.css( elem, type, extra ) :
+
+ // Set width or height on the element
+ jQuery.style( elem, type, value, extra );
+ }, type, chainable ? margin : undefined, chainable );
+ };
+ } );
+} );
+
+
+jQuery.each( ( "blur focus focusin focusout resize scroll click dblclick " +
+ "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
+ "change select submit keydown keypress keyup contextmenu" ).split( " " ),
+ function( i, name ) {
+
+ // Handle event binding
+ jQuery.fn[ name ] = function( data, fn ) {
+ return arguments.length > 0 ?
+ this.on( name, null, data, fn ) :
+ this.trigger( name );
+ };
+} );
+
+jQuery.fn.extend( {
+ hover: function( fnOver, fnOut ) {
+ return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
+ }
+} );
+
+
+
+
+jQuery.fn.extend( {
+
+ bind: function( types, data, fn ) {
+ return this.on( types, null, data, fn );
+ },
+ unbind: function( types, fn ) {
+ return this.off( types, null, fn );
+ },
+
+ delegate: function( selector, types, data, fn ) {
+ return this.on( types, selector, data, fn );
+ },
+ undelegate: function( selector, types, fn ) {
+
+ // ( namespace ) or ( selector, types [, fn] )
+ return arguments.length === 1 ?
+ this.off( selector, "**" ) :
+ this.off( types, selector || "**", fn );
+ }
+} );
+
+// Bind a function to a context, optionally partially applying any
+// arguments.
+// jQuery.proxy is deprecated to promote standards (specifically Function#bind)
+// However, it is not slated for removal any time soon
+jQuery.proxy = function( fn, context ) {
+ var tmp, args, proxy;
+
+ if ( typeof context === "string" ) {
+ tmp = fn[ context ];
+ context = fn;
+ fn = tmp;
+ }
+
+ // Quick check to determine if target is callable, in the spec
+ // this throws a TypeError, but we will just return undefined.
+ if ( !isFunction( fn ) ) {
+ return undefined;
+ }
+
+ // Simulated bind
+ args = slice.call( arguments, 2 );
+ proxy = function() {
+ return fn.apply( context || this, args.concat( slice.call( arguments ) ) );
+ };
+
+ // Set the guid of unique handler to the same of original handler, so it can be removed
+ proxy.guid = fn.guid = fn.guid || jQuery.guid++;
+
+ return proxy;
+};
+
+jQuery.holdReady = function( hold ) {
+ if ( hold ) {
+ jQuery.readyWait++;
+ } else {
+ jQuery.ready( true );
+ }
+};
+jQuery.isArray = Array.isArray;
+jQuery.parseJSON = JSON.parse;
+jQuery.nodeName = nodeName;
+jQuery.isFunction = isFunction;
+jQuery.isWindow = isWindow;
+jQuery.camelCase = camelCase;
+jQuery.type = toType;
+
+jQuery.now = Date.now;
+
+jQuery.isNumeric = function( obj ) {
+
+ // As of jQuery 3.0, isNumeric is limited to
+ // strings and numbers (primitives or objects)
+ // that can be coerced to finite numbers (gh-2662)
+ var type = jQuery.type( obj );
+ return ( type === "number" || type === "string" ) &&
+
+ // parseFloat NaNs numeric-cast false positives ("")
+ // ...but misinterprets leading-number strings, particularly hex literals ("0x...")
+ // subtraction forces infinities to NaN
+ !isNaN( obj - parseFloat( obj ) );
+};
+
+
+
+
+// Register as a named AMD module, since jQuery can be concatenated with other
+// files that may use define, but not via a proper concatenation script that
+// understands anonymous AMD modules. A named AMD is safest and most robust
+// way to register. Lowercase jquery is used because AMD module names are
+// derived from file names, and jQuery is normally delivered in a lowercase
+// file name. Do this after creating the global so that if an AMD module wants
+// to call noConflict to hide this version of jQuery, it will work.
+
+// Note that for maximum portability, libraries that are not jQuery should
+// declare themselves as anonymous modules, and avoid setting a global if an
+// AMD loader is present. jQuery is a special case. For more information, see
+// https://github.com/jrburke/requirejs/wiki/Updating-existing-libraries#wiki-anon
+
+if ( typeof define === "function" && define.amd ) {
+ define( "jquery", [], function() {
+ return jQuery;
+ } );
+}
+
+
+
+
+var
+
+ // Map over jQuery in case of overwrite
+ _jQuery = window.jQuery,
+
+ // Map over the $ in case of overwrite
+ _$ = window.$;
+
+jQuery.noConflict = function( deep ) {
+ if ( window.$ === jQuery ) {
+ window.$ = _$;
+ }
+
+ if ( deep && window.jQuery === jQuery ) {
+ window.jQuery = _jQuery;
+ }
+
+ return jQuery;
+};
+
+// Expose jQuery and $ identifiers, even in AMD
+// (#7102#comment:10, https://github.com/jquery/jquery/pull/557)
+// and CommonJS for browser emulators (#13566)
+if ( !noGlobal ) {
+ window.jQuery = window.$ = jQuery;
+}
+
+
+
+
+return jQuery;
+} );
diff --git a/doc/html/_static/searchtools.js b/doc/html/_static/searchtools.js
index 6031f991319e4a258c6aba6ad0512fd7b91fe5cb..5ff318066d83f9da7a5a97f34f7d78e1a7696c7c 100644
--- a/doc/html/_static/searchtools.js
+++ b/doc/html/_static/searchtools.js
@@ -36,10 +36,8 @@ if (!Scorer) {
// query found in title
title: 15,
- partialTitle: 7,
// query found in terms
- term: 5,
- partialTerm: 2
+ term: 5
};
}
@@ -58,14 +56,6 @@ var Search = {
_queued_query : null,
_pulse_status : -1,
- htmlToText : function(htmlString) {
- var htmlElement = document.createElement('span');
- htmlElement.innerHTML = htmlString;
- $(htmlElement).find('.headerlink').remove();
- docContent = $(htmlElement).find('[role=main]')[0];
- return docContent.textContent || docContent.innerText;
- },
-
init : function() {
var params = $.getQueryParameters();
if (params.q) {
@@ -130,7 +120,7 @@ var Search = {
this.out = $('#search-results');
this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
this.dots = $('<span></span>').appendTo(this.title);
- this.status = $('<p class="search-summary"> </p>').appendTo(this.out);
+ this.status = $('<p style="display: none"></p>').appendTo(this.out);
this.output = $('<ul class="search"/>').appendTo(this.out);
$('#search-progress').text(_('Preparing search...'));
@@ -269,7 +259,11 @@ var Search = {
displayNextItem();
});
} else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
- $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX,
+ var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
+ if (suffix === undefined) {
+ suffix = '.txt';
+ }
+ $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
dataType: "text",
complete: function(jqxhr, textstatus) {
var data = jqxhr.responseText;
@@ -319,13 +313,12 @@ var Search = {
for (var prefix in objects) {
for (var name in objects[prefix]) {
var fullname = (prefix ? prefix + '.' : '') + name;
- var fullnameLower = fullname.toLowerCase()
- if (fullnameLower.indexOf(object) > -1) {
+ if (fullname.toLowerCase().indexOf(object) > -1) {
var score = 0;
- var parts = fullnameLower.split('.');
+ var parts = fullname.split('.');
// check for different match types: exact matches of full name or
// "last name" (i.e. last dotted part)
- if (fullnameLower == object || parts[parts.length - 1] == object) {
+ if (fullname == object || parts[parts.length - 1] == object) {
score += Scorer.objNameMatch;
// matches in last name
} else if (parts[parts.length - 1].indexOf(object) > -1) {
@@ -392,19 +385,6 @@ var Search = {
{files: terms[word], score: Scorer.term},
{files: titleterms[word], score: Scorer.title}
];
- // add support for partial matches
- if (word.length > 2) {
- for (var w in terms) {
- if (w.match(word) && !terms[word]) {
- _o.push({files: terms[w], score: Scorer.partialTerm})
- }
- }
- for (var w in titleterms) {
- if (w.match(word) && !titleterms[word]) {
- _o.push({files: titleterms[w], score: Scorer.partialTitle})
- }
- }
- }
// no match but word was a required one
if ($u.every(_o, function(o){return o.files === undefined;})) {
@@ -444,12 +424,8 @@ var Search = {
var valid = true;
// check if all requirements are matched
- var filteredTermCount = // as search terms with length < 3 are discarded: ignore
- searchterms.filter(function(term){return term.length > 2}).length
- if (
- fileMap[file].length != searchterms.length &&
- fileMap[file].length != filteredTermCount
- ) continue;
+ if (fileMap[file].length != searchterms.length)
+ continue;
// ensure that none of the excluded terms is in the search result
for (i = 0; i < excluded.length; i++) {
@@ -480,8 +456,7 @@ var Search = {
* words. the first one is used to find the occurrence, the
* latter for highlighting it.
*/
- makeSearchSummary : function(htmlText, keywords, hlwords) {
- var text = Search.htmlToText(htmlText);
+ makeSearchSummary : function(text, keywords, hlwords) {
var textLower = text.toLowerCase();
var start = 0;
$.each(keywords, function() {
diff --git a/doc/html/_static/underscore-1.3.1.js b/doc/html/_static/underscore-1.3.1.js
deleted file mode 100644
index 208d4cd890c3183d946092ebe982738ade565061..0000000000000000000000000000000000000000
--- a/doc/html/_static/underscore-1.3.1.js
+++ /dev/null
@@ -1,999 +0,0 @@
-// Underscore.js 1.3.1
-// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore is freely distributable under the MIT license.
-// Portions of Underscore are inspired or borrowed from Prototype,
-// Oliver Steele's Functional, and John Resig's Micro-Templating.
-// For all details and documentation:
-// http://documentcloud.github.com/underscore
-
-(function() {
-
- // Baseline setup
- // --------------
-
- // Establish the root object, `window` in the browser, or `global` on the server.
- var root = this;
-
- // Save the previous value of the `_` variable.
- var previousUnderscore = root._;
-
- // Establish the object that gets returned to break out of a loop iteration.
- var breaker = {};
-
- // Save bytes in the minified (but not gzipped) version:
- var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype;
-
- // Create quick reference variables for speed access to core prototypes.
- var slice = ArrayProto.slice,
- unshift = ArrayProto.unshift,
- toString = ObjProto.toString,
- hasOwnProperty = ObjProto.hasOwnProperty;
-
- // All **ECMAScript 5** native function implementations that we hope to use
- // are declared here.
- var
- nativeForEach = ArrayProto.forEach,
- nativeMap = ArrayProto.map,
- nativeReduce = ArrayProto.reduce,
- nativeReduceRight = ArrayProto.reduceRight,
- nativeFilter = ArrayProto.filter,
- nativeEvery = ArrayProto.every,
- nativeSome = ArrayProto.some,
- nativeIndexOf = ArrayProto.indexOf,
- nativeLastIndexOf = ArrayProto.lastIndexOf,
- nativeIsArray = Array.isArray,
- nativeKeys = Object.keys,
- nativeBind = FuncProto.bind;
-
- // Create a safe reference to the Underscore object for use below.
- var _ = function(obj) { return new wrapper(obj); };
-
- // Export the Underscore object for **Node.js**, with
- // backwards-compatibility for the old `require()` API. If we're in
- // the browser, add `_` as a global object via a string identifier,
- // for Closure Compiler "advanced" mode.
- if (typeof exports !== 'undefined') {
- if (typeof module !== 'undefined' && module.exports) {
- exports = module.exports = _;
- }
- exports._ = _;
- } else {
- root['_'] = _;
- }
-
- // Current version.
- _.VERSION = '1.3.1';
-
- // Collection Functions
- // --------------------
-
- // The cornerstone, an `each` implementation, aka `forEach`.
- // Handles objects with the built-in `forEach`, arrays, and raw objects.
- // Delegates to **ECMAScript 5**'s native `forEach` if available.
- var each = _.each = _.forEach = function(obj, iterator, context) {
- if (obj == null) return;
- if (nativeForEach && obj.forEach === nativeForEach) {
- obj.forEach(iterator, context);
- } else if (obj.length === +obj.length) {
- for (var i = 0, l = obj.length; i < l; i++) {
- if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return;
- }
- } else {
- for (var key in obj) {
- if (_.has(obj, key)) {
- if (iterator.call(context, obj[key], key, obj) === breaker) return;
- }
- }
- }
- };
-
- // Return the results of applying the iterator to each element.
- // Delegates to **ECMAScript 5**'s native `map` if available.
- _.map = _.collect = function(obj, iterator, context) {
- var results = [];
- if (obj == null) return results;
- if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context);
- each(obj, function(value, index, list) {
- results[results.length] = iterator.call(context, value, index, list);
- });
- if (obj.length === +obj.length) results.length = obj.length;
- return results;
- };
-
- // **Reduce** builds up a single result from a list of values, aka `inject`,
- // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available.
- _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) {
- var initial = arguments.length > 2;
- if (obj == null) obj = [];
- if (nativeReduce && obj.reduce === nativeReduce) {
- if (context) iterator = _.bind(iterator, context);
- return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator);
- }
- each(obj, function(value, index, list) {
- if (!initial) {
- memo = value;
- initial = true;
- } else {
- memo = iterator.call(context, memo, value, index, list);
- }
- });
- if (!initial) throw new TypeError('Reduce of empty array with no initial value');
- return memo;
- };
-
- // The right-associative version of reduce, also known as `foldr`.
- // Delegates to **ECMAScript 5**'s native `reduceRight` if available.
- _.reduceRight = _.foldr = function(obj, iterator, memo, context) {
- var initial = arguments.length > 2;
- if (obj == null) obj = [];
- if (nativeReduceRight && obj.reduceRight === nativeReduceRight) {
- if (context) iterator = _.bind(iterator, context);
- return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator);
- }
- var reversed = _.toArray(obj).reverse();
- if (context && !initial) iterator = _.bind(iterator, context);
- return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator);
- };
-
- // Return the first value which passes a truth test. Aliased as `detect`.
- _.find = _.detect = function(obj, iterator, context) {
- var result;
- any(obj, function(value, index, list) {
- if (iterator.call(context, value, index, list)) {
- result = value;
- return true;
- }
- });
- return result;
- };
-
- // Return all the elements that pass a truth test.
- // Delegates to **ECMAScript 5**'s native `filter` if available.
- // Aliased as `select`.
- _.filter = _.select = function(obj, iterator, context) {
- var results = [];
- if (obj == null) return results;
- if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context);
- each(obj, function(value, index, list) {
- if (iterator.call(context, value, index, list)) results[results.length] = value;
- });
- return results;
- };
-
- // Return all the elements for which a truth test fails.
- _.reject = function(obj, iterator, context) {
- var results = [];
- if (obj == null) return results;
- each(obj, function(value, index, list) {
- if (!iterator.call(context, value, index, list)) results[results.length] = value;
- });
- return results;
- };
-
- // Determine whether all of the elements match a truth test.
- // Delegates to **ECMAScript 5**'s native `every` if available.
- // Aliased as `all`.
- _.every = _.all = function(obj, iterator, context) {
- var result = true;
- if (obj == null) return result;
- if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context);
- each(obj, function(value, index, list) {
- if (!(result = result && iterator.call(context, value, index, list))) return breaker;
- });
- return result;
- };
-
- // Determine if at least one element in the object matches a truth test.
- // Delegates to **ECMAScript 5**'s native `some` if available.
- // Aliased as `any`.
- var any = _.some = _.any = function(obj, iterator, context) {
- iterator || (iterator = _.identity);
- var result = false;
- if (obj == null) return result;
- if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context);
- each(obj, function(value, index, list) {
- if (result || (result = iterator.call(context, value, index, list))) return breaker;
- });
- return !!result;
- };
-
- // Determine if a given value is included in the array or object using `===`.
- // Aliased as `contains`.
- _.include = _.contains = function(obj, target) {
- var found = false;
- if (obj == null) return found;
- if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1;
- found = any(obj, function(value) {
- return value === target;
- });
- return found;
- };
-
- // Invoke a method (with arguments) on every item in a collection.
- _.invoke = function(obj, method) {
- var args = slice.call(arguments, 2);
- return _.map(obj, function(value) {
- return (_.isFunction(method) ? method || value : value[method]).apply(value, args);
- });
- };
-
- // Convenience version of a common use case of `map`: fetching a property.
- _.pluck = function(obj, key) {
- return _.map(obj, function(value){ return value[key]; });
- };
-
- // Return the maximum element or (element-based computation).
- _.max = function(obj, iterator, context) {
- if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj);
- if (!iterator && _.isEmpty(obj)) return -Infinity;
- var result = {computed : -Infinity};
- each(obj, function(value, index, list) {
- var computed = iterator ? iterator.call(context, value, index, list) : value;
- computed >= result.computed && (result = {value : value, computed : computed});
- });
- return result.value;
- };
-
- // Return the minimum element (or element-based computation).
- _.min = function(obj, iterator, context) {
- if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj);
- if (!iterator && _.isEmpty(obj)) return Infinity;
- var result = {computed : Infinity};
- each(obj, function(value, index, list) {
- var computed = iterator ? iterator.call(context, value, index, list) : value;
- computed < result.computed && (result = {value : value, computed : computed});
- });
- return result.value;
- };
-
- // Shuffle an array.
- _.shuffle = function(obj) {
- var shuffled = [], rand;
- each(obj, function(value, index, list) {
- if (index == 0) {
- shuffled[0] = value;
- } else {
- rand = Math.floor(Math.random() * (index + 1));
- shuffled[index] = shuffled[rand];
- shuffled[rand] = value;
- }
- });
- return shuffled;
- };
-
- // Sort the object's values by a criterion produced by an iterator.
- _.sortBy = function(obj, iterator, context) {
- return _.pluck(_.map(obj, function(value, index, list) {
- return {
- value : value,
- criteria : iterator.call(context, value, index, list)
- };
- }).sort(function(left, right) {
- var a = left.criteria, b = right.criteria;
- return a < b ? -1 : a > b ? 1 : 0;
- }), 'value');
- };
-
- // Groups the object's values by a criterion. Pass either a string attribute
- // to group by, or a function that returns the criterion.
- _.groupBy = function(obj, val) {
- var result = {};
- var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; };
- each(obj, function(value, index) {
- var key = iterator(value, index);
- (result[key] || (result[key] = [])).push(value);
- });
- return result;
- };
-
- // Use a comparator function to figure out at what index an object should
- // be inserted so as to maintain order. Uses binary search.
- _.sortedIndex = function(array, obj, iterator) {
- iterator || (iterator = _.identity);
- var low = 0, high = array.length;
- while (low < high) {
- var mid = (low + high) >> 1;
- iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid;
- }
- return low;
- };
-
- // Safely convert anything iterable into a real, live array.
- _.toArray = function(iterable) {
- if (!iterable) return [];
- if (iterable.toArray) return iterable.toArray();
- if (_.isArray(iterable)) return slice.call(iterable);
- if (_.isArguments(iterable)) return slice.call(iterable);
- return _.values(iterable);
- };
-
- // Return the number of elements in an object.
- _.size = function(obj) {
- return _.toArray(obj).length;
- };
-
- // Array Functions
- // ---------------
-
- // Get the first element of an array. Passing **n** will return the first N
- // values in the array. Aliased as `head`. The **guard** check allows it to work
- // with `_.map`.
- _.first = _.head = function(array, n, guard) {
- return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
- };
-
- // Returns everything but the last entry of the array. Especcialy useful on
- // the arguments object. Passing **n** will return all the values in
- // the array, excluding the last N. The **guard** check allows it to work with
- // `_.map`.
- _.initial = function(array, n, guard) {
- return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
- };
-
- // Get the last element of an array. Passing **n** will return the last N
- // values in the array. The **guard** check allows it to work with `_.map`.
- _.last = function(array, n, guard) {
- if ((n != null) && !guard) {
- return slice.call(array, Math.max(array.length - n, 0));
- } else {
- return array[array.length - 1];
- }
- };
-
- // Returns everything but the first entry of the array. Aliased as `tail`.
- // Especially useful on the arguments object. Passing an **index** will return
- // the rest of the values in the array from that index onward. The **guard**
- // check allows it to work with `_.map`.
- _.rest = _.tail = function(array, index, guard) {
- return slice.call(array, (index == null) || guard ? 1 : index);
- };
-
- // Trim out all falsy values from an array.
- _.compact = function(array) {
- return _.filter(array, function(value){ return !!value; });
- };
-
- // Return a completely flattened version of an array.
- _.flatten = function(array, shallow) {
- return _.reduce(array, function(memo, value) {
- if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value));
- memo[memo.length] = value;
- return memo;
- }, []);
- };
-
- // Return a version of the array that does not contain the specified value(s).
- _.without = function(array) {
- return _.difference(array, slice.call(arguments, 1));
- };
-
- // Produce a duplicate-free version of the array. If the array has already
- // been sorted, you have the option of using a faster algorithm.
- // Aliased as `unique`.
- _.uniq = _.unique = function(array, isSorted, iterator) {
- var initial = iterator ? _.map(array, iterator) : array;
- var result = [];
- _.reduce(initial, function(memo, el, i) {
- if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) {
- memo[memo.length] = el;
- result[result.length] = array[i];
- }
- return memo;
- }, []);
- return result;
- };
-
- // Produce an array that contains the union: each distinct element from all of
- // the passed-in arrays.
- _.union = function() {
- return _.uniq(_.flatten(arguments, true));
- };
-
- // Produce an array that contains every item shared between all the
- // passed-in arrays. (Aliased as "intersect" for back-compat.)
- _.intersection = _.intersect = function(array) {
- var rest = slice.call(arguments, 1);
- return _.filter(_.uniq(array), function(item) {
- return _.every(rest, function(other) {
- return _.indexOf(other, item) >= 0;
- });
- });
- };
-
- // Take the difference between one array and a number of other arrays.
- // Only the elements present in just the first array will remain.
- _.difference = function(array) {
- var rest = _.flatten(slice.call(arguments, 1));
- return _.filter(array, function(value){ return !_.include(rest, value); });
- };
-
- // Zip together multiple lists into a single array -- elements that share
- // an index go together.
- _.zip = function() {
- var args = slice.call(arguments);
- var length = _.max(_.pluck(args, 'length'));
- var results = new Array(length);
- for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i);
- return results;
- };
-
- // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
- // we need this function. Return the position of the first occurrence of an
- // item in an array, or -1 if the item is not included in the array.
- // Delegates to **ECMAScript 5**'s native `indexOf` if available.
- // If the array is large and already in sort order, pass `true`
- // for **isSorted** to use binary search.
- _.indexOf = function(array, item, isSorted) {
- if (array == null) return -1;
- var i, l;
- if (isSorted) {
- i = _.sortedIndex(array, item);
- return array[i] === item ? i : -1;
- }
- if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item);
- for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i;
- return -1;
- };
-
- // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
- _.lastIndexOf = function(array, item) {
- if (array == null) return -1;
- if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item);
- var i = array.length;
- while (i--) if (i in array && array[i] === item) return i;
- return -1;
- };
-
- // Generate an integer Array containing an arithmetic progression. A port of
- // the native Python `range()` function. See
- // [the Python documentation](http://docs.python.org/library/functions.html#range).
- _.range = function(start, stop, step) {
- if (arguments.length <= 1) {
- stop = start || 0;
- start = 0;
- }
- step = arguments[2] || 1;
-
- var len = Math.max(Math.ceil((stop - start) / step), 0);
- var idx = 0;
- var range = new Array(len);
-
- while(idx < len) {
- range[idx++] = start;
- start += step;
- }
-
- return range;
- };
-
- // Function (ahem) Functions
- // ------------------
-
- // Reusable constructor function for prototype setting.
- var ctor = function(){};
-
- // Create a function bound to a given object (assigning `this`, and arguments,
- // optionally). Binding with arguments is also known as `curry`.
- // Delegates to **ECMAScript 5**'s native `Function.bind` if available.
- // We check for `func.bind` first, to fail fast when `func` is undefined.
- _.bind = function bind(func, context) {
- var bound, args;
- if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
- if (!_.isFunction(func)) throw new TypeError;
- args = slice.call(arguments, 2);
- return bound = function() {
- if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
- ctor.prototype = func.prototype;
- var self = new ctor;
- var result = func.apply(self, args.concat(slice.call(arguments)));
- if (Object(result) === result) return result;
- return self;
- };
- };
-
- // Bind all of an object's methods to that object. Useful for ensuring that
- // all callbacks defined on an object belong to it.
- _.bindAll = function(obj) {
- var funcs = slice.call(arguments, 1);
- if (funcs.length == 0) funcs = _.functions(obj);
- each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
- return obj;
- };
-
- // Memoize an expensive function by storing its results.
- _.memoize = function(func, hasher) {
- var memo = {};
- hasher || (hasher = _.identity);
- return function() {
- var key = hasher.apply(this, arguments);
- return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
- };
- };
-
- // Delays a function for the given number of milliseconds, and then calls
- // it with the arguments supplied.
- _.delay = function(func, wait) {
- var args = slice.call(arguments, 2);
- return setTimeout(function(){ return func.apply(func, args); }, wait);
- };
-
- // Defers a function, scheduling it to run after the current call stack has
- // cleared.
- _.defer = function(func) {
- return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
- };
-
- // Returns a function, that, when invoked, will only be triggered at most once
- // during a given window of time.
- _.throttle = function(func, wait) {
- var context, args, timeout, throttling, more;
- var whenDone = _.debounce(function(){ more = throttling = false; }, wait);
- return function() {
- context = this; args = arguments;
- var later = function() {
- timeout = null;
- if (more) func.apply(context, args);
- whenDone();
- };
- if (!timeout) timeout = setTimeout(later, wait);
- if (throttling) {
- more = true;
- } else {
- func.apply(context, args);
- }
- whenDone();
- throttling = true;
- };
- };
-
- // Returns a function, that, as long as it continues to be invoked, will not
- // be triggered. The function will be called after it stops being called for
- // N milliseconds.
- _.debounce = function(func, wait) {
- var timeout;
- return function() {
- var context = this, args = arguments;
- var later = function() {
- timeout = null;
- func.apply(context, args);
- };
- clearTimeout(timeout);
- timeout = setTimeout(later, wait);
- };
- };
-
- // Returns a function that will be executed at most one time, no matter how
- // often you call it. Useful for lazy initialization.
- _.once = function(func) {
- var ran = false, memo;
- return function() {
- if (ran) return memo;
- ran = true;
- return memo = func.apply(this, arguments);
- };
- };
-
- // Returns the first function passed as an argument to the second,
- // allowing you to adjust arguments, run code before and after, and
- // conditionally execute the original function.
- _.wrap = function(func, wrapper) {
- return function() {
- var args = [func].concat(slice.call(arguments, 0));
- return wrapper.apply(this, args);
- };
- };
-
- // Returns a function that is the composition of a list of functions, each
- // consuming the return value of the function that follows.
- _.compose = function() {
- var funcs = arguments;
- return function() {
- var args = arguments;
- for (var i = funcs.length - 1; i >= 0; i--) {
- args = [funcs[i].apply(this, args)];
- }
- return args[0];
- };
- };
-
- // Returns a function that will only be executed after being called N times.
- _.after = function(times, func) {
- if (times <= 0) return func();
- return function() {
- if (--times < 1) { return func.apply(this, arguments); }
- };
- };
-
- // Object Functions
- // ----------------
-
- // Retrieve the names of an object's properties.
- // Delegates to **ECMAScript 5**'s native `Object.keys`
- _.keys = nativeKeys || function(obj) {
- if (obj !== Object(obj)) throw new TypeError('Invalid object');
- var keys = [];
- for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
- return keys;
- };
-
- // Retrieve the values of an object's properties.
- _.values = function(obj) {
- return _.map(obj, _.identity);
- };
-
- // Return a sorted list of the function names available on the object.
- // Aliased as `methods`
- _.functions = _.methods = function(obj) {
- var names = [];
- for (var key in obj) {
- if (_.isFunction(obj[key])) names.push(key);
- }
- return names.sort();
- };
-
- // Extend a given object with all the properties in passed-in object(s).
- _.extend = function(obj) {
- each(slice.call(arguments, 1), function(source) {
- for (var prop in source) {
- obj[prop] = source[prop];
- }
- });
- return obj;
- };
-
- // Fill in a given object with default properties.
- _.defaults = function(obj) {
- each(slice.call(arguments, 1), function(source) {
- for (var prop in source) {
- if (obj[prop] == null) obj[prop] = source[prop];
- }
- });
- return obj;
- };
-
- // Create a (shallow-cloned) duplicate of an object.
- _.clone = function(obj) {
- if (!_.isObject(obj)) return obj;
- return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
- };
-
- // Invokes interceptor with the obj, and then returns obj.
- // The primary purpose of this method is to "tap into" a method chain, in
- // order to perform operations on intermediate results within the chain.
- _.tap = function(obj, interceptor) {
- interceptor(obj);
- return obj;
- };
-
- // Internal recursive comparison function.
- function eq(a, b, stack) {
- // Identical objects are equal. `0 === -0`, but they aren't identical.
- // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
- if (a === b) return a !== 0 || 1 / a == 1 / b;
- // A strict comparison is necessary because `null == undefined`.
- if (a == null || b == null) return a === b;
- // Unwrap any wrapped objects.
- if (a._chain) a = a._wrapped;
- if (b._chain) b = b._wrapped;
- // Invoke a custom `isEqual` method if one is provided.
- if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b);
- if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a);
- // Compare `[[Class]]` names.
- var className = toString.call(a);
- if (className != toString.call(b)) return false;
- switch (className) {
- // Strings, numbers, dates, and booleans are compared by value.
- case '[object String]':
- // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
- // equivalent to `new String("5")`.
- return a == String(b);
- case '[object Number]':
- // `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
- // other numeric values.
- return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
- case '[object Date]':
- case '[object Boolean]':
- // Coerce dates and booleans to numeric primitive values. Dates are compared by their
- // millisecond representations. Note that invalid dates with millisecond representations
- // of `NaN` are not equivalent.
- return +a == +b;
- // RegExps are compared by their source patterns and flags.
- case '[object RegExp]':
- return a.source == b.source &&
- a.global == b.global &&
- a.multiline == b.multiline &&
- a.ignoreCase == b.ignoreCase;
- }
- if (typeof a != 'object' || typeof b != 'object') return false;
- // Assume equality for cyclic structures. The algorithm for detecting cyclic
- // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
- var length = stack.length;
- while (length--) {
- // Linear search. Performance is inversely proportional to the number of
- // unique nested structures.
- if (stack[length] == a) return true;
- }
- // Add the first object to the stack of traversed objects.
- stack.push(a);
- var size = 0, result = true;
- // Recursively compare objects and arrays.
- if (className == '[object Array]') {
- // Compare array lengths to determine if a deep comparison is necessary.
- size = a.length;
- result = size == b.length;
- if (result) {
- // Deep compare the contents, ignoring non-numeric properties.
- while (size--) {
- // Ensure commutative equality for sparse arrays.
- if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break;
- }
- }
- } else {
- // Objects with different constructors are not equivalent.
- if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false;
- // Deep compare objects.
- for (var key in a) {
- if (_.has(a, key)) {
- // Count the expected number of properties.
- size++;
- // Deep compare each member.
- if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break;
- }
- }
- // Ensure that both objects contain the same number of properties.
- if (result) {
- for (key in b) {
- if (_.has(b, key) && !(size--)) break;
- }
- result = !size;
- }
- }
- // Remove the first object from the stack of traversed objects.
- stack.pop();
- return result;
- }
-
- // Perform a deep comparison to check if two objects are equal.
- _.isEqual = function(a, b) {
- return eq(a, b, []);
- };
-
- // Is a given array, string, or object empty?
- // An "empty" object has no enumerable own-properties.
- _.isEmpty = function(obj) {
- if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
- for (var key in obj) if (_.has(obj, key)) return false;
- return true;
- };
-
- // Is a given value a DOM element?
- _.isElement = function(obj) {
- return !!(obj && obj.nodeType == 1);
- };
-
- // Is a given value an array?
- // Delegates to ECMA5's native Array.isArray
- _.isArray = nativeIsArray || function(obj) {
- return toString.call(obj) == '[object Array]';
- };
-
- // Is a given variable an object?
- _.isObject = function(obj) {
- return obj === Object(obj);
- };
-
- // Is a given variable an arguments object?
- _.isArguments = function(obj) {
- return toString.call(obj) == '[object Arguments]';
- };
- if (!_.isArguments(arguments)) {
- _.isArguments = function(obj) {
- return !!(obj && _.has(obj, 'callee'));
- };
- }
-
- // Is a given value a function?
- _.isFunction = function(obj) {
- return toString.call(obj) == '[object Function]';
- };
-
- // Is a given value a string?
- _.isString = function(obj) {
- return toString.call(obj) == '[object String]';
- };
-
- // Is a given value a number?
- _.isNumber = function(obj) {
- return toString.call(obj) == '[object Number]';
- };
-
- // Is the given value `NaN`?
- _.isNaN = function(obj) {
- // `NaN` is the only value for which `===` is not reflexive.
- return obj !== obj;
- };
-
- // Is a given value a boolean?
- _.isBoolean = function(obj) {
- return obj === true || obj === false || toString.call(obj) == '[object Boolean]';
- };
-
- // Is a given value a date?
- _.isDate = function(obj) {
- return toString.call(obj) == '[object Date]';
- };
-
- // Is the given value a regular expression?
- _.isRegExp = function(obj) {
- return toString.call(obj) == '[object RegExp]';
- };
-
- // Is a given value equal to null?
- _.isNull = function(obj) {
- return obj === null;
- };
-
- // Is a given variable undefined?
- _.isUndefined = function(obj) {
- return obj === void 0;
- };
-
- // Has own property?
- _.has = function(obj, key) {
- return hasOwnProperty.call(obj, key);
- };
-
- // Utility Functions
- // -----------------
-
- // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
- // previous owner. Returns a reference to the Underscore object.
- _.noConflict = function() {
- root._ = previousUnderscore;
- return this;
- };
-
- // Keep the identity function around for default iterators.
- _.identity = function(value) {
- return value;
- };
-
- // Run a function **n** times.
- _.times = function (n, iterator, context) {
- for (var i = 0; i < n; i++) iterator.call(context, i);
- };
-
- // Escape a string for HTML interpolation.
- _.escape = function(string) {
- return (''+string).replace(/&/g, '&').replace(/</g, '<').replace(/>/g, '>').replace(/"/g, '"').replace(/'/g, ''').replace(/\//g,'/');
- };
-
- // Add your own custom functions to the Underscore object, ensuring that
- // they're correctly added to the OOP wrapper as well.
- _.mixin = function(obj) {
- each(_.functions(obj), function(name){
- addToWrapper(name, _[name] = obj[name]);
- });
- };
-
- // Generate a unique integer id (unique within the entire client session).
- // Useful for temporary DOM ids.
- var idCounter = 0;
- _.uniqueId = function(prefix) {
- var id = idCounter++;
- return prefix ? prefix + id : id;
- };
-
- // By default, Underscore uses ERB-style template delimiters, change the
- // following template settings to use alternative delimiters.
- _.templateSettings = {
- evaluate : /<%([\s\S]+?)%>/g,
- interpolate : /<%=([\s\S]+?)%>/g,
- escape : /<%-([\s\S]+?)%>/g
- };
-
- // When customizing `templateSettings`, if you don't want to define an
- // interpolation, evaluation or escaping regex, we need one that is
- // guaranteed not to match.
- var noMatch = /.^/;
-
- // Within an interpolation, evaluation, or escaping, remove HTML escaping
- // that had been previously added.
- var unescape = function(code) {
- return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'");
- };
-
- // JavaScript micro-templating, similar to John Resig's implementation.
- // Underscore templating handles arbitrary delimiters, preserves whitespace,
- // and correctly escapes quotes within interpolated code.
- _.template = function(str, data) {
- var c = _.templateSettings;
- var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' +
- 'with(obj||{}){__p.push(\'' +
- str.replace(/\\/g, '\\\\')
- .replace(/'/g, "\\'")
- .replace(c.escape || noMatch, function(match, code) {
- return "',_.escape(" + unescape(code) + "),'";
- })
- .replace(c.interpolate || noMatch, function(match, code) {
- return "'," + unescape(code) + ",'";
- })
- .replace(c.evaluate || noMatch, function(match, code) {
- return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('";
- })
- .replace(/\r/g, '\\r')
- .replace(/\n/g, '\\n')
- .replace(/\t/g, '\\t')
- + "');}return __p.join('');";
- var func = new Function('obj', '_', tmpl);
- if (data) return func(data, _);
- return function(data) {
- return func.call(this, data, _);
- };
- };
-
- // Add a "chain" function, which will delegate to the wrapper.
- _.chain = function(obj) {
- return _(obj).chain();
- };
-
- // The OOP Wrapper
- // ---------------
-
- // If Underscore is called as a function, it returns a wrapped object that
- // can be used OO-style. This wrapper holds altered versions of all the
- // underscore functions. Wrapped objects may be chained.
- var wrapper = function(obj) { this._wrapped = obj; };
-
- // Expose `wrapper.prototype` as `_.prototype`
- _.prototype = wrapper.prototype;
-
- // Helper function to continue chaining intermediate results.
- var result = function(obj, chain) {
- return chain ? _(obj).chain() : obj;
- };
-
- // A method to easily add functions to the OOP wrapper.
- var addToWrapper = function(name, func) {
- wrapper.prototype[name] = function() {
- var args = slice.call(arguments);
- unshift.call(args, this._wrapped);
- return result(func.apply(_, args), this._chain);
- };
- };
-
- // Add all of the Underscore functions to the wrapper object.
- _.mixin(_);
-
- // Add all mutator Array functions to the wrapper.
- each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
- var method = ArrayProto[name];
- wrapper.prototype[name] = function() {
- var wrapped = this._wrapped;
- method.apply(wrapped, arguments);
- var length = wrapped.length;
- if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0];
- return result(wrapped, this._chain);
- };
- });
-
- // Add all accessor Array functions to the wrapper.
- each(['concat', 'join', 'slice'], function(name) {
- var method = ArrayProto[name];
- wrapper.prototype[name] = function() {
- return result(method.apply(this._wrapped, arguments), this._chain);
- };
- });
-
- // Start chaining a wrapped Underscore object.
- wrapper.prototype.chain = function() {
- this._chain = true;
- return this;
- };
-
- // Extracts the result from a wrapped and chained object.
- wrapper.prototype.value = function() {
- return this._wrapped;
- };
-
-}).call(this);
diff --git a/doc/html/_static/underscore.js b/doc/html/_static/underscore.js
index 5b55f32beaca186f84cca115514f02cddbd1bbd5..709ae8e30b066fa10e18e77dac51551ec5bc4719 100644
--- a/doc/html/_static/underscore.js
+++ b/doc/html/_static/underscore.js
@@ -1,31 +1,1707 @@
-// Underscore.js 1.3.1
-// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
-// Underscore is freely distributable under the MIT license.
-// Portions of Underscore are inspired or borrowed from Prototype,
-// Oliver Steele's Functional, and John Resig's Micro-Templating.
-// For all details and documentation:
-// http://documentcloud.github.com/underscore
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+// Underscore.js 1.9.1
+// http://underscorejs.org
+// (c) 2009-2018 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors
+// Underscore may be freely distributed under the MIT license.
+
+(function() {
+
+ // Baseline setup
+ // --------------
+
+ // Establish the root object, `window` (`self`) in the browser, `global`
+ // on the server, or `this` in some virtual machines. We use `self`
+ // instead of `window` for `WebWorker` support.
+ var root = typeof self == 'object' && self.self === self && self ||
+ typeof global == 'object' && global.global === global && global ||
+ this ||
+ {};
+
+ // Save the previous value of the `_` variable.
+ var previousUnderscore = root._;
+
+ // Save bytes in the minified (but not gzipped) version:
+ var ArrayProto = Array.prototype, ObjProto = Object.prototype;
+ var SymbolProto = typeof Symbol !== 'undefined' ? Symbol.prototype : null;
+
+ // Create quick reference variables for speed access to core prototypes.
+ var push = ArrayProto.push,
+ slice = ArrayProto.slice,
+ toString = ObjProto.toString,
+ hasOwnProperty = ObjProto.hasOwnProperty;
+
+ // All **ECMAScript 5** native function implementations that we hope to use
+ // are declared here.
+ var nativeIsArray = Array.isArray,
+ nativeKeys = Object.keys,
+ nativeCreate = Object.create;
+
+ // Naked function reference for surrogate-prototype-swapping.
+ var Ctor = function(){};
+
+ // Create a safe reference to the Underscore object for use below.
+ var _ = function(obj) {
+ if (obj instanceof _) return obj;
+ if (!(this instanceof _)) return new _(obj);
+ this._wrapped = obj;
+ };
+
+ // Export the Underscore object for **Node.js**, with
+ // backwards-compatibility for their old module API. If we're in
+ // the browser, add `_` as a global object.
+ // (`nodeType` is checked to ensure that `module`
+ // and `exports` are not HTML elements.)
+ if (typeof exports != 'undefined' && !exports.nodeType) {
+ if (typeof module != 'undefined' && !module.nodeType && module.exports) {
+ exports = module.exports = _;
+ }
+ exports._ = _;
+ } else {
+ root._ = _;
+ }
+
+ // Current version.
+ _.VERSION = '1.9.1';
+
+ // Internal function that returns an efficient (for current engines) version
+ // of the passed-in callback, to be repeatedly applied in other Underscore
+ // functions.
+ var optimizeCb = function(func, context, argCount) {
+ if (context === void 0) return func;
+ switch (argCount == null ? 3 : argCount) {
+ case 1: return function(value) {
+ return func.call(context, value);
+ };
+ // The 2-argument case is omitted because we’re not using it.
+ case 3: return function(value, index, collection) {
+ return func.call(context, value, index, collection);
+ };
+ case 4: return function(accumulator, value, index, collection) {
+ return func.call(context, accumulator, value, index, collection);
+ };
+ }
+ return function() {
+ return func.apply(context, arguments);
+ };
+ };
+
+ var builtinIteratee;
+
+ // An internal function to generate callbacks that can be applied to each
+ // element in a collection, returning the desired result — either `identity`,
+ // an arbitrary callback, a property matcher, or a property accessor.
+ var cb = function(value, context, argCount) {
+ if (_.iteratee !== builtinIteratee) return _.iteratee(value, context);
+ if (value == null) return _.identity;
+ if (_.isFunction(value)) return optimizeCb(value, context, argCount);
+ if (_.isObject(value) && !_.isArray(value)) return _.matcher(value);
+ return _.property(value);
+ };
+
+ // External wrapper for our callback generator. Users may customize
+ // `_.iteratee` if they want additional predicate/iteratee shorthand styles.
+ // This abstraction hides the internal-only argCount argument.
+ _.iteratee = builtinIteratee = function(value, context) {
+ return cb(value, context, Infinity);
+ };
+
+ // Some functions take a variable number of arguments, or a few expected
+ // arguments at the beginning and then a variable number of values to operate
+ // on. This helper accumulates all remaining arguments past the function’s
+ // argument length (or an explicit `startIndex`), into an array that becomes
+ // the last argument. Similar to ES6’s "rest parameter".
+ var restArguments = function(func, startIndex) {
+ startIndex = startIndex == null ? func.length - 1 : +startIndex;
+ return function() {
+ var length = Math.max(arguments.length - startIndex, 0),
+ rest = Array(length),
+ index = 0;
+ for (; index < length; index++) {
+ rest[index] = arguments[index + startIndex];
+ }
+ switch (startIndex) {
+ case 0: return func.call(this, rest);
+ case 1: return func.call(this, arguments[0], rest);
+ case 2: return func.call(this, arguments[0], arguments[1], rest);
+ }
+ var args = Array(startIndex + 1);
+ for (index = 0; index < startIndex; index++) {
+ args[index] = arguments[index];
+ }
+ args[startIndex] = rest;
+ return func.apply(this, args);
+ };
+ };
+
+ // An internal function for creating a new object that inherits from another.
+ var baseCreate = function(prototype) {
+ if (!_.isObject(prototype)) return {};
+ if (nativeCreate) return nativeCreate(prototype);
+ Ctor.prototype = prototype;
+ var result = new Ctor;
+ Ctor.prototype = null;
+ return result;
+ };
+
+ var shallowProperty = function(key) {
+ return function(obj) {
+ return obj == null ? void 0 : obj[key];
+ };
+ };
+
+ var has = function(obj, path) {
+ return obj != null && hasOwnProperty.call(obj, path);
+ }
+
+ var deepGet = function(obj, path) {
+ var length = path.length;
+ for (var i = 0; i < length; i++) {
+ if (obj == null) return void 0;
+ obj = obj[path[i]];
+ }
+ return length ? obj : void 0;
+ };
+
+ // Helper for collection methods to determine whether a collection
+ // should be iterated as an array or as an object.
+ // Related: http://people.mozilla.org/~jorendorff/es6-draft.html#sec-tolength
+ // Avoids a very nasty iOS 8 JIT bug on ARM-64. #2094
+ var MAX_ARRAY_INDEX = Math.pow(2, 53) - 1;
+ var getLength = shallowProperty('length');
+ var isArrayLike = function(collection) {
+ var length = getLength(collection);
+ return typeof length == 'number' && length >= 0 && length <= MAX_ARRAY_INDEX;
+ };
+
+ // Collection Functions
+ // --------------------
+
+ // The cornerstone, an `each` implementation, aka `forEach`.
+ // Handles raw objects in addition to array-likes. Treats all
+ // sparse array-likes as if they were dense.
+ _.each = _.forEach = function(obj, iteratee, context) {
+ iteratee = optimizeCb(iteratee, context);
+ var i, length;
+ if (isArrayLike(obj)) {
+ for (i = 0, length = obj.length; i < length; i++) {
+ iteratee(obj[i], i, obj);
+ }
+ } else {
+ var keys = _.keys(obj);
+ for (i = 0, length = keys.length; i < length; i++) {
+ iteratee(obj[keys[i]], keys[i], obj);
+ }
+ }
+ return obj;
+ };
+
+ // Return the results of applying the iteratee to each element.
+ _.map = _.collect = function(obj, iteratee, context) {
+ iteratee = cb(iteratee, context);
+ var keys = !isArrayLike(obj) && _.keys(obj),
+ length = (keys || obj).length,
+ results = Array(length);
+ for (var index = 0; index < length; index++) {
+ var currentKey = keys ? keys[index] : index;
+ results[index] = iteratee(obj[currentKey], currentKey, obj);
+ }
+ return results;
+ };
+
+ // Create a reducing function iterating left or right.
+ var createReduce = function(dir) {
+ // Wrap code that reassigns argument variables in a separate function than
+ // the one that accesses `arguments.length` to avoid a perf hit. (#1991)
+ var reducer = function(obj, iteratee, memo, initial) {
+ var keys = !isArrayLike(obj) && _.keys(obj),
+ length = (keys || obj).length,
+ index = dir > 0 ? 0 : length - 1;
+ if (!initial) {
+ memo = obj[keys ? keys[index] : index];
+ index += dir;
+ }
+ for (; index >= 0 && index < length; index += dir) {
+ var currentKey = keys ? keys[index] : index;
+ memo = iteratee(memo, obj[currentKey], currentKey, obj);
+ }
+ return memo;
+ };
+
+ return function(obj, iteratee, memo, context) {
+ var initial = arguments.length >= 3;
+ return reducer(obj, optimizeCb(iteratee, context, 4), memo, initial);
+ };
+ };
+
+ // **Reduce** builds up a single result from a list of values, aka `inject`,
+ // or `foldl`.
+ _.reduce = _.foldl = _.inject = createReduce(1);
+
+ // The right-associative version of reduce, also known as `foldr`.
+ _.reduceRight = _.foldr = createReduce(-1);
+
+ // Return the first value which passes a truth test. Aliased as `detect`.
+ _.find = _.detect = function(obj, predicate, context) {
+ var keyFinder = isArrayLike(obj) ? _.findIndex : _.findKey;
+ var key = keyFinder(obj, predicate, context);
+ if (key !== void 0 && key !== -1) return obj[key];
+ };
+
+ // Return all the elements that pass a truth test.
+ // Aliased as `select`.
+ _.filter = _.select = function(obj, predicate, context) {
+ var results = [];
+ predicate = cb(predicate, context);
+ _.each(obj, function(value, index, list) {
+ if (predicate(value, index, list)) results.push(value);
+ });
+ return results;
+ };
+
+ // Return all the elements for which a truth test fails.
+ _.reject = function(obj, predicate, context) {
+ return _.filter(obj, _.negate(cb(predicate)), context);
+ };
+
+ // Determine whether all of the elements match a truth test.
+ // Aliased as `all`.
+ _.every = _.all = function(obj, predicate, context) {
+ predicate = cb(predicate, context);
+ var keys = !isArrayLike(obj) && _.keys(obj),
+ length = (keys || obj).length;
+ for (var index = 0; index < length; index++) {
+ var currentKey = keys ? keys[index] : index;
+ if (!predicate(obj[currentKey], currentKey, obj)) return false;
+ }
+ return true;
+ };
+
+ // Determine if at least one element in the object matches a truth test.
+ // Aliased as `any`.
+ _.some = _.any = function(obj, predicate, context) {
+ predicate = cb(predicate, context);
+ var keys = !isArrayLike(obj) && _.keys(obj),
+ length = (keys || obj).length;
+ for (var index = 0; index < length; index++) {
+ var currentKey = keys ? keys[index] : index;
+ if (predicate(obj[currentKey], currentKey, obj)) return true;
+ }
+ return false;
+ };
+
+ // Determine if the array or object contains a given item (using `===`).
+ // Aliased as `includes` and `include`.
+ _.contains = _.includes = _.include = function(obj, item, fromIndex, guard) {
+ if (!isArrayLike(obj)) obj = _.values(obj);
+ if (typeof fromIndex != 'number' || guard) fromIndex = 0;
+ return _.indexOf(obj, item, fromIndex) >= 0;
+ };
+
+ // Invoke a method (with arguments) on every item in a collection.
+ _.invoke = restArguments(function(obj, path, args) {
+ var contextPath, func;
+ if (_.isFunction(path)) {
+ func = path;
+ } else if (_.isArray(path)) {
+ contextPath = path.slice(0, -1);
+ path = path[path.length - 1];
+ }
+ return _.map(obj, function(context) {
+ var method = func;
+ if (!method) {
+ if (contextPath && contextPath.length) {
+ context = deepGet(context, contextPath);
+ }
+ if (context == null) return void 0;
+ method = context[path];
+ }
+ return method == null ? method : method.apply(context, args);
+ });
+ });
+
+ // Convenience version of a common use case of `map`: fetching a property.
+ _.pluck = function(obj, key) {
+ return _.map(obj, _.property(key));
+ };
+
+ // Convenience version of a common use case of `filter`: selecting only objects
+ // containing specific `key:value` pairs.
+ _.where = function(obj, attrs) {
+ return _.filter(obj, _.matcher(attrs));
+ };
+
+ // Convenience version of a common use case of `find`: getting the first object
+ // containing specific `key:value` pairs.
+ _.findWhere = function(obj, attrs) {
+ return _.find(obj, _.matcher(attrs));
+ };
+
+ // Return the maximum element (or element-based computation).
+ _.max = function(obj, iteratee, context) {
+ var result = -Infinity, lastComputed = -Infinity,
+ value, computed;
+ if (iteratee == null || typeof iteratee == 'number' && typeof obj[0] != 'object' && obj != null) {
+ obj = isArrayLike(obj) ? obj : _.values(obj);
+ for (var i = 0, length = obj.length; i < length; i++) {
+ value = obj[i];
+ if (value != null && value > result) {
+ result = value;
+ }
+ }
+ } else {
+ iteratee = cb(iteratee, context);
+ _.each(obj, function(v, index, list) {
+ computed = iteratee(v, index, list);
+ if (computed > lastComputed || computed === -Infinity && result === -Infinity) {
+ result = v;
+ lastComputed = computed;
+ }
+ });
+ }
+ return result;
+ };
+
+ // Return the minimum element (or element-based computation).
+ _.min = function(obj, iteratee, context) {
+ var result = Infinity, lastComputed = Infinity,
+ value, computed;
+ if (iteratee == null || typeof iteratee == 'number' && typeof obj[0] != 'object' && obj != null) {
+ obj = isArrayLike(obj) ? obj : _.values(obj);
+ for (var i = 0, length = obj.length; i < length; i++) {
+ value = obj[i];
+ if (value != null && value < result) {
+ result = value;
+ }
+ }
+ } else {
+ iteratee = cb(iteratee, context);
+ _.each(obj, function(v, index, list) {
+ computed = iteratee(v, index, list);
+ if (computed < lastComputed || computed === Infinity && result === Infinity) {
+ result = v;
+ lastComputed = computed;
+ }
+ });
+ }
+ return result;
+ };
+
+ // Shuffle a collection.
+ _.shuffle = function(obj) {
+ return _.sample(obj, Infinity);
+ };
+
+ // Sample **n** random values from a collection using the modern version of the
+ // [Fisher-Yates shuffle](http://en.wikipedia.org/wiki/Fisher–Yates_shuffle).
+ // If **n** is not specified, returns a single random element.
+ // The internal `guard` argument allows it to work with `map`.
+ _.sample = function(obj, n, guard) {
+ if (n == null || guard) {
+ if (!isArrayLike(obj)) obj = _.values(obj);
+ return obj[_.random(obj.length - 1)];
+ }
+ var sample = isArrayLike(obj) ? _.clone(obj) : _.values(obj);
+ var length = getLength(sample);
+ n = Math.max(Math.min(n, length), 0);
+ var last = length - 1;
+ for (var index = 0; index < n; index++) {
+ var rand = _.random(index, last);
+ var temp = sample[index];
+ sample[index] = sample[rand];
+ sample[rand] = temp;
+ }
+ return sample.slice(0, n);
+ };
+
+ // Sort the object's values by a criterion produced by an iteratee.
+ _.sortBy = function(obj, iteratee, context) {
+ var index = 0;
+ iteratee = cb(iteratee, context);
+ return _.pluck(_.map(obj, function(value, key, list) {
+ return {
+ value: value,
+ index: index++,
+ criteria: iteratee(value, key, list)
+ };
+ }).sort(function(left, right) {
+ var a = left.criteria;
+ var b = right.criteria;
+ if (a !== b) {
+ if (a > b || a === void 0) return 1;
+ if (a < b || b === void 0) return -1;
+ }
+ return left.index - right.index;
+ }), 'value');
+ };
+
+ // An internal function used for aggregate "group by" operations.
+ var group = function(behavior, partition) {
+ return function(obj, iteratee, context) {
+ var result = partition ? [[], []] : {};
+ iteratee = cb(iteratee, context);
+ _.each(obj, function(value, index) {
+ var key = iteratee(value, index, obj);
+ behavior(result, value, key);
+ });
+ return result;
+ };
+ };
+
+ // Groups the object's values by a criterion. Pass either a string attribute
+ // to group by, or a function that returns the criterion.
+ _.groupBy = group(function(result, value, key) {
+ if (has(result, key)) result[key].push(value); else result[key] = [value];
+ });
+
+ // Indexes the object's values by a criterion, similar to `groupBy`, but for
+ // when you know that your index values will be unique.
+ _.indexBy = group(function(result, value, key) {
+ result[key] = value;
+ });
+
+ // Counts instances of an object that group by a certain criterion. Pass
+ // either a string attribute to count by, or a function that returns the
+ // criterion.
+ _.countBy = group(function(result, value, key) {
+ if (has(result, key)) result[key]++; else result[key] = 1;
+ });
+
+ var reStrSymbol = /[^\ud800-\udfff]|[\ud800-\udbff][\udc00-\udfff]|[\ud800-\udfff]/g;
+ // Safely create a real, live array from anything iterable.
+ _.toArray = function(obj) {
+ if (!obj) return [];
+ if (_.isArray(obj)) return slice.call(obj);
+ if (_.isString(obj)) {
+ // Keep surrogate pair characters together
+ return obj.match(reStrSymbol);
+ }
+ if (isArrayLike(obj)) return _.map(obj, _.identity);
+ return _.values(obj);
+ };
+
+ // Return the number of elements in an object.
+ _.size = function(obj) {
+ if (obj == null) return 0;
+ return isArrayLike(obj) ? obj.length : _.keys(obj).length;
+ };
+
+ // Split a collection into two arrays: one whose elements all satisfy the given
+ // predicate, and one whose elements all do not satisfy the predicate.
+ _.partition = group(function(result, value, pass) {
+ result[pass ? 0 : 1].push(value);
+ }, true);
+
+ // Array Functions
+ // ---------------
+
+ // Get the first element of an array. Passing **n** will return the first N
+ // values in the array. Aliased as `head` and `take`. The **guard** check
+ // allows it to work with `_.map`.
+ _.first = _.head = _.take = function(array, n, guard) {
+ if (array == null || array.length < 1) return n == null ? void 0 : [];
+ if (n == null || guard) return array[0];
+ return _.initial(array, array.length - n);
+ };
+
+ // Returns everything but the last entry of the array. Especially useful on
+ // the arguments object. Passing **n** will return all the values in
+ // the array, excluding the last N.
+ _.initial = function(array, n, guard) {
+ return slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 : n)));
+ };
+
+ // Get the last element of an array. Passing **n** will return the last N
+ // values in the array.
+ _.last = function(array, n, guard) {
+ if (array == null || array.length < 1) return n == null ? void 0 : [];
+ if (n == null || guard) return array[array.length - 1];
+ return _.rest(array, Math.max(0, array.length - n));
+ };
+
+ // Returns everything but the first entry of the array. Aliased as `tail` and `drop`.
+ // Especially useful on the arguments object. Passing an **n** will return
+ // the rest N values in the array.
+ _.rest = _.tail = _.drop = function(array, n, guard) {
+ return slice.call(array, n == null || guard ? 1 : n);
+ };
+
+ // Trim out all falsy values from an array.
+ _.compact = function(array) {
+ return _.filter(array, Boolean);
+ };
+
+ // Internal implementation of a recursive `flatten` function.
+ var flatten = function(input, shallow, strict, output) {
+ output = output || [];
+ var idx = output.length;
+ for (var i = 0, length = getLength(input); i < length; i++) {
+ var value = input[i];
+ if (isArrayLike(value) && (_.isArray(value) || _.isArguments(value))) {
+ // Flatten current level of array or arguments object.
+ if (shallow) {
+ var j = 0, len = value.length;
+ while (j < len) output[idx++] = value[j++];
+ } else {
+ flatten(value, shallow, strict, output);
+ idx = output.length;
+ }
+ } else if (!strict) {
+ output[idx++] = value;
+ }
+ }
+ return output;
+ };
+
+ // Flatten out an array, either recursively (by default), or just one level.
+ _.flatten = function(array, shallow) {
+ return flatten(array, shallow, false);
+ };
+
+ // Return a version of the array that does not contain the specified value(s).
+ _.without = restArguments(function(array, otherArrays) {
+ return _.difference(array, otherArrays);
+ });
+
+ // Produce a duplicate-free version of the array. If the array has already
+ // been sorted, you have the option of using a faster algorithm.
+ // The faster algorithm will not work with an iteratee if the iteratee
+ // is not a one-to-one function, so providing an iteratee will disable
+ // the faster algorithm.
+ // Aliased as `unique`.
+ _.uniq = _.unique = function(array, isSorted, iteratee, context) {
+ if (!_.isBoolean(isSorted)) {
+ context = iteratee;
+ iteratee = isSorted;
+ isSorted = false;
+ }
+ if (iteratee != null) iteratee = cb(iteratee, context);
+ var result = [];
+ var seen = [];
+ for (var i = 0, length = getLength(array); i < length; i++) {
+ var value = array[i],
+ computed = iteratee ? iteratee(value, i, array) : value;
+ if (isSorted && !iteratee) {
+ if (!i || seen !== computed) result.push(value);
+ seen = computed;
+ } else if (iteratee) {
+ if (!_.contains(seen, computed)) {
+ seen.push(computed);
+ result.push(value);
+ }
+ } else if (!_.contains(result, value)) {
+ result.push(value);
+ }
+ }
+ return result;
+ };
+
+ // Produce an array that contains the union: each distinct element from all of
+ // the passed-in arrays.
+ _.union = restArguments(function(arrays) {
+ return _.uniq(flatten(arrays, true, true));
+ });
+
+ // Produce an array that contains every item shared between all the
+ // passed-in arrays.
+ _.intersection = function(array) {
+ var result = [];
+ var argsLength = arguments.length;
+ for (var i = 0, length = getLength(array); i < length; i++) {
+ var item = array[i];
+ if (_.contains(result, item)) continue;
+ var j;
+ for (j = 1; j < argsLength; j++) {
+ if (!_.contains(arguments[j], item)) break;
+ }
+ if (j === argsLength) result.push(item);
+ }
+ return result;
+ };
+
+ // Take the difference between one array and a number of other arrays.
+ // Only the elements present in just the first array will remain.
+ _.difference = restArguments(function(array, rest) {
+ rest = flatten(rest, true, true);
+ return _.filter(array, function(value){
+ return !_.contains(rest, value);
+ });
+ });
+
+ // Complement of _.zip. Unzip accepts an array of arrays and groups
+ // each array's elements on shared indices.
+ _.unzip = function(array) {
+ var length = array && _.max(array, getLength).length || 0;
+ var result = Array(length);
+
+ for (var index = 0; index < length; index++) {
+ result[index] = _.pluck(array, index);
+ }
+ return result;
+ };
+
+ // Zip together multiple lists into a single array -- elements that share
+ // an index go together.
+ _.zip = restArguments(_.unzip);
+
+ // Converts lists into objects. Pass either a single array of `[key, value]`
+ // pairs, or two parallel arrays of the same length -- one of keys, and one of
+ // the corresponding values. Passing by pairs is the reverse of _.pairs.
+ _.object = function(list, values) {
+ var result = {};
+ for (var i = 0, length = getLength(list); i < length; i++) {
+ if (values) {
+ result[list[i]] = values[i];
+ } else {
+ result[list[i][0]] = list[i][1];
+ }
+ }
+ return result;
+ };
+
+ // Generator function to create the findIndex and findLastIndex functions.
+ var createPredicateIndexFinder = function(dir) {
+ return function(array, predicate, context) {
+ predicate = cb(predicate, context);
+ var length = getLength(array);
+ var index = dir > 0 ? 0 : length - 1;
+ for (; index >= 0 && index < length; index += dir) {
+ if (predicate(array[index], index, array)) return index;
+ }
+ return -1;
+ };
+ };
+
+ // Returns the first index on an array-like that passes a predicate test.
+ _.findIndex = createPredicateIndexFinder(1);
+ _.findLastIndex = createPredicateIndexFinder(-1);
+
+ // Use a comparator function to figure out the smallest index at which
+ // an object should be inserted so as to maintain order. Uses binary search.
+ _.sortedIndex = function(array, obj, iteratee, context) {
+ iteratee = cb(iteratee, context, 1);
+ var value = iteratee(obj);
+ var low = 0, high = getLength(array);
+ while (low < high) {
+ var mid = Math.floor((low + high) / 2);
+ if (iteratee(array[mid]) < value) low = mid + 1; else high = mid;
+ }
+ return low;
+ };
+
+ // Generator function to create the indexOf and lastIndexOf functions.
+ var createIndexFinder = function(dir, predicateFind, sortedIndex) {
+ return function(array, item, idx) {
+ var i = 0, length = getLength(array);
+ if (typeof idx == 'number') {
+ if (dir > 0) {
+ i = idx >= 0 ? idx : Math.max(idx + length, i);
+ } else {
+ length = idx >= 0 ? Math.min(idx + 1, length) : idx + length + 1;
+ }
+ } else if (sortedIndex && idx && length) {
+ idx = sortedIndex(array, item);
+ return array[idx] === item ? idx : -1;
+ }
+ if (item !== item) {
+ idx = predicateFind(slice.call(array, i, length), _.isNaN);
+ return idx >= 0 ? idx + i : -1;
+ }
+ for (idx = dir > 0 ? i : length - 1; idx >= 0 && idx < length; idx += dir) {
+ if (array[idx] === item) return idx;
+ }
+ return -1;
+ };
+ };
+
+ // Return the position of the first occurrence of an item in an array,
+ // or -1 if the item is not included in the array.
+ // If the array is large and already in sort order, pass `true`
+ // for **isSorted** to use binary search.
+ _.indexOf = createIndexFinder(1, _.findIndex, _.sortedIndex);
+ _.lastIndexOf = createIndexFinder(-1, _.findLastIndex);
+
+ // Generate an integer Array containing an arithmetic progression. A port of
+ // the native Python `range()` function. See
+ // [the Python documentation](http://docs.python.org/library/functions.html#range).
+ _.range = function(start, stop, step) {
+ if (stop == null) {
+ stop = start || 0;
+ start = 0;
+ }
+ if (!step) {
+ step = stop < start ? -1 : 1;
+ }
+
+ var length = Math.max(Math.ceil((stop - start) / step), 0);
+ var range = Array(length);
+
+ for (var idx = 0; idx < length; idx++, start += step) {
+ range[idx] = start;
+ }
+
+ return range;
+ };
+
+ // Chunk a single array into multiple arrays, each containing `count` or fewer
+ // items.
+ _.chunk = function(array, count) {
+ if (count == null || count < 1) return [];
+ var result = [];
+ var i = 0, length = array.length;
+ while (i < length) {
+ result.push(slice.call(array, i, i += count));
+ }
+ return result;
+ };
+
+ // Function (ahem) Functions
+ // ------------------
+
+ // Determines whether to execute a function as a constructor
+ // or a normal function with the provided arguments.
+ var executeBound = function(sourceFunc, boundFunc, context, callingContext, args) {
+ if (!(callingContext instanceof boundFunc)) return sourceFunc.apply(context, args);
+ var self = baseCreate(sourceFunc.prototype);
+ var result = sourceFunc.apply(self, args);
+ if (_.isObject(result)) return result;
+ return self;
+ };
+
+ // Create a function bound to a given object (assigning `this`, and arguments,
+ // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if
+ // available.
+ _.bind = restArguments(function(func, context, args) {
+ if (!_.isFunction(func)) throw new TypeError('Bind must be called on a function');
+ var bound = restArguments(function(callArgs) {
+ return executeBound(func, bound, context, this, args.concat(callArgs));
+ });
+ return bound;
+ });
+
+ // Partially apply a function by creating a version that has had some of its
+ // arguments pre-filled, without changing its dynamic `this` context. _ acts
+ // as a placeholder by default, allowing any combination of arguments to be
+ // pre-filled. Set `_.partial.placeholder` for a custom placeholder argument.
+ _.partial = restArguments(function(func, boundArgs) {
+ var placeholder = _.partial.placeholder;
+ var bound = function() {
+ var position = 0, length = boundArgs.length;
+ var args = Array(length);
+ for (var i = 0; i < length; i++) {
+ args[i] = boundArgs[i] === placeholder ? arguments[position++] : boundArgs[i];
+ }
+ while (position < arguments.length) args.push(arguments[position++]);
+ return executeBound(func, bound, this, this, args);
+ };
+ return bound;
+ });
+
+ _.partial.placeholder = _;
+
+ // Bind a number of an object's methods to that object. Remaining arguments
+ // are the method names to be bound. Useful for ensuring that all callbacks
+ // defined on an object belong to it.
+ _.bindAll = restArguments(function(obj, keys) {
+ keys = flatten(keys, false, false);
+ var index = keys.length;
+ if (index < 1) throw new Error('bindAll must be passed function names');
+ while (index--) {
+ var key = keys[index];
+ obj[key] = _.bind(obj[key], obj);
+ }
+ });
+
+ // Memoize an expensive function by storing its results.
+ _.memoize = function(func, hasher) {
+ var memoize = function(key) {
+ var cache = memoize.cache;
+ var address = '' + (hasher ? hasher.apply(this, arguments) : key);
+ if (!has(cache, address)) cache[address] = func.apply(this, arguments);
+ return cache[address];
+ };
+ memoize.cache = {};
+ return memoize;
+ };
+
+ // Delays a function for the given number of milliseconds, and then calls
+ // it with the arguments supplied.
+ _.delay = restArguments(function(func, wait, args) {
+ return setTimeout(function() {
+ return func.apply(null, args);
+ }, wait);
+ });
+
+ // Defers a function, scheduling it to run after the current call stack has
+ // cleared.
+ _.defer = _.partial(_.delay, _, 1);
+
+ // Returns a function, that, when invoked, will only be triggered at most once
+ // during a given window of time. Normally, the throttled function will run
+ // as much as it can, without ever going more than once per `wait` duration;
+ // but if you'd like to disable the execution on the leading edge, pass
+ // `{leading: false}`. To disable execution on the trailing edge, ditto.
+ _.throttle = function(func, wait, options) {
+ var timeout, context, args, result;
+ var previous = 0;
+ if (!options) options = {};
+
+ var later = function() {
+ previous = options.leading === false ? 0 : _.now();
+ timeout = null;
+ result = func.apply(context, args);
+ if (!timeout) context = args = null;
+ };
+
+ var throttled = function() {
+ var now = _.now();
+ if (!previous && options.leading === false) previous = now;
+ var remaining = wait - (now - previous);
+ context = this;
+ args = arguments;
+ if (remaining <= 0 || remaining > wait) {
+ if (timeout) {
+ clearTimeout(timeout);
+ timeout = null;
+ }
+ previous = now;
+ result = func.apply(context, args);
+ if (!timeout) context = args = null;
+ } else if (!timeout && options.trailing !== false) {
+ timeout = setTimeout(later, remaining);
+ }
+ return result;
+ };
+
+ throttled.cancel = function() {
+ clearTimeout(timeout);
+ previous = 0;
+ timeout = context = args = null;
+ };
+
+ return throttled;
+ };
+
+ // Returns a function, that, as long as it continues to be invoked, will not
+ // be triggered. The function will be called after it stops being called for
+ // N milliseconds. If `immediate` is passed, trigger the function on the
+ // leading edge, instead of the trailing.
+ _.debounce = function(func, wait, immediate) {
+ var timeout, result;
+
+ var later = function(context, args) {
+ timeout = null;
+ if (args) result = func.apply(context, args);
+ };
+
+ var debounced = restArguments(function(args) {
+ if (timeout) clearTimeout(timeout);
+ if (immediate) {
+ var callNow = !timeout;
+ timeout = setTimeout(later, wait);
+ if (callNow) result = func.apply(this, args);
+ } else {
+ timeout = _.delay(later, wait, this, args);
+ }
+
+ return result;
+ });
+
+ debounced.cancel = function() {
+ clearTimeout(timeout);
+ timeout = null;
+ };
+
+ return debounced;
+ };
+
+ // Returns the first function passed as an argument to the second,
+ // allowing you to adjust arguments, run code before and after, and
+ // conditionally execute the original function.
+ _.wrap = function(func, wrapper) {
+ return _.partial(wrapper, func);
+ };
+
+ // Returns a negated version of the passed-in predicate.
+ _.negate = function(predicate) {
+ return function() {
+ return !predicate.apply(this, arguments);
+ };
+ };
+
+ // Returns a function that is the composition of a list of functions, each
+ // consuming the return value of the function that follows.
+ _.compose = function() {
+ var args = arguments;
+ var start = args.length - 1;
+ return function() {
+ var i = start;
+ var result = args[start].apply(this, arguments);
+ while (i--) result = args[i].call(this, result);
+ return result;
+ };
+ };
+
+ // Returns a function that will only be executed on and after the Nth call.
+ _.after = function(times, func) {
+ return function() {
+ if (--times < 1) {
+ return func.apply(this, arguments);
+ }
+ };
+ };
+
+ // Returns a function that will only be executed up to (but not including) the Nth call.
+ _.before = function(times, func) {
+ var memo;
+ return function() {
+ if (--times > 0) {
+ memo = func.apply(this, arguments);
+ }
+ if (times <= 1) func = null;
+ return memo;
+ };
+ };
+
+ // Returns a function that will be executed at most one time, no matter how
+ // often you call it. Useful for lazy initialization.
+ _.once = _.partial(_.before, 2);
+
+ _.restArguments = restArguments;
+
+ // Object Functions
+ // ----------------
+
+ // Keys in IE < 9 that won't be iterated by `for key in ...` and thus missed.
+ var hasEnumBug = !{toString: null}.propertyIsEnumerable('toString');
+ var nonEnumerableProps = ['valueOf', 'isPrototypeOf', 'toString',
+ 'propertyIsEnumerable', 'hasOwnProperty', 'toLocaleString'];
+
+ var collectNonEnumProps = function(obj, keys) {
+ var nonEnumIdx = nonEnumerableProps.length;
+ var constructor = obj.constructor;
+ var proto = _.isFunction(constructor) && constructor.prototype || ObjProto;
+
+ // Constructor is a special case.
+ var prop = 'constructor';
+ if (has(obj, prop) && !_.contains(keys, prop)) keys.push(prop);
+
+ while (nonEnumIdx--) {
+ prop = nonEnumerableProps[nonEnumIdx];
+ if (prop in obj && obj[prop] !== proto[prop] && !_.contains(keys, prop)) {
+ keys.push(prop);
+ }
+ }
+ };
+
+ // Retrieve the names of an object's own properties.
+ // Delegates to **ECMAScript 5**'s native `Object.keys`.
+ _.keys = function(obj) {
+ if (!_.isObject(obj)) return [];
+ if (nativeKeys) return nativeKeys(obj);
+ var keys = [];
+ for (var key in obj) if (has(obj, key)) keys.push(key);
+ // Ahem, IE < 9.
+ if (hasEnumBug) collectNonEnumProps(obj, keys);
+ return keys;
+ };
+
+ // Retrieve all the property names of an object.
+ _.allKeys = function(obj) {
+ if (!_.isObject(obj)) return [];
+ var keys = [];
+ for (var key in obj) keys.push(key);
+ // Ahem, IE < 9.
+ if (hasEnumBug) collectNonEnumProps(obj, keys);
+ return keys;
+ };
+
+ // Retrieve the values of an object's properties.
+ _.values = function(obj) {
+ var keys = _.keys(obj);
+ var length = keys.length;
+ var values = Array(length);
+ for (var i = 0; i < length; i++) {
+ values[i] = obj[keys[i]];
+ }
+ return values;
+ };
+
+ // Returns the results of applying the iteratee to each element of the object.
+ // In contrast to _.map it returns an object.
+ _.mapObject = function(obj, iteratee, context) {
+ iteratee = cb(iteratee, context);
+ var keys = _.keys(obj),
+ length = keys.length,
+ results = {};
+ for (var index = 0; index < length; index++) {
+ var currentKey = keys[index];
+ results[currentKey] = iteratee(obj[currentKey], currentKey, obj);
+ }
+ return results;
+ };
+
+ // Convert an object into a list of `[key, value]` pairs.
+ // The opposite of _.object.
+ _.pairs = function(obj) {
+ var keys = _.keys(obj);
+ var length = keys.length;
+ var pairs = Array(length);
+ for (var i = 0; i < length; i++) {
+ pairs[i] = [keys[i], obj[keys[i]]];
+ }
+ return pairs;
+ };
+
+ // Invert the keys and values of an object. The values must be serializable.
+ _.invert = function(obj) {
+ var result = {};
+ var keys = _.keys(obj);
+ for (var i = 0, length = keys.length; i < length; i++) {
+ result[obj[keys[i]]] = keys[i];
+ }
+ return result;
+ };
+
+ // Return a sorted list of the function names available on the object.
+ // Aliased as `methods`.
+ _.functions = _.methods = function(obj) {
+ var names = [];
+ for (var key in obj) {
+ if (_.isFunction(obj[key])) names.push(key);
+ }
+ return names.sort();
+ };
+
+ // An internal function for creating assigner functions.
+ var createAssigner = function(keysFunc, defaults) {
+ return function(obj) {
+ var length = arguments.length;
+ if (defaults) obj = Object(obj);
+ if (length < 2 || obj == null) return obj;
+ for (var index = 1; index < length; index++) {
+ var source = arguments[index],
+ keys = keysFunc(source),
+ l = keys.length;
+ for (var i = 0; i < l; i++) {
+ var key = keys[i];
+ if (!defaults || obj[key] === void 0) obj[key] = source[key];
+ }
+ }
+ return obj;
+ };
+ };
+
+ // Extend a given object with all the properties in passed-in object(s).
+ _.extend = createAssigner(_.allKeys);
+
+ // Assigns a given object with all the own properties in the passed-in object(s).
+ // (https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object/assign)
+ _.extendOwn = _.assign = createAssigner(_.keys);
+
+ // Returns the first key on an object that passes a predicate test.
+ _.findKey = function(obj, predicate, context) {
+ predicate = cb(predicate, context);
+ var keys = _.keys(obj), key;
+ for (var i = 0, length = keys.length; i < length; i++) {
+ key = keys[i];
+ if (predicate(obj[key], key, obj)) return key;
+ }
+ };
+
+ // Internal pick helper function to determine if `obj` has key `key`.
+ var keyInObj = function(value, key, obj) {
+ return key in obj;
+ };
+
+ // Return a copy of the object only containing the whitelisted properties.
+ _.pick = restArguments(function(obj, keys) {
+ var result = {}, iteratee = keys[0];
+ if (obj == null) return result;
+ if (_.isFunction(iteratee)) {
+ if (keys.length > 1) iteratee = optimizeCb(iteratee, keys[1]);
+ keys = _.allKeys(obj);
+ } else {
+ iteratee = keyInObj;
+ keys = flatten(keys, false, false);
+ obj = Object(obj);
+ }
+ for (var i = 0, length = keys.length; i < length; i++) {
+ var key = keys[i];
+ var value = obj[key];
+ if (iteratee(value, key, obj)) result[key] = value;
+ }
+ return result;
+ });
+
+ // Return a copy of the object without the blacklisted properties.
+ _.omit = restArguments(function(obj, keys) {
+ var iteratee = keys[0], context;
+ if (_.isFunction(iteratee)) {
+ iteratee = _.negate(iteratee);
+ if (keys.length > 1) context = keys[1];
+ } else {
+ keys = _.map(flatten(keys, false, false), String);
+ iteratee = function(value, key) {
+ return !_.contains(keys, key);
+ };
+ }
+ return _.pick(obj, iteratee, context);
+ });
+
+ // Fill in a given object with default properties.
+ _.defaults = createAssigner(_.allKeys, true);
+
+ // Creates an object that inherits from the given prototype object.
+ // If additional properties are provided then they will be added to the
+ // created object.
+ _.create = function(prototype, props) {
+ var result = baseCreate(prototype);
+ if (props) _.extendOwn(result, props);
+ return result;
+ };
+
+ // Create a (shallow-cloned) duplicate of an object.
+ _.clone = function(obj) {
+ if (!_.isObject(obj)) return obj;
+ return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
+ };
+
+ // Invokes interceptor with the obj, and then returns obj.
+ // The primary purpose of this method is to "tap into" a method chain, in
+ // order to perform operations on intermediate results within the chain.
+ _.tap = function(obj, interceptor) {
+ interceptor(obj);
+ return obj;
+ };
+
+ // Returns whether an object has a given set of `key:value` pairs.
+ _.isMatch = function(object, attrs) {
+ var keys = _.keys(attrs), length = keys.length;
+ if (object == null) return !length;
+ var obj = Object(object);
+ for (var i = 0; i < length; i++) {
+ var key = keys[i];
+ if (attrs[key] !== obj[key] || !(key in obj)) return false;
+ }
+ return true;
+ };
+
+
+ // Internal recursive comparison function for `isEqual`.
+ var eq, deepEq;
+ eq = function(a, b, aStack, bStack) {
+ // Identical objects are equal. `0 === -0`, but they aren't identical.
+ // See the [Harmony `egal` proposal](http://wiki.ecmascript.org/doku.php?id=harmony:egal).
+ if (a === b) return a !== 0 || 1 / a === 1 / b;
+ // `null` or `undefined` only equal to itself (strict comparison).
+ if (a == null || b == null) return false;
+ // `NaN`s are equivalent, but non-reflexive.
+ if (a !== a) return b !== b;
+ // Exhaust primitive checks
+ var type = typeof a;
+ if (type !== 'function' && type !== 'object' && typeof b != 'object') return false;
+ return deepEq(a, b, aStack, bStack);
+ };
+
+ // Internal recursive comparison function for `isEqual`.
+ deepEq = function(a, b, aStack, bStack) {
+ // Unwrap any wrapped objects.
+ if (a instanceof _) a = a._wrapped;
+ if (b instanceof _) b = b._wrapped;
+ // Compare `[[Class]]` names.
+ var className = toString.call(a);
+ if (className !== toString.call(b)) return false;
+ switch (className) {
+ // Strings, numbers, regular expressions, dates, and booleans are compared by value.
+ case '[object RegExp]':
+ // RegExps are coerced to strings for comparison (Note: '' + /a/i === '/a/i')
+ case '[object String]':
+ // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
+ // equivalent to `new String("5")`.
+ return '' + a === '' + b;
+ case '[object Number]':
+ // `NaN`s are equivalent, but non-reflexive.
+ // Object(NaN) is equivalent to NaN.
+ if (+a !== +a) return +b !== +b;
+ // An `egal` comparison is performed for other numeric values.
+ return +a === 0 ? 1 / +a === 1 / b : +a === +b;
+ case '[object Date]':
+ case '[object Boolean]':
+ // Coerce dates and booleans to numeric primitive values. Dates are compared by their
+ // millisecond representations. Note that invalid dates with millisecond representations
+ // of `NaN` are not equivalent.
+ return +a === +b;
+ case '[object Symbol]':
+ return SymbolProto.valueOf.call(a) === SymbolProto.valueOf.call(b);
+ }
+
+ var areArrays = className === '[object Array]';
+ if (!areArrays) {
+ if (typeof a != 'object' || typeof b != 'object') return false;
+
+ // Objects with different constructors are not equivalent, but `Object`s or `Array`s
+ // from different frames are.
+ var aCtor = a.constructor, bCtor = b.constructor;
+ if (aCtor !== bCtor && !(_.isFunction(aCtor) && aCtor instanceof aCtor &&
+ _.isFunction(bCtor) && bCtor instanceof bCtor)
+ && ('constructor' in a && 'constructor' in b)) {
+ return false;
+ }
+ }
+ // Assume equality for cyclic structures. The algorithm for detecting cyclic
+ // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
+
+ // Initializing stack of traversed objects.
+ // It's done here since we only need them for objects and arrays comparison.
+ aStack = aStack || [];
+ bStack = bStack || [];
+ var length = aStack.length;
+ while (length--) {
+ // Linear search. Performance is inversely proportional to the number of
+ // unique nested structures.
+ if (aStack[length] === a) return bStack[length] === b;
+ }
+
+ // Add the first object to the stack of traversed objects.
+ aStack.push(a);
+ bStack.push(b);
+
+ // Recursively compare objects and arrays.
+ if (areArrays) {
+ // Compare array lengths to determine if a deep comparison is necessary.
+ length = a.length;
+ if (length !== b.length) return false;
+ // Deep compare the contents, ignoring non-numeric properties.
+ while (length--) {
+ if (!eq(a[length], b[length], aStack, bStack)) return false;
+ }
+ } else {
+ // Deep compare objects.
+ var keys = _.keys(a), key;
+ length = keys.length;
+ // Ensure that both objects contain the same number of properties before comparing deep equality.
+ if (_.keys(b).length !== length) return false;
+ while (length--) {
+ // Deep compare each member
+ key = keys[length];
+ if (!(has(b, key) && eq(a[key], b[key], aStack, bStack))) return false;
+ }
+ }
+ // Remove the first object from the stack of traversed objects.
+ aStack.pop();
+ bStack.pop();
+ return true;
+ };
+
+ // Perform a deep comparison to check if two objects are equal.
+ _.isEqual = function(a, b) {
+ return eq(a, b);
+ };
+
+ // Is a given array, string, or object empty?
+ // An "empty" object has no enumerable own-properties.
+ _.isEmpty = function(obj) {
+ if (obj == null) return true;
+ if (isArrayLike(obj) && (_.isArray(obj) || _.isString(obj) || _.isArguments(obj))) return obj.length === 0;
+ return _.keys(obj).length === 0;
+ };
+
+ // Is a given value a DOM element?
+ _.isElement = function(obj) {
+ return !!(obj && obj.nodeType === 1);
+ };
+
+ // Is a given value an array?
+ // Delegates to ECMA5's native Array.isArray
+ _.isArray = nativeIsArray || function(obj) {
+ return toString.call(obj) === '[object Array]';
+ };
+
+ // Is a given variable an object?
+ _.isObject = function(obj) {
+ var type = typeof obj;
+ return type === 'function' || type === 'object' && !!obj;
+ };
+
+ // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp, isError, isMap, isWeakMap, isSet, isWeakSet.
+ _.each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp', 'Error', 'Symbol', 'Map', 'WeakMap', 'Set', 'WeakSet'], function(name) {
+ _['is' + name] = function(obj) {
+ return toString.call(obj) === '[object ' + name + ']';
+ };
+ });
+
+ // Define a fallback version of the method in browsers (ahem, IE < 9), where
+ // there isn't any inspectable "Arguments" type.
+ if (!_.isArguments(arguments)) {
+ _.isArguments = function(obj) {
+ return has(obj, 'callee');
+ };
+ }
+
+ // Optimize `isFunction` if appropriate. Work around some typeof bugs in old v8,
+ // IE 11 (#1621), Safari 8 (#1929), and PhantomJS (#2236).
+ var nodelist = root.document && root.document.childNodes;
+ if (typeof /./ != 'function' && typeof Int8Array != 'object' && typeof nodelist != 'function') {
+ _.isFunction = function(obj) {
+ return typeof obj == 'function' || false;
+ };
+ }
+
+ // Is a given object a finite number?
+ _.isFinite = function(obj) {
+ return !_.isSymbol(obj) && isFinite(obj) && !isNaN(parseFloat(obj));
+ };
+
+ // Is the given value `NaN`?
+ _.isNaN = function(obj) {
+ return _.isNumber(obj) && isNaN(obj);
+ };
+
+ // Is a given value a boolean?
+ _.isBoolean = function(obj) {
+ return obj === true || obj === false || toString.call(obj) === '[object Boolean]';
+ };
+
+ // Is a given value equal to null?
+ _.isNull = function(obj) {
+ return obj === null;
+ };
+
+ // Is a given variable undefined?
+ _.isUndefined = function(obj) {
+ return obj === void 0;
+ };
+
+ // Shortcut function for checking if an object has a given property directly
+ // on itself (in other words, not on a prototype).
+ _.has = function(obj, path) {
+ if (!_.isArray(path)) {
+ return has(obj, path);
+ }
+ var length = path.length;
+ for (var i = 0; i < length; i++) {
+ var key = path[i];
+ if (obj == null || !hasOwnProperty.call(obj, key)) {
+ return false;
+ }
+ obj = obj[key];
+ }
+ return !!length;
+ };
+
+ // Utility Functions
+ // -----------------
+
+ // Run Underscore.js in *noConflict* mode, returning the `_` variable to its
+ // previous owner. Returns a reference to the Underscore object.
+ _.noConflict = function() {
+ root._ = previousUnderscore;
+ return this;
+ };
+
+ // Keep the identity function around for default iteratees.
+ _.identity = function(value) {
+ return value;
+ };
+
+ // Predicate-generating functions. Often useful outside of Underscore.
+ _.constant = function(value) {
+ return function() {
+ return value;
+ };
+ };
+
+ _.noop = function(){};
+
+ // Creates a function that, when passed an object, will traverse that object’s
+ // properties down the given `path`, specified as an array of keys or indexes.
+ _.property = function(path) {
+ if (!_.isArray(path)) {
+ return shallowProperty(path);
+ }
+ return function(obj) {
+ return deepGet(obj, path);
+ };
+ };
+
+ // Generates a function for a given object that returns a given property.
+ _.propertyOf = function(obj) {
+ if (obj == null) {
+ return function(){};
+ }
+ return function(path) {
+ return !_.isArray(path) ? obj[path] : deepGet(obj, path);
+ };
+ };
+
+ // Returns a predicate for checking whether an object has a given set of
+ // `key:value` pairs.
+ _.matcher = _.matches = function(attrs) {
+ attrs = _.extendOwn({}, attrs);
+ return function(obj) {
+ return _.isMatch(obj, attrs);
+ };
+ };
+
+ // Run a function **n** times.
+ _.times = function(n, iteratee, context) {
+ var accum = Array(Math.max(0, n));
+ iteratee = optimizeCb(iteratee, context, 1);
+ for (var i = 0; i < n; i++) accum[i] = iteratee(i);
+ return accum;
+ };
+
+ // Return a random integer between min and max (inclusive).
+ _.random = function(min, max) {
+ if (max == null) {
+ max = min;
+ min = 0;
+ }
+ return min + Math.floor(Math.random() * (max - min + 1));
+ };
+
+ // A (possibly faster) way to get the current timestamp as an integer.
+ _.now = Date.now || function() {
+ return new Date().getTime();
+ };
+
+ // List of HTML entities for escaping.
+ var escapeMap = {
+ '&': '&',
+ '<': '<',
+ '>': '>',
+ '"': '"',
+ "'": ''',
+ '`': '`'
+ };
+ var unescapeMap = _.invert(escapeMap);
+
+ // Functions for escaping and unescaping strings to/from HTML interpolation.
+ var createEscaper = function(map) {
+ var escaper = function(match) {
+ return map[match];
+ };
+ // Regexes for identifying a key that needs to be escaped.
+ var source = '(?:' + _.keys(map).join('|') + ')';
+ var testRegexp = RegExp(source);
+ var replaceRegexp = RegExp(source, 'g');
+ return function(string) {
+ string = string == null ? '' : '' + string;
+ return testRegexp.test(string) ? string.replace(replaceRegexp, escaper) : string;
+ };
+ };
+ _.escape = createEscaper(escapeMap);
+ _.unescape = createEscaper(unescapeMap);
+
+ // Traverses the children of `obj` along `path`. If a child is a function, it
+ // is invoked with its parent as context. Returns the value of the final
+ // child, or `fallback` if any child is undefined.
+ _.result = function(obj, path, fallback) {
+ if (!_.isArray(path)) path = [path];
+ var length = path.length;
+ if (!length) {
+ return _.isFunction(fallback) ? fallback.call(obj) : fallback;
+ }
+ for (var i = 0; i < length; i++) {
+ var prop = obj == null ? void 0 : obj[path[i]];
+ if (prop === void 0) {
+ prop = fallback;
+ i = length; // Ensure we don't continue iterating.
+ }
+ obj = _.isFunction(prop) ? prop.call(obj) : prop;
+ }
+ return obj;
+ };
+
+ // Generate a unique integer id (unique within the entire client session).
+ // Useful for temporary DOM ids.
+ var idCounter = 0;
+ _.uniqueId = function(prefix) {
+ var id = ++idCounter + '';
+ return prefix ? prefix + id : id;
+ };
+
+ // By default, Underscore uses ERB-style template delimiters, change the
+ // following template settings to use alternative delimiters.
+ _.templateSettings = {
+ evaluate: /<%([\s\S]+?)%>/g,
+ interpolate: /<%=([\s\S]+?)%>/g,
+ escape: /<%-([\s\S]+?)%>/g
+ };
+
+ // When customizing `templateSettings`, if you don't want to define an
+ // interpolation, evaluation or escaping regex, we need one that is
+ // guaranteed not to match.
+ var noMatch = /(.)^/;
+
+ // Certain characters need to be escaped so that they can be put into a
+ // string literal.
+ var escapes = {
+ "'": "'",
+ '\\': '\\',
+ '\r': 'r',
+ '\n': 'n',
+ '\u2028': 'u2028',
+ '\u2029': 'u2029'
+ };
+
+ var escapeRegExp = /\\|'|\r|\n|\u2028|\u2029/g;
+
+ var escapeChar = function(match) {
+ return '\\' + escapes[match];
+ };
+
+ // In order to prevent third-party code injection through
+ // `_.templateSettings.variable`, we test it against the following regular
+ // expression. It is intentionally a bit more liberal than just matching valid
+ // identifiers, but still prevents possible loopholes through defaults or
+ // destructuring assignment.
+ var bareIdentifier = /^\s*(\w|\$)+\s*$/;
+
+ // JavaScript micro-templating, similar to John Resig's implementation.
+ // Underscore templating handles arbitrary delimiters, preserves whitespace,
+ // and correctly escapes quotes within interpolated code.
+ // NB: `oldSettings` only exists for backwards compatibility.
+ _.template = function(text, settings, oldSettings) {
+ if (!settings && oldSettings) settings = oldSettings;
+ settings = _.defaults({}, settings, _.templateSettings);
+
+ // Combine delimiters into one regular expression via alternation.
+ var matcher = RegExp([
+ (settings.escape || noMatch).source,
+ (settings.interpolate || noMatch).source,
+ (settings.evaluate || noMatch).source
+ ].join('|') + '|$', 'g');
+
+ // Compile the template source, escaping string literals appropriately.
+ var index = 0;
+ var source = "__p+='";
+ text.replace(matcher, function(match, escape, interpolate, evaluate, offset) {
+ source += text.slice(index, offset).replace(escapeRegExp, escapeChar);
+ index = offset + match.length;
+
+ if (escape) {
+ source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'";
+ } else if (interpolate) {
+ source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'";
+ } else if (evaluate) {
+ source += "';\n" + evaluate + "\n__p+='";
+ }
+
+ // Adobe VMs need the match returned to produce the correct offset.
+ return match;
+ });
+ source += "';\n";
+
+ var argument = settings.variable;
+ if (argument) {
+ // Insure against third-party code injection.
+ if (!bareIdentifier.test(argument)) throw new Error(
+ 'variable is not a bare identifier: ' + argument
+ );
+ } else {
+ // If a variable is not specified, place data values in local scope.
+ source = 'with(obj||{}){\n' + source + '}\n';
+ argument = 'obj';
+ }
+
+ source = "var __t,__p='',__j=Array.prototype.join," +
+ "print=function(){__p+=__j.call(arguments,'');};\n" +
+ source + 'return __p;\n';
+
+ var render;
+ try {
+ render = new Function(argument, '_', source);
+ } catch (e) {
+ e.source = source;
+ throw e;
+ }
+
+ var template = function(data) {
+ return render.call(this, data, _);
+ };
+
+ // Provide the compiled source as a convenience for precompilation.
+ template.source = 'function(' + argument + '){\n' + source + '}';
+
+ return template;
+ };
+
+ // Add a "chain" function. Start chaining a wrapped Underscore object.
+ _.chain = function(obj) {
+ var instance = _(obj);
+ instance._chain = true;
+ return instance;
+ };
+
+ // OOP
+ // ---------------
+ // If Underscore is called as a function, it returns a wrapped object that
+ // can be used OO-style. This wrapper holds altered versions of all the
+ // underscore functions. Wrapped objects may be chained.
+
+ // Helper function to continue chaining intermediate results.
+ var chainResult = function(instance, obj) {
+ return instance._chain ? _(obj).chain() : obj;
+ };
+
+ // Add your own custom functions to the Underscore object.
+ _.mixin = function(obj) {
+ _.each(_.functions(obj), function(name) {
+ var func = _[name] = obj[name];
+ _.prototype[name] = function() {
+ var args = [this._wrapped];
+ push.apply(args, arguments);
+ return chainResult(this, func.apply(_, args));
+ };
+ });
+ return _;
+ };
+
+ // Add all of the Underscore functions to the wrapper object.
+ _.mixin(_);
+
+ // Add all mutator Array functions to the wrapper.
+ _.each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
+ var method = ArrayProto[name];
+ _.prototype[name] = function() {
+ var obj = this._wrapped;
+ method.apply(obj, arguments);
+ if ((name === 'shift' || name === 'splice') && obj.length === 0) delete obj[0];
+ return chainResult(this, obj);
+ };
+ });
+
+ // Add all accessor Array functions to the wrapper.
+ _.each(['concat', 'join', 'slice'], function(name) {
+ var method = ArrayProto[name];
+ _.prototype[name] = function() {
+ return chainResult(this, method.apply(this._wrapped, arguments));
+ };
+ });
+
+ // Extracts the result from a wrapped and chained object.
+ _.prototype.value = function() {
+ return this._wrapped;
+ };
+
+ // Provide unwrapping proxy for some methods used in engine operations
+ // such as arithmetic and JSON stringification.
+ _.prototype.valueOf = _.prototype.toJSON = _.prototype.value;
+
+ _.prototype.toString = function() {
+ return String(this._wrapped);
+ };
+
+ // AMD registration happens at the end for compatibility with AMD loaders
+ // that may not enforce next-turn semantics on modules. Even though general
+ // practice for AMD registration is to be anonymous, underscore registers
+ // as a named module because, like jQuery, it is a base library that is
+ // popular enough to be bundled in a third party lib, but not be part of
+ // an AMD load request. Those cases could generate an error when an
+ // anonymous define() is called outside of a loader request.
+ if (typeof define == 'function' && define.amd) {
+ define('underscore', [], function() {
+ return _;
+ });
+ }
+}());
diff --git a/doc/html/_static/up-pressed.png b/doc/html/_static/up-pressed.png
new file mode 100644
index 0000000000000000000000000000000000000000..acee3b68efbbfb9de3bfa73fce2531380f4bd820
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diff --git a/doc/html/_static/up.png b/doc/html/_static/up.png
new file mode 100644
index 0000000000000000000000000000000000000000..2a940a7da7c14e6a36901e83306849ba7efad4d4
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diff --git a/doc/html/_static/websupport.js b/doc/html/_static/websupport.js
new file mode 100644
index 0000000000000000000000000000000000000000..3b4999ebf2ee4d35d8bbe05dc6636c3f64b2dfa8
--- /dev/null
+++ b/doc/html/_static/websupport.js
@@ -0,0 +1,808 @@
+/*
+ * websupport.js
+ * ~~~~~~~~~~~~~
+ *
+ * sphinx.websupport utilities for all documentation.
+ *
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+(function($) {
+ $.fn.autogrow = function() {
+ return this.each(function() {
+ var textarea = this;
+
+ $.fn.autogrow.resize(textarea);
+
+ $(textarea)
+ .focus(function() {
+ textarea.interval = setInterval(function() {
+ $.fn.autogrow.resize(textarea);
+ }, 500);
+ })
+ .blur(function() {
+ clearInterval(textarea.interval);
+ });
+ });
+ };
+
+ $.fn.autogrow.resize = function(textarea) {
+ var lineHeight = parseInt($(textarea).css('line-height'), 10);
+ var lines = textarea.value.split('\n');
+ var columns = textarea.cols;
+ var lineCount = 0;
+ $.each(lines, function() {
+ lineCount += Math.ceil(this.length / columns) || 1;
+ });
+ var height = lineHeight * (lineCount + 1);
+ $(textarea).css('height', height);
+ };
+})(jQuery);
+
+(function($) {
+ var comp, by;
+
+ function init() {
+ initEvents();
+ initComparator();
+ }
+
+ function initEvents() {
+ $(document).on("click", 'a.comment-close', function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ });
+ $(document).on("click", 'a.vote', function(event) {
+ event.preventDefault();
+ handleVote($(this));
+ });
+ $(document).on("click", 'a.reply', function(event) {
+ event.preventDefault();
+ openReply($(this).attr('id').substring(2));
+ });
+ $(document).on("click", 'a.close-reply', function(event) {
+ event.preventDefault();
+ closeReply($(this).attr('id').substring(2));
+ });
+ $(document).on("click", 'a.sort-option', function(event) {
+ event.preventDefault();
+ handleReSort($(this));
+ });
+ $(document).on("click", 'a.show-proposal', function(event) {
+ event.preventDefault();
+ showProposal($(this).attr('id').substring(2));
+ });
+ $(document).on("click", 'a.hide-proposal', function(event) {
+ event.preventDefault();
+ hideProposal($(this).attr('id').substring(2));
+ });
+ $(document).on("click", 'a.show-propose-change', function(event) {
+ event.preventDefault();
+ showProposeChange($(this).attr('id').substring(2));
+ });
+ $(document).on("click", 'a.hide-propose-change', function(event) {
+ event.preventDefault();
+ hideProposeChange($(this).attr('id').substring(2));
+ });
+ $(document).on("click", 'a.accept-comment', function(event) {
+ event.preventDefault();
+ acceptComment($(this).attr('id').substring(2));
+ });
+ $(document).on("click", 'a.delete-comment', function(event) {
+ event.preventDefault();
+ deleteComment($(this).attr('id').substring(2));
+ });
+ $(document).on("click", 'a.comment-markup', function(event) {
+ event.preventDefault();
+ toggleCommentMarkupBox($(this).attr('id').substring(2));
+ });
+ }
+
+ /**
+ * Set comp, which is a comparator function used for sorting and
+ * inserting comments into the list.
+ */
+ function setComparator() {
+ // If the first three letters are "asc", sort in ascending order
+ // and remove the prefix.
+ if (by.substring(0,3) == 'asc') {
+ var i = by.substring(3);
+ comp = function(a, b) { return a[i] - b[i]; };
+ } else {
+ // Otherwise sort in descending order.
+ comp = function(a, b) { return b[by] - a[by]; };
+ }
+
+ // Reset link styles and format the selected sort option.
+ $('a.sel').attr('href', '#').removeClass('sel');
+ $('a.by' + by).removeAttr('href').addClass('sel');
+ }
+
+ /**
+ * Create a comp function. If the user has preferences stored in
+ * the sortBy cookie, use those, otherwise use the default.
+ */
+ function initComparator() {
+ by = 'rating'; // Default to sort by rating.
+ // If the sortBy cookie is set, use that instead.
+ if (document.cookie.length > 0) {
+ var start = document.cookie.indexOf('sortBy=');
+ if (start != -1) {
+ start = start + 7;
+ var end = document.cookie.indexOf(";", start);
+ if (end == -1) {
+ end = document.cookie.length;
+ by = unescape(document.cookie.substring(start, end));
+ }
+ }
+ }
+ setComparator();
+ }
+
+ /**
+ * Show a comment div.
+ */
+ function show(id) {
+ $('#ao' + id).hide();
+ $('#ah' + id).show();
+ var context = $.extend({id: id}, opts);
+ var popup = $(renderTemplate(popupTemplate, context)).hide();
+ popup.find('textarea[name="proposal"]').hide();
+ popup.find('a.by' + by).addClass('sel');
+ var form = popup.find('#cf' + id);
+ form.submit(function(event) {
+ event.preventDefault();
+ addComment(form);
+ });
+ $('#s' + id).after(popup);
+ popup.slideDown('fast', function() {
+ getComments(id);
+ });
+ }
+
+ /**
+ * Hide a comment div.
+ */
+ function hide(id) {
+ $('#ah' + id).hide();
+ $('#ao' + id).show();
+ var div = $('#sc' + id);
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ }
+
+ /**
+ * Perform an ajax request to get comments for a node
+ * and insert the comments into the comments tree.
+ */
+ function getComments(id) {
+ $.ajax({
+ type: 'GET',
+ url: opts.getCommentsURL,
+ data: {node: id},
+ success: function(data, textStatus, request) {
+ var ul = $('#cl' + id);
+ var speed = 100;
+ $('#cf' + id)
+ .find('textarea[name="proposal"]')
+ .data('source', data.source);
+
+ if (data.comments.length === 0) {
+ ul.html('<li>No comments yet.</li>');
+ ul.data('empty', true);
+ } else {
+ // If there are comments, sort them and put them in the list.
+ var comments = sortComments(data.comments);
+ speed = data.comments.length * 100;
+ appendComments(comments, ul);
+ ul.data('empty', false);
+ }
+ $('#cn' + id).slideUp(speed + 200);
+ ul.slideDown(speed);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem retrieving the comments.');
+ },
+ dataType: 'json'
+ });
+ }
+
+ /**
+ * Add a comment via ajax and insert the comment into the comment tree.
+ */
+ function addComment(form) {
+ var node_id = form.find('input[name="node"]').val();
+ var parent_id = form.find('input[name="parent"]').val();
+ var text = form.find('textarea[name="comment"]').val();
+ var proposal = form.find('textarea[name="proposal"]').val();
+
+ if (text == '') {
+ showError('Please enter a comment.');
+ return;
+ }
+
+ // Disable the form that is being submitted.
+ form.find('textarea,input').attr('disabled', 'disabled');
+
+ // Send the comment to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.addCommentURL,
+ dataType: 'json',
+ data: {
+ node: node_id,
+ parent: parent_id,
+ text: text,
+ proposal: proposal
+ },
+ success: function(data, textStatus, error) {
+ // Reset the form.
+ if (node_id) {
+ hideProposeChange(node_id);
+ }
+ form.find('textarea')
+ .val('')
+ .add(form.find('input'))
+ .removeAttr('disabled');
+ var ul = $('#cl' + (node_id || parent_id));
+ if (ul.data('empty')) {
+ $(ul).empty();
+ ul.data('empty', false);
+ }
+ insertComment(data.comment);
+ var ao = $('#ao' + node_id);
+ ao.find('img').attr({'src': opts.commentBrightImage});
+ if (node_id) {
+ // if this was a "root" comment, remove the commenting box
+ // (the user can get it back by reopening the comment popup)
+ $('#ca' + node_id).slideUp();
+ }
+ },
+ error: function(request, textStatus, error) {
+ form.find('textarea,input').removeAttr('disabled');
+ showError('Oops, there was a problem adding the comment.');
+ }
+ });
+ }
+
+ /**
+ * Recursively append comments to the main comment list and children
+ * lists, creating the comment tree.
+ */
+ function appendComments(comments, ul) {
+ $.each(comments, function() {
+ var div = createCommentDiv(this);
+ ul.append($(document.createElement('li')).html(div));
+ appendComments(this.children, div.find('ul.comment-children'));
+ // To avoid stagnating data, don't store the comments children in data.
+ this.children = null;
+ div.data('comment', this);
+ });
+ }
+
+ /**
+ * After adding a new comment, it must be inserted in the correct
+ * location in the comment tree.
+ */
+ function insertComment(comment) {
+ var div = createCommentDiv(comment);
+
+ // To avoid stagnating data, don't store the comments children in data.
+ comment.children = null;
+ div.data('comment', comment);
+
+ var ul = $('#cl' + (comment.node || comment.parent));
+ var siblings = getChildren(ul);
+
+ var li = $(document.createElement('li'));
+ li.hide();
+
+ // Determine where in the parents children list to insert this comment.
+ for(var i=0; i < siblings.length; i++) {
+ if (comp(comment, siblings[i]) <= 0) {
+ $('#cd' + siblings[i].id)
+ .parent()
+ .before(li.html(div));
+ li.slideDown('fast');
+ return;
+ }
+ }
+
+ // If we get here, this comment rates lower than all the others,
+ // or it is the only comment in the list.
+ ul.append(li.html(div));
+ li.slideDown('fast');
+ }
+
+ function acceptComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.acceptCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ $('#cm' + id).fadeOut('fast');
+ $('#cd' + id).removeClass('moderate');
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem accepting the comment.');
+ }
+ });
+ }
+
+ function deleteComment(id) {
+ $.ajax({
+ type: 'POST',
+ url: opts.deleteCommentURL,
+ data: {id: id},
+ success: function(data, textStatus, request) {
+ var div = $('#cd' + id);
+ if (data == 'delete') {
+ // Moderator mode: remove the comment and all children immediately
+ div.slideUp('fast', function() {
+ div.remove();
+ });
+ return;
+ }
+ // User mode: only mark the comment as deleted
+ div
+ .find('span.user-id:first')
+ .text('[deleted]').end()
+ .find('div.comment-text:first')
+ .text('[deleted]').end()
+ .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
+ ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
+ .remove();
+ var comment = div.data('comment');
+ comment.username = '[deleted]';
+ comment.text = '[deleted]';
+ div.data('comment', comment);
+ },
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem deleting the comment.');
+ }
+ });
+ }
+
+ function showProposal(id) {
+ $('#sp' + id).hide();
+ $('#hp' + id).show();
+ $('#pr' + id).slideDown('fast');
+ }
+
+ function hideProposal(id) {
+ $('#hp' + id).hide();
+ $('#sp' + id).show();
+ $('#pr' + id).slideUp('fast');
+ }
+
+ function showProposeChange(id) {
+ $('#pc' + id).hide();
+ $('#hc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val(textarea.data('source'));
+ $.fn.autogrow.resize(textarea[0]);
+ textarea.slideDown('fast');
+ }
+
+ function hideProposeChange(id) {
+ $('#hc' + id).hide();
+ $('#pc' + id).show();
+ var textarea = $('#pt' + id);
+ textarea.val('').removeAttr('disabled');
+ textarea.slideUp('fast');
+ }
+
+ function toggleCommentMarkupBox(id) {
+ $('#mb' + id).toggle();
+ }
+
+ /** Handle when the user clicks on a sort by link. */
+ function handleReSort(link) {
+ var classes = link.attr('class').split(/\s+/);
+ for (var i=0; i<classes.length; i++) {
+ if (classes[i] != 'sort-option') {
+ by = classes[i].substring(2);
+ }
+ }
+ setComparator();
+ // Save/update the sortBy cookie.
+ var expiration = new Date();
+ expiration.setDate(expiration.getDate() + 365);
+ document.cookie= 'sortBy=' + escape(by) +
+ ';expires=' + expiration.toUTCString();
+ $('ul.comment-ul').each(function(index, ul) {
+ var comments = getChildren($(ul), true);
+ comments = sortComments(comments);
+ appendComments(comments, $(ul).empty());
+ });
+ }
+
+ /**
+ * Function to process a vote when a user clicks an arrow.
+ */
+ function handleVote(link) {
+ if (!opts.voting) {
+ showError("You'll need to login to vote.");
+ return;
+ }
+
+ var id = link.attr('id');
+ if (!id) {
+ // Didn't click on one of the voting arrows.
+ return;
+ }
+ // If it is an unvote, the new vote value is 0,
+ // Otherwise it's 1 for an upvote, or -1 for a downvote.
+ var value = 0;
+ if (id.charAt(1) != 'u') {
+ value = id.charAt(0) == 'u' ? 1 : -1;
+ }
+ // The data to be sent to the server.
+ var d = {
+ comment_id: id.substring(2),
+ value: value
+ };
+
+ // Swap the vote and unvote links.
+ link.hide();
+ $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
+ .show();
+
+ // The div the comment is displayed in.
+ var div = $('div#cd' + d.comment_id);
+ var data = div.data('comment');
+
+ // If this is not an unvote, and the other vote arrow has
+ // already been pressed, unpress it.
+ if ((d.value !== 0) && (data.vote === d.value * -1)) {
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
+ $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
+ }
+
+ // Update the comments rating in the local data.
+ data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
+ data.vote = d.value;
+ div.data('comment', data);
+
+ // Change the rating text.
+ div.find('.rating:first')
+ .text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
+
+ // Send the vote information to the server.
+ $.ajax({
+ type: "POST",
+ url: opts.processVoteURL,
+ data: d,
+ error: function(request, textStatus, error) {
+ showError('Oops, there was a problem casting that vote.');
+ }
+ });
+ }
+
+ /**
+ * Open a reply form used to reply to an existing comment.
+ */
+ function openReply(id) {
+ // Swap out the reply link for the hide link
+ $('#rl' + id).hide();
+ $('#cr' + id).show();
+
+ // Add the reply li to the children ul.
+ var div = $(renderTemplate(replyTemplate, {id: id})).hide();
+ $('#cl' + id)
+ .prepend(div)
+ // Setup the submit handler for the reply form.
+ .find('#rf' + id)
+ .submit(function(event) {
+ event.preventDefault();
+ addComment($('#rf' + id));
+ closeReply(id);
+ })
+ .find('input[type=button]')
+ .click(function() {
+ closeReply(id);
+ });
+ div.slideDown('fast', function() {
+ $('#rf' + id).find('textarea').focus();
+ });
+ }
+
+ /**
+ * Close the reply form opened with openReply.
+ */
+ function closeReply(id) {
+ // Remove the reply div from the DOM.
+ $('#rd' + id).slideUp('fast', function() {
+ $(this).remove();
+ });
+
+ // Swap out the hide link for the reply link
+ $('#cr' + id).hide();
+ $('#rl' + id).show();
+ }
+
+ /**
+ * Recursively sort a tree of comments using the comp comparator.
+ */
+ function sortComments(comments) {
+ comments.sort(comp);
+ $.each(comments, function() {
+ this.children = sortComments(this.children);
+ });
+ return comments;
+ }
+
+ /**
+ * Get the children comments from a ul. If recursive is true,
+ * recursively include childrens' children.
+ */
+ function getChildren(ul, recursive) {
+ var children = [];
+ ul.children().children("[id^='cd']")
+ .each(function() {
+ var comment = $(this).data('comment');
+ if (recursive)
+ comment.children = getChildren($(this).find('#cl' + comment.id), true);
+ children.push(comment);
+ });
+ return children;
+ }
+
+ /** Create a div to display a comment in. */
+ function createCommentDiv(comment) {
+ if (!comment.displayed && !opts.moderator) {
+ return $('<div class="moderate">Thank you! Your comment will show up '
+ + 'once it is has been approved by a moderator.</div>');
+ }
+ // Prettify the comment rating.
+ comment.pretty_rating = comment.rating + ' point' +
+ (comment.rating == 1 ? '' : 's');
+ // Make a class (for displaying not yet moderated comments differently)
+ comment.css_class = comment.displayed ? '' : ' moderate';
+ // Create a div for this comment.
+ var context = $.extend({}, opts, comment);
+ var div = $(renderTemplate(commentTemplate, context));
+
+ // If the user has voted on this comment, highlight the correct arrow.
+ if (comment.vote) {
+ var direction = (comment.vote == 1) ? 'u' : 'd';
+ div.find('#' + direction + 'v' + comment.id).hide();
+ div.find('#' + direction + 'u' + comment.id).show();
+ }
+
+ if (opts.moderator || comment.text != '[deleted]') {
+ div.find('a.reply').show();
+ if (comment.proposal_diff)
+ div.find('#sp' + comment.id).show();
+ if (opts.moderator && !comment.displayed)
+ div.find('#cm' + comment.id).show();
+ if (opts.moderator || (opts.username == comment.username))
+ div.find('#dc' + comment.id).show();
+ }
+ return div;
+ }
+
+ /**
+ * A simple template renderer. Placeholders such as <%id%> are replaced
+ * by context['id'] with items being escaped. Placeholders such as <#id#>
+ * are not escaped.
+ */
+ function renderTemplate(template, context) {
+ var esc = $(document.createElement('div'));
+
+ function handle(ph, escape) {
+ var cur = context;
+ $.each(ph.split('.'), function() {
+ cur = cur[this];
+ });
+ return escape ? esc.text(cur || "").html() : cur;
+ }
+
+ return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
+ return handle(arguments[2], arguments[1] == '%' ? true : false);
+ });
+ }
+
+ /** Flash an error message briefly. */
+ function showError(message) {
+ $(document.createElement('div')).attr({'class': 'popup-error'})
+ .append($(document.createElement('div'))
+ .attr({'class': 'error-message'}).text(message))
+ .appendTo('body')
+ .fadeIn("slow")
+ .delay(2000)
+ .fadeOut("slow");
+ }
+
+ /** Add a link the user uses to open the comments popup. */
+ $.fn.comment = function() {
+ return this.each(function() {
+ var id = $(this).attr('id').substring(1);
+ var count = COMMENT_METADATA[id];
+ var title = count + ' comment' + (count == 1 ? '' : 's');
+ var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
+ var addcls = count == 0 ? ' nocomment' : '';
+ $(this)
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-open' + addcls,
+ id: 'ao' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: image,
+ alt: 'comment',
+ title: title
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ show($(this).attr('id').substring(2));
+ })
+ )
+ .append(
+ $(document.createElement('a')).attr({
+ href: '#',
+ 'class': 'sphinx-comment-close hidden',
+ id: 'ah' + id
+ })
+ .append($(document.createElement('img')).attr({
+ src: opts.closeCommentImage,
+ alt: 'close',
+ title: 'close'
+ }))
+ .click(function(event) {
+ event.preventDefault();
+ hide($(this).attr('id').substring(2));
+ })
+ );
+ });
+ };
+
+ var opts = {
+ processVoteURL: '/_process_vote',
+ addCommentURL: '/_add_comment',
+ getCommentsURL: '/_get_comments',
+ acceptCommentURL: '/_accept_comment',
+ deleteCommentURL: '/_delete_comment',
+ commentImage: '/static/_static/comment.png',
+ closeCommentImage: '/static/_static/comment-close.png',
+ loadingImage: '/static/_static/ajax-loader.gif',
+ commentBrightImage: '/static/_static/comment-bright.png',
+ upArrow: '/static/_static/up.png',
+ downArrow: '/static/_static/down.png',
+ upArrowPressed: '/static/_static/up-pressed.png',
+ downArrowPressed: '/static/_static/down-pressed.png',
+ voting: false,
+ moderator: false
+ };
+
+ if (typeof COMMENT_OPTIONS != "undefined") {
+ opts = jQuery.extend(opts, COMMENT_OPTIONS);
+ }
+
+ var popupTemplate = '\
+ <div class="sphinx-comments" id="sc<%id%>">\
+ <p class="sort-options">\
+ Sort by:\
+ <a href="#" class="sort-option byrating">best rated</a>\
+ <a href="#" class="sort-option byascage">newest</a>\
+ <a href="#" class="sort-option byage">oldest</a>\
+ </p>\
+ <div class="comment-header">Comments</div>\
+ <div class="comment-loading" id="cn<%id%>">\
+ loading comments... <img src="<%loadingImage%>" alt="" /></div>\
+ <ul id="cl<%id%>" class="comment-ul"></ul>\
+ <div id="ca<%id%>">\
+ <p class="add-a-comment">Add a comment\
+ (<a href="#" class="comment-markup" id="ab<%id%>">markup</a>):</p>\
+ <div class="comment-markup-box" id="mb<%id%>">\
+ reStructured text markup: <i>*emph*</i>, <b>**strong**</b>, \
+ <code>``code``</code>, \
+ code blocks: <code>::</code> and an indented block after blank line</div>\
+ <form method="post" id="cf<%id%>" class="comment-form" action="">\
+ <textarea name="comment" cols="80"></textarea>\
+ <p class="propose-button">\
+ <a href="#" id="pc<%id%>" class="show-propose-change">\
+ Propose a change ▹\
+ </a>\
+ <a href="#" id="hc<%id%>" class="hide-propose-change">\
+ Propose a change ▿\
+ </a>\
+ </p>\
+ <textarea name="proposal" id="pt<%id%>" cols="80"\
+ spellcheck="false"></textarea>\
+ <input type="submit" value="Add comment" />\
+ <input type="hidden" name="node" value="<%id%>" />\
+ <input type="hidden" name="parent" value="" />\
+ </form>\
+ </div>\
+ </div>';
+
+ var commentTemplate = '\
+ <div id="cd<%id%>" class="sphinx-comment<%css_class%>">\
+ <div class="vote">\
+ <div class="arrow">\
+ <a href="#" id="uv<%id%>" class="vote" title="vote up">\
+ <img src="<%upArrow%>" />\
+ </a>\
+ <a href="#" id="uu<%id%>" class="un vote" title="vote up">\
+ <img src="<%upArrowPressed%>" />\
+ </a>\
+ </div>\
+ <div class="arrow">\
+ <a href="#" id="dv<%id%>" class="vote" title="vote down">\
+ <img src="<%downArrow%>" id="da<%id%>" />\
+ </a>\
+ <a href="#" id="du<%id%>" class="un vote" title="vote down">\
+ <img src="<%downArrowPressed%>" />\
+ </a>\
+ </div>\
+ </div>\
+ <div class="comment-content">\
+ <p class="tagline comment">\
+ <span class="user-id"><%username%></span>\
+ <span class="rating"><%pretty_rating%></span>\
+ <span class="delta"><%time.delta%></span>\
+ </p>\
+ <div class="comment-text comment"><#text#></div>\
+ <p class="comment-opts comment">\
+ <a href="#" class="reply hidden" id="rl<%id%>">reply ▹</a>\
+ <a href="#" class="close-reply" id="cr<%id%>">reply ▿</a>\
+ <a href="#" id="sp<%id%>" class="show-proposal">proposal ▹</a>\
+ <a href="#" id="hp<%id%>" class="hide-proposal">proposal ▿</a>\
+ <a href="#" id="dc<%id%>" class="delete-comment hidden">delete</a>\
+ <span id="cm<%id%>" class="moderation hidden">\
+ <a href="#" id="ac<%id%>" class="accept-comment">accept</a>\
+ </span>\
+ </p>\
+ <pre class="proposal" id="pr<%id%>">\
+<#proposal_diff#>\
+ </pre>\
+ <ul class="comment-children" id="cl<%id%>"></ul>\
+ </div>\
+ <div class="clearleft"></div>\
+ </div>\
+ </div>';
+
+ var replyTemplate = '\
+ <li>\
+ <div class="reply-div" id="rd<%id%>">\
+ <form id="rf<%id%>">\
+ <textarea name="comment" cols="80"></textarea>\
+ <input type="submit" value="Add reply" />\
+ <input type="button" value="Cancel" />\
+ <input type="hidden" name="parent" value="<%id%>" />\
+ <input type="hidden" name="node" value="" />\
+ </form>\
+ </div>\
+ </li>';
+
+ $(document).ready(function() {
+ init();
+ });
+})(jQuery);
+
+$(document).ready(function() {
+ // add comment anchors for all paragraphs that are commentable
+ $('.sphinx-has-comment').comment();
+
+ // highlight search words in search results
+ $("div.context").each(function() {
+ var params = $.getQueryParameters();
+ var terms = (params.q) ? params.q[0].split(/\s+/) : [];
+ var result = $(this);
+ $.each(terms, function() {
+ result.highlightText(this.toLowerCase(), 'highlighted');
+ });
+ });
+
+ // directly open comment window if requested
+ var anchor = document.location.hash;
+ if (anchor.substring(0, 9) == '#comment-') {
+ $('#ao' + anchor.substring(9)).click();
+ document.location.hash = '#s' + anchor.substring(9);
+ }
+});
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index 03acc8c078ac24d3ae060b4247b3658346ecdff9..c17396d63f79bdf26a29d16e85d25dc278ef95b4 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>ProMod3 Actions — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>ProMod3 Actions — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="project-actions">
@@ -63,8 +62,9 @@ given order. The chains of the target model are named with default chain names
(A, B, C, …, see <a class="reference internal" href="../modelling/pipeline.html#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a>).
Notes on the input formats:</p>
<ul>
-<li><p>Leading/trailing whitespaces of sequence names will always be deleted</p></li>
-<li><p>FASTA input example:</p>
+<li><p class="first">Leading/trailing whitespaces of sequence names will always be deleted</p>
+</li>
+<li><p class="first">FASTA input example:</p>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>>target
HGFHVHEFGDNTNGCMSSGPHFNPYGKEHGAPVDENRHLG
>2jlp-1.A|55
@@ -76,8 +76,9 @@ used. Template sequence names can encode an identifier for the chain to attach
to it and optionally an offset (here: 55, see below for details).
Leading whitespaces of fasta headers will be deleted</p>
</li>
-<li><p>CLUSTAL input follows the same logic as FASTA input</p></li>
-<li><p>JSON input: filenames are not allowed to start with ‘{‘.
+<li><p class="first">CLUSTAL input follows the same logic as FASTA input</p>
+</li>
+<li><p class="first">JSON input: filenames are not allowed to start with ‘{‘.
JSON objects contain an entry with key ‘alignmentlist’.
That in turn is an array of objects with keys ‘target’ and ‘template’.
Those in turn are objects with keys
@@ -110,16 +111,16 @@ chain to attach to which template sequence. Chains for each sequence are
identified based on the sequence name of the templates in the alignments. Valid
sequence names are:</p>
<ul class="simple">
-<li><p>anything, if only one structure with one chain</p></li>
-<li><p>“<FILE>.<CHAIN>”, where <FILE> is the base file name of an imported structure
+<li>anything, if only one structure with one chain</li>
+<li>“<FILE>.<CHAIN>”, where <FILE> is the base file name of an imported structure
with no extensions and <CHAIN> is the identifier of the chain in the imported
-structure.</p></li>
-<li><p>“<FILE>” if only one chain in file</p></li>
-<li><p>“<CHAIN>” if only one file imported</p></li>
-<li><p>“<CHAINID>|<OFFSET>”, where <CHAINID> identifies the chain as above and
+structure.</li>
+<li>“<FILE>” if only one chain in file</li>
+<li>“<CHAIN>” if only one file imported</li>
+<li>“<CHAINID>|<OFFSET>”, where <CHAINID> identifies the chain as above and
<OFFSET> is the number of residues to skip for that chain to reach the first
residue in the aligned sequence. Leading/trailing whitespaces of <CHAINID> and
-<OFFSET> are ignored.</p></li>
+<OFFSET> are ignored.</li>
</ul>
<p>Example: <code class="docutils literal notranslate"><span class="pre">...</span> <span class="pre">-p</span> <span class="pre">data/2jlp.pdb.gz</span></code>, where the pdb file has chains <code class="docutils literal notranslate"><span class="pre">A</span></code>,
<code class="docutils literal notranslate"><span class="pre">B</span></code>, <code class="docutils literal notranslate"><span class="pre">C</span></code> and the template sequence is named <code class="docutils literal notranslate"><span class="pre">2jlp.A|55</span></code>.</p>
@@ -131,12 +132,12 @@ extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
Consider to use <code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code> if you have a
file in a3m format at hand.</p>
<ul class="simple">
-<li><p>The profiles are mapped based on exact matches towards the gapless
+<li>The profiles are mapped based on exact matches towards the gapless
target sequences from the provided alignment files,
-i.e. one profile is mapped to several chains in case of homo-oligomers</p></li>
-<li><p>Every profile must have a unique sequence to avoid ambiguities</p></li>
-<li><p>All or nothing - You cannot provide profiles for only a subset of
-target sequences</p></li>
+i.e. one profile is mapped to several chains in case of homo-oligomers</li>
+<li>Every profile must have a unique sequence to avoid ambiguities</li>
+<li>All or nothing - You cannot provide profiles for only a subset of
+target sequences</li>
</ul>
<p>Example usage:</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb -s prof.hhm
@@ -158,13 +159,13 @@ that the accuracy of those termini is likely to be limited. Termini of length 1
won’t be modelled.</p>
<p>Possible exit codes of the action:</p>
<ul class="simple">
-<li><p>0: all went well</p></li>
-<li><p>1: an unhandled exception was raised</p></li>
-<li><p>2: arguments cannot be parsed or required arguments are missing</p></li>
-<li><p>3: failed to perform modelling (internal error)</p></li>
-<li><p>4: failed to write results to file</p></li>
-<li><p>other non-zero: failure in argument checking
-(see <a class="reference internal" href="../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.core.pm3argparse.PM3ArgumentParser</span></code></a>)</p></li>
+<li>0: all went well</li>
+<li>1: an unhandled exception was raised</li>
+<li>2: arguments cannot be parsed or required arguments are missing</li>
+<li>3: failed to perform modelling (internal error)</li>
+<li>4: failed to write results to file</li>
+<li>other non-zero: failure in argument checking
+(see <a class="reference internal" href="../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser" title="promod3.core.pm3argparse.PM3ArgumentParser"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.core.pm3argparse.PM3ArgumentParser</span></code></a>)</li>
</ul>
</div>
<div class="section" id="sidechain-modelling">
@@ -189,25 +190,25 @@ chosen by file ending. Recognized File Extensions: <code class="docutils literal
<p>Several flags control the modelling behaviour:</p>
<dl class="option">
<dt id="cmdoption-k">
-<code class="sig-name descname">-k</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--keep-sidechains</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-k" title="Permalink to this definition">¶</a></dt>
+<code class="descname">-k</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--keep-sidechains</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-k" title="Permalink to this definition">¶</a></dt>
<dd><p>Keep existing sidechains.</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-n">
-<code class="sig-name descname">-n</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--no-disulfids</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-n" title="Permalink to this definition">¶</a></dt>
+<code class="descname">-n</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--no-disulfids</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-n" title="Permalink to this definition">¶</a></dt>
<dd><p>Do not build disulfid bonds before sidechain optimization</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-r">
-<code class="sig-name descname">-r</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--rigid-rotamers</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-r" title="Permalink to this definition">¶</a></dt>
+<code class="descname">-r</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--rigid-rotamers</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-r" title="Permalink to this definition">¶</a></dt>
<dd><p>Do not use rotamers with subrotamers</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-i">
-<code class="sig-name descname">-i</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--backbone-independent</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-i" title="Permalink to this definition">¶</a></dt>
+<code class="descname">-i</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--backbone-independent</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-i" title="Permalink to this definition">¶</a></dt>
<dd><p>Use backbone independent rotamer library
(from <a class="reference internal" href="../sidechain/loading.html#promod3.sidechain.LoadLib" title="promod3.sidechain.LoadLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.sidechain.LoadLib()</span></code></a>) instead of the default backbone
dependent one (from <a class="reference internal" href="../sidechain/loading.html#promod3.sidechain.LoadBBDepLib" title="promod3.sidechain.LoadBBDepLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.sidechain.LoadBBDepLib()</span></code></a>)</p>
@@ -215,13 +216,13 @@ dependent one (from <a class="reference internal" href="../sidechain/loading.htm
<dl class="option">
<dt id="cmdoption-s">
-<code class="sig-name descname">-s</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--no-subrotamer-optimization</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-s" title="Permalink to this definition">¶</a></dt>
+<code class="descname">-s</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--no-subrotamer-optimization</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-s" title="Permalink to this definition">¶</a></dt>
<dd><p>Dont do subrotamer optimization if flexible rotamer model is used</p>
</dd></dl>
<dl class="option">
<dt id="cmdoption-f">
-<code class="sig-name descname">-f</code><code class="sig-prename descclassname"></code><code class="sig-prename descclassname">, </code><code class="sig-name descname">--energy_function</code><code class="sig-prename descclassname"></code><a class="headerlink" href="#cmdoption-f" title="Permalink to this definition">¶</a></dt>
+<code class="descname">-f</code><code class="descclassname"></code><code class="descclassname">, </code><code class="descname">--energy_function</code><code class="descclassname"></code><a class="headerlink" href="#cmdoption-f" title="Permalink to this definition">¶</a></dt>
<dd><p>The energy function to be used. Default is SCWRL4, can be any function
supported by <a class="reference internal" href="../modelling/sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a>.</p>
</dd></dl>
@@ -231,7 +232,6 @@ supported by <a class="reference internal" href="../modelling/sidechain_reconstr
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -252,12 +252,12 @@ supported by <a class="reference internal" href="../modelling/sidechain_reconstr
<li class="toctree-l2 current"><a class="current reference internal" href="#">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -281,33 +281,27 @@ supported by <a class="reference internal" href="../modelling/sidechain_reconstr
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/actions/index.rst.txt"
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 35c893b404ddcfc8d33fcb0c1e49ea75a90a83cf..408223d63c3356f2cbddee7f22175516ff007228 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>test_actions - Testing Actions — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>test_actions - Testing Actions — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="module-test_actions">
@@ -41,8 +40,8 @@ distribution intended to help developing ProMod3. Basically it supports you
creating new actions along immediate tests, which will be stored as unit tests
and stay available to monitor later changes.</p>
<div class="admonition note">
-<p class="admonition-title">Note</p>
-<p>A couple of different paths will be mentioned in the following. To make
+<p class="first admonition-title">Note</p>
+<p class="last">A couple of different paths will be mentioned in the following. To make
things easier to tell apart, a prefix <code class="file docutils literal notranslate"><span class="pre"><SOURCE></span></code> refers to the code
repository, <code class="file docutils literal notranslate"><span class="pre"><BUILD></span></code> to the build directory tree.</p>
</div>
@@ -252,7 +251,7 @@ output will be separated into <code class="file docutils literal notranslate"><s
<h2>Unit Test Actions API<a class="headerlink" href="#unit-test-actions-api" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="test_actions.ActionTestCase">
-<em class="property">class </em><code class="sig-prename descclassname">test_actions.</code><code class="sig-name descname">ActionTestCase</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">test_actions.</code><code class="descname">ActionTestCase</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase" title="Permalink to this definition">¶</a></dt>
<dd><p>Class to help developing actions. Comes with a lot of convenience wrappers
around what should be tested and serves as a recorder for test calls…
just for in two years when you come back to rewrite the whole action…</p>
@@ -260,68 +259,82 @@ just for in two years when you come back to rewrite the whole action…</p>
Otherwise the whole idea does not work.</p>
<dl class="attribute">
<dt id="test_actions.ActionTestCase.pm_bin">
-<code class="sig-name descname">pm_bin</code><a class="headerlink" href="#test_actions.ActionTestCase.pm_bin" title="Permalink to this definition">¶</a></dt>
+<code class="descname">pm_bin</code><a class="headerlink" href="#test_actions.ActionTestCase.pm_bin" title="Permalink to this definition">¶</a></dt>
<dd><p>This is the path of the <code class="docutils literal notranslate"><span class="pre">pm</span></code> binary. Automatically set by calling
<code class="xref py py-meth docutils literal notranslate"><span class="pre">__init__()</span></code> inside the initialisation of your class.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="test_actions.ActionTestCase.pm_action">
-<code class="sig-name descname">pm_action</code><a class="headerlink" href="#test_actions.ActionTestCase.pm_action" title="Permalink to this definition">¶</a></dt>
+<code class="descname">pm_action</code><a class="headerlink" href="#test_actions.ActionTestCase.pm_action" title="Permalink to this definition">¶</a></dt>
<dd><p>The action to be tested. Needs to be set by your initialisation routine,
<strong>after</strong> calling <code class="xref py py-meth docutils literal notranslate"><span class="pre">__init__()</span></code> from here. Skip the
“pm-” in front of the action name.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="test_actions.ActionTestCase.RunAction">
-<code class="sig-name descname">RunAction</code><span class="sig-paren">(</span><em class="sig-param">arguments</em>, <em class="sig-param">verbose=False</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.RunAction" title="Permalink to this definition">¶</a></dt>
+<code class="descname">RunAction</code><span class="sig-paren">(</span><em>arguments</em>, <em>verbose=False</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.RunAction" title="Permalink to this definition">¶</a></dt>
<dd><p>Call an action, return the exit status (<code class="docutils literal notranslate"><span class="pre">$?</span></code> shell variable). May be
set to <code class="docutils literal notranslate"><span class="pre">verbose</span></code> to print the actions terminal output. The action to
be executed needs to be stored in <a class="reference internal" href="#test_actions.ActionTestCase.pm_action" title="test_actions.ActionTestCase.pm_action"><code class="xref py py-attr docutils literal notranslate"><span class="pre">pm_action</span></code></a> first.</p>
<p>If in verbose mode, output to <code class="file docutils literal notranslate"><span class="pre">stdout</span></code> of the action will be
printed first followed by <code class="file docutils literal notranslate"><span class="pre">stderr</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>arguments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of arguments for the call.</p></li>
-<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If <code class="docutils literal notranslate"><span class="pre">True</span></code>, report output of the action.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>arguments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of arguments for the call.</li>
+<li><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If <code class="docutils literal notranslate"><span class="pre">True</span></code>, report output of the action.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The exit code of the action (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>).</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The exit code of the action (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>).</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="test_actions.ActionTestCase.RunExitStatusTest">
-<code class="sig-name descname">RunExitStatusTest</code><span class="sig-paren">(</span><em class="sig-param">exit_code</em>, <em class="sig-param">arguments</em>, <em class="sig-param">verbose=False</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.RunExitStatusTest" title="Permalink to this definition">¶</a></dt>
+<code class="descname">RunExitStatusTest</code><span class="sig-paren">(</span><em>exit_code</em>, <em>arguments</em>, <em>verbose=False</em><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.RunExitStatusTest" title="Permalink to this definition">¶</a></dt>
<dd><p>Run the action with given arguments and check the exit code.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>exit_code</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The expected return code, <code class="docutils literal notranslate"><span class="pre">$?</span></code> in a shell.</p></li>
-<li><p><strong>arguments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of arguments for the call.</p></li>
-<li><p><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If <code class="docutils literal notranslate"><span class="pre">True</span></code>, report output of the action.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>exit_code</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The expected return code, <code class="docutils literal notranslate"><span class="pre">$?</span></code> in a shell.</li>
+<li><strong>arguments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of arguments for the call.</li>
+<li><strong>verbose</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If <code class="docutils literal notranslate"><span class="pre">True</span></code>, report output of the action.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="test_actions.ActionTestCase.testPMExists">
-<code class="sig-name descname">testPMExists</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.testPMExists" title="Permalink to this definition">¶</a></dt>
+<code class="descname">testPMExists</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#test_actions.ActionTestCase.testPMExists" title="Permalink to this definition">¶</a></dt>
<dd><p>This is an internal test, executed when the source code of the test
class is run as unit test. Verifies that <a class="reference internal" href="#test_actions.ActionTestCase.pm_bin" title="test_actions.ActionTestCase.pm_bin"><code class="xref py py-attr docutils literal notranslate"><span class="pre">pm_bin</span></code></a> is an existing
file (also complains if a directory is found instead).</p>
@@ -334,7 +347,6 @@ file (also complains if a directory is found instead).</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -371,33 +383,27 @@ file (also complains if a directory is found instead).</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/actions/index_dev.rst.txt"
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index bb112e4cd94fc8a049138175171891ebc7fd8d46..d013cbc79d4fb5dd10f9d668518e7e7ce0e40c8b 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Building ProMod3 — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Building ProMod3 — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="building-project">
@@ -38,7 +37,7 @@
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
<p>ProMod3 is build on top of <a class="reference external" href="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
-2.2.0. OST must be configured and compiled with <code class="docutils literal notranslate"><span class="pre">ENABLE_MM=1</span></code> to
+2.3.0. OST must be configured and compiled with <code class="docutils literal notranslate"><span class="pre">ENABLE_MM=1</span></code> to
use <a class="reference external" href="https://github.com/openmm/openmm">OpenMM</a>. To create the build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required. The same
versions of <a class="reference external" href="https://www.python.org/">Python</a> and <a class="reference external" href="https://www.boost.org/">Boost</a> are needed as used in OST. For <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a>
we need at least version 3.3.0. To build the documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> is
@@ -47,13 +46,13 @@ release supporting Python 2.7 is 2.1.0 which also requires OST to be
compiled with Python 2.7.</p>
<p>The currently preferred versions are:</p>
<ul class="simple">
-<li><p><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.2.0</p></li>
-<li><p><a class="reference external" href="https://github.com/openmm/openmm">OpenMM</a> 7.1.1</p></li>
-<li><p><a class="reference external" href="https://cmake.org/">CMake</a> 3.12.1</p></li>
-<li><p><a class="reference external" href="https://www.python.org/">Python</a> 3.6.0</p></li>
-<li><p><a class="reference external" href="https://www.boost.org/">Boost</a> 1.68.0</p></li>
-<li><p><a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> 3.3.1</p></li>
-<li><p><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.4.9</p></li>
+<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 2.3.0</li>
+<li><a class="reference external" href="https://github.com/openmm/openmm">OpenMM</a> 7.1.1</li>
+<li><a class="reference external" href="https://cmake.org/">CMake</a> 3.12.1</li>
+<li><a class="reference external" href="https://www.python.org/">Python</a> 3.6.0</li>
+<li><a class="reference external" href="https://www.boost.org/">Boost</a> 1.68.0</li>
+<li><a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> 3.3.1</li>
+<li><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.4.9</li>
</ul>
</div>
<div class="section" id="using-cmake">
@@ -78,15 +77,15 @@ These are set with the <code class="docutils literal notranslate"><span class="p
<code class="docutils literal notranslate"><span class="pre">Python_ROOT_DIR</span></code> and <code class="docutils literal notranslate"><span class="pre">EIGEN3_INCLUDE_DIR</span></code>.</p>
<p>Here is a list of more options used within ProMod3:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">DISABLE_DOCUMENTATION</span></code> Don’t build documentation, don’t search for Sphinx</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">DISABLE_DOCTEST</span></code> Don’t run example code from documentation on
-<code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> (implicit by <code class="docutils literal notranslate"><span class="pre">DISABLE_DOCUMENTATION</span></code>)</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">DISABLE_LINKCHECK</span></code> Don’t test links from documentation on <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code>
-(implicit by <code class="docutils literal notranslate"><span class="pre">DISABLE_DOCUMENTATION</span></code>)</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">ENABLE_SSE</span></code> Allow for more agressive optimization by adding -msse4 flag to
+<li><code class="docutils literal notranslate"><span class="pre">DISABLE_DOCUMENTATION</span></code> Don’t build documentation, don’t search for Sphinx</li>
+<li><code class="docutils literal notranslate"><span class="pre">DISABLE_DOCTEST</span></code> Don’t run example code from documentation on
+<code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> (implicit by <code class="docutils literal notranslate"><span class="pre">DISABLE_DOCUMENTATION</span></code>)</li>
+<li><code class="docutils literal notranslate"><span class="pre">DISABLE_LINKCHECK</span></code> Don’t test links from documentation on <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code>
+(implicit by <code class="docutils literal notranslate"><span class="pre">DISABLE_DOCUMENTATION</span></code>)</li>
+<li><code class="docutils literal notranslate"><span class="pre">ENABLE_SSE</span></code> Allow for more agressive optimization by adding -msse4 flag to
the compiler. At some places within the code, we use SSE intrinsics explicitely.
This is only enabled if OST has been compiled with single precision.
-(<code class="docutils literal notranslate"><span class="pre">OST_DOUBLE_PRECISION</span></code> flag)</p></li>
+(<code class="docutils literal notranslate"><span class="pre">OST_DOUBLE_PRECISION</span></code> flag)</li>
</ul>
<p>Since we use OST in the background, some of its options for CMake are
also relevant, here. Basically they need to be set to exactly the same value.
@@ -94,8 +93,8 @@ Even if ProMod3 builds with different settings, it may start producing funny
results at an unexpected point. If you do not know the values, grep the option
in the <code class="file docutils literal notranslate"><span class="pre">CMakeCache.txt</span></code> of OST:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">OPTIMIZE</span></code></p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">OST_DOUBLE_PRECISION</span></code></p></li>
+<li><code class="docutils literal notranslate"><span class="pre">OPTIMIZE</span></code></li>
+<li><code class="docutils literal notranslate"><span class="pre">OST_DOUBLE_PRECISION</span></code></li>
</ul>
<p>Instead of calling CMake by yourself, there is the <code class="file docutils literal notranslate"><span class="pre">conf-scripts</span></code>
directory, providing smallish scripts to invoke CMake the right way for
@@ -118,16 +117,16 @@ latest code.</p>
<p id="index-0">Beside the usual <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">all</span></code> and other default targets, there are a few
special targets:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">check</span></code> <span class="target" id="index-1"></span>make check Runs unit tests and if CMake was invoked in
+<li><code class="docutils literal notranslate"><span class="pre">check</span></code> <span class="target" id="index-1"></span>make check Runs unit tests and if CMake was invoked in
its standard configuration also documentation examples (<code class="docutils literal notranslate"><span class="pre">doctest</span></code>) and
-links in the doc. (<code class="docutils literal notranslate"><span class="pre">linkcheck</span></code>) are checked</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">html</span></code> <span class="target" id="index-2"></span>make html Creates documentation as web page using the
-Sphinx <code class="docutils literal notranslate"><span class="pre">html</span></code> builder</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">man</span></code> <span class="target" id="index-3"></span>make man Creates a manual page using the Sphinx <code class="docutils literal notranslate"><span class="pre">man</span></code>
-builder</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">doc</span></code> <span class="target" id="index-4"></span>make doc Creates documentation using the <code class="docutils literal notranslate"><span class="pre">html</span></code> and
-<code class="docutils literal notranslate"><span class="pre">man</span></code> targets</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">help</span></code> <span class="target" id="index-5"></span>make help Prints a list of targets available</p></li>
+links in the doc. (<code class="docutils literal notranslate"><span class="pre">linkcheck</span></code>) are checked</li>
+<li><code class="docutils literal notranslate"><span class="pre">html</span></code> <span class="target" id="index-2"></span>make html Creates documentation as web page using the
+Sphinx <code class="docutils literal notranslate"><span class="pre">html</span></code> builder</li>
+<li><code class="docutils literal notranslate"><span class="pre">man</span></code> <span class="target" id="index-3"></span>make man Creates a manual page using the Sphinx <code class="docutils literal notranslate"><span class="pre">man</span></code>
+builder</li>
+<li><code class="docutils literal notranslate"><span class="pre">doc</span></code> <span class="target" id="index-4"></span>make doc Creates documentation using the <code class="docutils literal notranslate"><span class="pre">html</span></code> and
+<code class="docutils literal notranslate"><span class="pre">man</span></code> targets</li>
+<li><code class="docutils literal notranslate"><span class="pre">help</span></code> <span class="target" id="index-5"></span>make help Prints a list of targets available</li>
</ul>
</div>
<div class="section" id="installing-project">
@@ -150,7 +149,6 @@ safely delete the whole source folder.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -171,12 +169,12 @@ safely delete the whole source folder.</p>
<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -200,33 +198,27 @@ safely delete the whole source folder.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/buildsystem.rst.txt"
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 4a4a2b2289b4f433726fef935582650615500669..9f00e07757540e4ddd5bc2b3b7a0a744fcda935f 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Changelog — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Changelog — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -19,7 +21,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -28,163 +29,166 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="changelog">
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="release-3-2-1">
+<h2>Release 3.2.1<a class="headerlink" href="#release-3-2-1" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li>Bugfix release: Updates OpenStructure dependency to 2.3.0</li>
+</ul>
+</div>
<div class="section" id="release-3-2-0">
<h2>Release 3.2.0<a class="headerlink" href="#release-3-2-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li><p>Remove outdated configuration scripts (Fedora 19 / ancient Mac)</p></li>
-<li><p>Construct CB atoms if only N,CA and C atoms are present in
-ReconstructSidechains input structure.</p></li>
-<li><p>Detect Python using functionality provided by CMake instead of our own code.
+<li>Remove outdated configuration scripts (Fedora 19 / ancient Mac)</li>
+<li>Construct CB atoms if only N,CA and C atoms are present in
+ReconstructSidechains input structure.</li>
+<li>Detect Python using functionality provided by CMake instead of our own code.
You might have to adapt CMake flags when building ProMod3 to variables
-specified here: <a class="reference external" href="https://cmake.org/cmake/help/latest/module/FindPython.html">https://cmake.org/cmake/help/latest/module/FindPython.html</a></p></li>
-<li><p>Several minor bug fixes, improvements, and speed-ups.</p></li>
+specified here: <a class="reference external" href="https://cmake.org/cmake/help/latest/module/FindPython.html">https://cmake.org/cmake/help/latest/module/FindPython.html</a></li>
+<li>Several minor bug fixes, improvements, and speed-ups.</li>
</ul>
</div>
<div class="section" id="release-3-1-1">
<h2>Release 3.1.1<a class="headerlink" href="#release-3-1-1" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li><p>Bugfix release: reintroduces backwards compatibility in BuildRawModel.
-See commit 0288eced23a9a541a88005a7ed30b8f019e06226 for details</p></li>
+<li>Bugfix release: reintroduces backwards compatibility in BuildRawModel.
+See commit 0288eced23a9a541a88005a7ed30b8f019e06226 for details</li>
</ul>
</div>
<div class="section" id="release-3-1-0">
<h2>Release 3.1.0<a class="headerlink" href="#release-3-1-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li><p>Introduce alignment processing steps in BuildRawModel</p></li>
-<li><p>Several minor bug fixes, improvements, and speed-ups.</p></li>
+<li>Introduce alignment processing steps in BuildRawModel</li>
+<li>Several minor bug fixes, improvements, and speed-ups.</li>
</ul>
</div>
<div class="section" id="release-3-0-0">
<h2>Release 3.0.0<a class="headerlink" href="#release-3-0-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li><p>First release supporting Python 3. Python 2 support has been dropped.</p></li>
-<li><p>Updated versions of dependencies.</p></li>
-<li><p>Reduced amount of warnings during compilation.</p></li>
-<li><p>Improved and simplified use of Docker and Singularity containers.</p></li>
-<li><p>Several minor bug fixes, improvements, and speed-ups.</p></li>
+<li>First release supporting Python 3. Python 2 support has been dropped.</li>
+<li>Updated versions of dependencies.</li>
+<li>Reduced amount of warnings during compilation.</li>
+<li>Improved and simplified use of Docker and Singularity containers.</li>
+<li>Several minor bug fixes, improvements, and speed-ups.</li>
</ul>
</div>
<div class="section" id="release-2-1-0">
<h2>Release 2.1.0<a class="headerlink" href="#release-2-1-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li><p>This is expected to be the last release supporting Python 2.</p></li>
-<li><p>This project now requires a C++11 compatible compiler.</p></li>
-<li><p>Introduced VINA scoring function in the sidechain module. A scoring function
+<li>This is expected to be the last release supporting Python 2.</li>
+<li>This project now requires a C++11 compatible compiler.</li>
+<li>Introduced VINA scoring function in the sidechain module. A scoring function
specific RotamerConstructor is provided that comes with extensive heuristics
-to parametrize arbitrary compounds.</p></li>
-<li><p>Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
-The algorithm is based on principles of geometric hashing.</p></li>
-<li><p>Several minor bug fixes, improvements, and speed-ups</p></li>
+to parametrize arbitrary compounds.</li>
+<li>Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
+The algorithm is based on principles of geometric hashing.</li>
+<li>Several minor bug fixes, improvements, and speed-ups</li>
</ul>
</div>
<div class="section" id="release-2-0-0">
<h2>Release 2.0.0<a class="headerlink" href="#release-2-0-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li><p>Generalize particle scoring and rotamer construction in sidechain module.
+<li>Generalize particle scoring and rotamer construction in sidechain module.
This simplifies the addition of other scoring functions in the future.
Be aware of breaking changes introduced in the process!
(SCWRLRotamerConstructor -> SCWRL4RotamerConstructor, changed interface of
-Particle and RotamerConstructor classes).</p></li>
-<li><p>Enable possibility to use structural fragments in default modelling pipeline
-and build-model action</p></li>
-<li><p>Enable possibility to enforce full coverage models including termini without
-template coverage in default modelling pipeline and build-model action</p></li>
-<li><p>Modelling pipeline can track issues in the ModellingHandle object</p></li>
-<li><p>External example scripts can now be found in extras/external_scripts</p></li>
-<li><p>Improved support for recent compilers and libraries.</p></li>
-<li><p>Several minor bug fixes, improvements, and speed-ups</p></li>
+Particle and RotamerConstructor classes).</li>
+<li>Enable possibility to use structural fragments in default modelling pipeline
+and build-model action</li>
+<li>Enable possibility to enforce full coverage models including termini without
+template coverage in default modelling pipeline and build-model action</li>
+<li>Modelling pipeline can track issues in the ModellingHandle object</li>
+<li>External example scripts can now be found in extras/external_scripts</li>
+<li>Improved support for recent compilers and libraries.</li>
+<li>Several minor bug fixes, improvements, and speed-ups</li>
</ul>
</div>
<div class="section" id="release-1-3-0">
<h2>Release 1.3.0<a class="headerlink" href="#release-1-3-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li><p>Apply Apache Version 2.0 License to the project</p></li>
-<li><p>2010 Dunbrack rotamer library has been replaced by an own backbone dependent
+<li>Apply Apache Version 2.0 License to the project</li>
+<li>2010 Dunbrack rotamer library has been replaced by an own backbone dependent
rotamer library. All scripts required to reproduce the data are in
-extras/data_generation/rotamer_library</p></li>
-<li><p>Penultimate rotamer library has been replaced by an own backbone independent
+extras/data_generation/rotamer_library</li>
+<li>Penultimate rotamer library has been replaced by an own backbone independent
rotamer library. All scripts required to reproduce the data are in
-extras/data_generation/rotamer_library</p></li>
-<li><p>SampleMonteCarlo function moved to Python. This makes it possible to provide
-sampler/closer/scorer/cooler objects implemented in both, Python and C++</p></li>
-<li><p>Action script for sidechain modelling</p></li>
-<li><p>Allow sequence profiles as input for build-model action script.</p></li>
-<li><p>Recipe for Docker / Singularity container</p></li>
-<li><p>Check peptide bonds when building a RawModel. Treat as gap if bond is
-stereochemically problematic despite being in sequence.</p></li>
-<li><p>Several minor bug fixes, improvements, and speed-ups</p></li>
+extras/data_generation/rotamer_library</li>
+<li>SampleMonteCarlo function moved to Python. This makes it possible to provide
+sampler/closer/scorer/cooler objects implemented in both, Python and C++</li>
+<li>Action script for sidechain modelling</li>
+<li>Allow sequence profiles as input for build-model action script.</li>
+<li>Recipe for Docker / Singularity container</li>
+<li>Check peptide bonds when building a RawModel. Treat as gap if bond is
+stereochemically problematic despite being in sequence.</li>
+<li>Several minor bug fixes, improvements, and speed-ups</li>
</ul>
</div>
<div class="section" id="release-1-2-0">
<h2>Release 1.2.0<a class="headerlink" href="#release-1-2-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li><p>Graph optimizer has been separated from the sidechain module and can now be
+<li>Graph optimizer has been separated from the sidechain module and can now be
used for arbitrary optimization problems. Available optimization algorithms
-are TreePack, AStar and MonteCarlo.</p></li>
-<li><p>Make it possible to distinguish between the scores of a loop towards a constant
+are TreePack, AStar and MonteCarlo.</li>
+<li>Make it possible to distinguish between the scores of a loop towards a constant
environment (external scores) and the scores within the loop itself
-(internal scores).</p></li>
-<li><p>Most scores based on pairwise interactions are now pairwise decomposable.</p></li>
-<li><p>Disconnected loops at several locations can be scored at once.</p></li>
-<li><p>Avoid the usage of the DSSP executable and use the OpenStructure internal
-secondary structure assignment instead.</p></li>
-<li><p>Allow to decide whether the CB atom belongs to the actual rotamer or to the
+(internal scores).</li>
+<li>Most scores based on pairwise interactions are now pairwise decomposable.</li>
+<li>Disconnected loops at several locations can be scored at once.</li>
+<li>Avoid the usage of the DSSP executable and use the OpenStructure internal
+secondary structure assignment instead.</li>
+<li>Allow to decide whether the CB atom belongs to the actual rotamer or to the
constant frame in sidechain optimization. This can be useful in design
questions, where the identity of a rotamer is not given and you want to
-allow glycine or alanine.</p></li>
-<li><p>The naming of the entries in the StructureDB is not strictly limited to
-4 letter codes anymore, arbitrary strings can be used instead.</p></li>
-<li><p>Adding coordinates to the StructureDB does not require external tools anymore
-(msms, dssp etc.), internal implementations are used instead.</p></li>
-<li><p>The data that is stored in a StructureDB can be controlled at initialization,
-everything except the sequence and the actual coordinates is optional.</p></li>
-<li><p>Entries in the StructureDB can be removed again.</p></li>
-<li><p>Allow to search positions of arbitrary copies in DynamicSpatialOrganizer
-by providing RT operators.</p></li>
-<li><p>Several minor bug fixes, improvements, and speed-ups</p></li>
+allow glycine or alanine.</li>
+<li>The naming of the entries in the StructureDB is not strictly limited to
+4 letter codes anymore, arbitrary strings can be used instead.</li>
+<li>Adding coordinates to the StructureDB does not require external tools anymore
+(msms, dssp etc.), internal implementations are used instead.</li>
+<li>The data that is stored in a StructureDB can be controlled at initialization,
+everything except the sequence and the actual coordinates is optional.</li>
+<li>Entries in the StructureDB can be removed again.</li>
+<li>Allow to search positions of arbitrary copies in DynamicSpatialOrganizer
+by providing RT operators.</li>
+<li>Several minor bug fixes, improvements, and speed-ups</li>
</ul>
</div>
<div class="section" id="release-1-1-0">
<h2>Release 1.1.0<a class="headerlink" href="#release-1-1-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li><p>Updated dependencies: need Eigen 3.3.0 and OST 1.7</p></li>
-<li><p>Changes in modelling pipeline: remove clashing loop candidates early, new
+<li>Updated dependencies: need Eigen 3.3.0 and OST 1.7</li>
+<li>Changes in modelling pipeline: remove clashing loop candidates early, new
scores using sequence / structure profiles, new scoring weights, subrotamer
-optimization to reduce ring punches, and improved handling of ligands</p></li>
-<li><p>Improved build-model action to generate oligomeric models, input multiple
-files, and allow for residue offsets into structure files</p></li>
-<li><p>Improved computational runtime of relevant operations in pipeline (CCD,
+optimization to reduce ring punches, and improved handling of ligands</li>
+<li>Improved build-model action to generate oligomeric models, input multiple
+files, and allow for residue offsets into structure files</li>
+<li>Improved computational runtime of relevant operations in pipeline (CCD,
scorers, backbone list operations), superpositions and loop candidate
-clustering</p></li>
-<li><p>High-level functionality moved consistently to modelling module</p></li>
-<li><p>New modelling algorithms: rigid blocks to compare structures and improved
-fragment sampling for de novo modelling</p></li>
-<li><p>New rotamer graph solvers for sidechains: AStar and Monte Carlo</p></li>
-<li><p>Refactored backbone scoring to simplify extensions</p></li>
-<li><p>Added all atom scoring with possibilities to reconstruct sidechains for
-selected loops, reconstruct hydrogens and minimize energy with MM</p></li>
-<li><p>Refactored backbone list to speed it up</p></li>
-<li><p>Added runtime profiling for developers</p></li>
-<li><p>Several minor bug fixes, improvements, and speed-ups</p></li>
+clustering</li>
+<li>High-level functionality moved consistently to modelling module</li>
+<li>New modelling algorithms: rigid blocks to compare structures and improved
+fragment sampling for de novo modelling</li>
+<li>New rotamer graph solvers for sidechains: AStar and Monte Carlo</li>
+<li>Refactored backbone scoring to simplify extensions</li>
+<li>Added all atom scoring with possibilities to reconstruct sidechains for
+selected loops, reconstruct hydrogens and minimize energy with MM</li>
+<li>Refactored backbone list to speed it up</li>
+<li>Added runtime profiling for developers</li>
+<li>Several minor bug fixes, improvements, and speed-ups</li>
</ul>
</div>
<div class="section" id="release-1-0">
<h2>Release 1.0<a class="headerlink" href="#release-1-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
-<li><p>Initial release of ProMod3 for use in productive instances of SMNG</p></li>
+<li>Initial release of ProMod3 for use in productive instances of SMNG</li>
</ul>
</div>
</div>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -218,33 +222,27 @@ selected loops, reconstruct hydrogens and minimize energy with MM</p></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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<a href="_sources/changelog.rst.txt"
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index 094a5faeed083f11e84f969ed968e06283c38205..a18b6c781a3bb93cdd4087606e9e03e918e0d8be 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>ProMod3’s Share Of CMake — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>ProMod3’s Share Of CMake — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="project-s-share-of-cmake">
@@ -41,16 +40,16 @@
macros) fed from the <code class="file docutils literal notranslate"><span class="pre">cmake_support</span></code> directory. Those could be easily put
into three categories of varying relevance for you:</p>
<ol class="arabic simple">
-<li><p>Functions used to integrate your contribution into ProMod3. Its all about
+<li>Functions used to integrate your contribution into ProMod3. Its all about
adding files to the documentation, declaring unit tests and code management.
-Almost all of them have their home in the file <code class="file docutils literal notranslate"><span class="pre">PROMOD3.cmake</span></code>.</p></li>
-<li><p>Then there is a set of functions needed to set up CMake itself. Those are
+Almost all of them have their home in the file <code class="file docutils literal notranslate"><span class="pre">PROMOD3.cmake</span></code>.</li>
+<li>Then there is a set of functions needed to set up CMake itself. Those are
little helpers to find tools, external packages and such. These are found in
-<code class="file docutils literal notranslate"><span class="pre">Find<DEPENDENCY>.cmake</span></code> files.</p></li>
-<li><p>The last and probably least relevant category for you is also to be found in
+<code class="file docutils literal notranslate"><span class="pre">Find<DEPENDENCY>.cmake</span></code> files.</li>
+<li>The last and probably least relevant category for you is also to be found in
<code class="file docutils literal notranslate"><span class="pre">PROMOD3.cmake</span></code>. There is a set of functions used to define more
CMake functionality. You only need to consider those if you dare to extend
-this set up.</p></li>
+this set up.</li>
</ol>
<p>Best practices for using our home-brew CMake functions are found in the
various <code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code> files in the project’s directory tree.</p>
@@ -61,12 +60,12 @@ various <code class="file docutils literal notranslate"><span class="pre">CMakeL
<h3>Module definition<a class="headerlink" href="#module-definition" title="Permalink to this headline">¶</a></h3>
<p>Default dependencies in a module <code class="docutils literal notranslate"><span class="pre">NAME</span></code>:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">_NAME</span></code> depends on <code class="docutils literal notranslate"><span class="pre">NAME_pymod</span></code> and <code class="docutils literal notranslate"><span class="pre">promod3_NAME</span></code> (if that exists)</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">promod3_NAME</span></code> depends on <code class="docutils literal notranslate"><span class="pre">promod3_NAME_headers</span></code></p></li>
+<li><code class="docutils literal notranslate"><span class="pre">_NAME</span></code> depends on <code class="docutils literal notranslate"><span class="pre">NAME_pymod</span></code> and <code class="docutils literal notranslate"><span class="pre">promod3_NAME</span></code> (if that exists)</li>
+<li><code class="docutils literal notranslate"><span class="pre">promod3_NAME</span></code> depends on <code class="docutils literal notranslate"><span class="pre">promod3_NAME_headers</span></code></li>
</ul>
<dl class="command">
<dt id="command:module">
-<code class="sig-name descname">module</code><a class="headerlink" href="#command:module" title="Permalink to this definition">¶</a></dt>
+<code class="descname">module</code><a class="headerlink" href="#command:module" title="Permalink to this definition">¶</a></dt>
<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">module(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">SOURCES</span><span class="w"> </span><span class="nb">source1</span><span class="w"> </span><span class="nb">source2</span><span class="w"></span>
<span class="w"> </span><span class="no">HEADERS</span><span class="w"> </span><span class="nb">header1</span><span class="w"> </span><span class="nb">header2</span><span class="w"> </span><span class="p">[</span><span class="no">IN_DIR</span><span class="w"> </span><span class="nb">dir</span><span class="p">]</span><span class="w"></span>
@@ -79,35 +78,35 @@ various <code class="file docutils literal notranslate"><span class="pre">CMakeL
<p>Define a ProMod3 module from a set of C++ files. This will define the
following make targets (where <code class="docutils literal notranslate"><span class="pre">NAME</span></code> is the provided module name):</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">promod3_NAME</span></code>: builds library <code class="file docutils literal notranslate"><span class="pre">libpromod3_NAME</span></code></p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">promod3_NAME_headers</span></code>: copies all header files</p></li>
+<li><code class="docutils literal notranslate"><span class="pre">promod3_NAME</span></code>: builds library <code class="file docutils literal notranslate"><span class="pre">libpromod3_NAME</span></code></li>
+<li><code class="docutils literal notranslate"><span class="pre">promod3_NAME_headers</span></code>: copies all header files</li>
</ul>
<p>The parameters are:</p>
-<dl class="simple">
-<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt><dd><p>Specify the name of the module.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">SOURCES</span></code></dt><dd><p>Set of C++ source files to be compiled.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">HEADERS</span></code></dt><dd><p>Set of C++ header files to be copied. If the headers are located in
+<dl class="docutils">
+<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt>
+<dd>Specify the name of the module.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">SOURCES</span></code></dt>
+<dd>Set of C++ source files to be compiled.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">HEADERS</span></code></dt>
+<dd>Set of C++ header files to be copied. If the headers are located in
a different directory than the current one, you must group them by directory
and provide the directory name <code class="docutils literal notranslate"><span class="pre">dir</span></code> with <code class="docutils literal notranslate"><span class="pre">IN_DIR</span> <span class="pre">dir</span></code> after listing the
-header files in said directory.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">DEPENDS_ON</span></code></dt><dd><p>Add dependencies on other targets (e.g. <code class="docutils literal notranslate"><span class="pre">promod3_MOD</span></code> for another
-ProMod3 module).</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">HEADER_OUTPUT_DIR</span></code></dt><dd><p>Define alternative folder to which to copy header files. Default is
-<code class="file docutils literal notranslate"><span class="pre">promod3/NAME</span></code>.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">LINK</span></code></dt><dd><p>Add dependencies to external libraries. You may use some predefines set of
-libraries here, such as <code class="docutils literal notranslate"><span class="pre">${OST_LIBRARIES}</span></code> and <code class="docutils literal notranslate"><span class="pre">${BOOST_LIBRARIES}</span></code>.</p>
-</dd>
+header files in said directory.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">DEPENDS_ON</span></code></dt>
+<dd>Add dependencies on other targets (e.g. <code class="docutils literal notranslate"><span class="pre">promod3_MOD</span></code> for another
+ProMod3 module).</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">HEADER_OUTPUT_DIR</span></code></dt>
+<dd>Define alternative folder to which to copy header files. Default is
+<code class="file docutils literal notranslate"><span class="pre">promod3/NAME</span></code>.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">LINK</span></code></dt>
+<dd>Add dependencies to external libraries. You may use some predefines set of
+libraries here, such as <code class="docutils literal notranslate"><span class="pre">${OST_LIBRARIES}</span></code> and <code class="docutils literal notranslate"><span class="pre">${BOOST_LIBRARIES}</span></code>.</dd>
</dl>
</dd></dl>
<dl class="command">
<dt id="command:pymod">
-<code class="sig-name descname">pymod</code><a class="headerlink" href="#command:pymod" title="Permalink to this definition">¶</a></dt>
+<code class="descname">pymod</code><a class="headerlink" href="#command:pymod" title="Permalink to this definition">¶</a></dt>
<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">pymod(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">CPP</span><span class="w"> </span><span class="nb">source1</span><span class="w"> </span><span class="nb">source2</span><span class="w"></span>
<span class="w"> </span><span class="no">PY</span><span class="w"> </span><span class="nb">source</span><span class="w"> </span><span class="nb">source2</span><span class="w"> </span><span class="p">[</span><span class="no">IN_DIR</span><span class="w"> </span><span class="nb">dir</span><span class="p">]</span><span class="w"></span>
@@ -122,39 +121,40 @@ libraries here, such as <code class="docutils literal notranslate"><span class="
wrappers and/or Python files. This will define the following make targets
(where <code class="docutils literal notranslate"><span class="pre">NAME</span></code> is the provided module name):</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">_NAME</span></code>: builds library <code class="file docutils literal notranslate"><span class="pre">_NAME</span></code> for Python wrapper around C++</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">NAME_pymod</span></code>: copies (and/or translates) all Python files</p></li>
+<li><code class="docutils literal notranslate"><span class="pre">_NAME</span></code>: builds library <code class="file docutils literal notranslate"><span class="pre">_NAME</span></code> for Python wrapper around C++</li>
+<li><code class="docutils literal notranslate"><span class="pre">NAME_pymod</span></code>: copies (and/or translates) all Python files</li>
</ul>
<p>The parameters are:</p>
-<dl>
-<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt><dd><p>Specify the name of the module.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">CPP</span></code></dt><dd><p>Set of C++ source files to be compiled.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">PY</span></code></dt><dd><p>Set of Python source files to be copied. If the files are located in
+<dl class="docutils">
+<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt>
+<dd>Specify the name of the module.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">CPP</span></code></dt>
+<dd>Set of C++ source files to be compiled.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">PY</span></code></dt>
+<dd><p class="first">Set of Python source files to be copied. If the files are located in
a different directory than the current one, you must group them by directory
and provide the directory name <code class="docutils literal notranslate"><span class="pre">dir</span></code> with <code class="docutils literal notranslate"><span class="pre">IN_DIR</span> <span class="pre">dir</span></code> after listing the
header files in said directory.</p>
-<p>If a Python source file needs to be translated by CMake, provide the
+<p class="last">If a Python source file needs to be translated by CMake, provide the
dictionary after putting <code class="docutils literal notranslate"><span class="pre">TRANSLATE</span></code>. This assumes a <code class="docutils literal notranslate"><span class="pre"><FILE>.py.in</span></code> for
<code class="docutils literal notranslate"><span class="pre"><FILE>.py</span></code>. <code class="docutils literal notranslate"><span class="pre">END_TRANSLATE</span></code> marks the end of the translation
dictionary.</p>
</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">OUTPUT_DIR</span></code></dt><dd><p>Define alternative folder (within Python tree) to place python files.
-Default is <code class="file docutils literal notranslate"><span class="pre">promod3/NAME</span></code>.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">DEPENDS_ON</span></code></dt><dd><p>Add dependencies on other targets (e.g. <code class="docutils literal notranslate"><span class="pre">promod3_MOD</span></code> for another
-ProMod3 module).</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">NEED_CONFIG_HEADER</span></code></dt><dd><p>Makes the module depending on the config_header target, which provides the
-headers in the <code class="file docutils literal notranslate"><span class="pre">config</span></code> directory.</p>
-</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">OUTPUT_DIR</span></code></dt>
+<dd>Define alternative folder (within Python tree) to place python files.
+Default is <code class="file docutils literal notranslate"><span class="pre">promod3/NAME</span></code>.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">DEPENDS_ON</span></code></dt>
+<dd>Add dependencies on other targets (e.g. <code class="docutils literal notranslate"><span class="pre">promod3_MOD</span></code> for another
+ProMod3 module).</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">NEED_CONFIG_HEADER</span></code></dt>
+<dd>Makes the module depending on the config_header target, which provides the
+headers in the <code class="file docutils literal notranslate"><span class="pre">config</span></code> directory.</dd>
</dl>
</dd></dl>
<dl class="command">
<dt id="command:convert_module_data">
-<code class="sig-name descname">convert_module_data</code><a class="headerlink" href="#command:convert_module_data" title="Permalink to this definition">¶</a></dt>
+<code class="descname">convert_module_data</code><a class="headerlink" href="#command:convert_module_data" title="Permalink to this definition">¶</a></dt>
<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">convert_module_data(</span><span class="no">MODULE</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">FILE</span><span class="w"> </span><span class="nb">file</span><span class="w"></span>
<span class="w"> </span><span class="no">SCRIPT</span><span class="w"> </span><span class="nb">script</span><span class="w"></span>
@@ -176,7 +176,7 @@ If given, <code class="docutils literal notranslate"><span class="pre">args</spa
<h3>Unit Tests<a class="headerlink" href="#unit-tests" title="Permalink to this headline">¶</a></h3>
<dl class="command">
<dt id="command:promod3_unittest">
-<code class="sig-name descname">promod3_unittest</code><a class="headerlink" href="#command:promod3_unittest" title="Permalink to this definition">¶</a></dt>
+<code class="descname">promod3_unittest</code><a class="headerlink" href="#command:promod3_unittest" title="Permalink to this definition">¶</a></dt>
<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">promod3_unittest(</span><span class="no">MODULE</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">SOURCES</span><span class="w"> </span><span class="nb">source1</span><span class="w"> </span><span class="p">[</span><span class="nb">source2</span><span class="w"> </span><span class="p">...]</span><span class="w"></span>
<span class="w"> </span><span class="p">[</span><span class="no">LINK</span><span class="w"> </span><span class="na">library1/</span><span class="w"> </span><span class="nb">linker</span><span class="w"> </span><span class="nb">flag1</span><span class="w"> </span><span class="p">[</span><span class="na">library2/</span><span class="w"> </span><span class="nb">linker</span><span class="w"> </span><span class="nb">flag2</span><span class="w"> </span><span class="p">...]]</span><span class="w"></span>
@@ -194,36 +194,36 @@ it is out of the source tree, you may change test data as you like, without
the Git repository noticing. Calling <span class="target" id="index-1-command:promod3_unittest"></span><a class="reference internal" href="#command:promod3_unittest" title="promod3_unittest"><code class="xref cmake cmake-command docutils literal notranslate"><span class="pre">promod3_unittest()</span></code></a> will
create a set of certain <code class="docutils literal notranslate"><span class="pre">make</span></code> targets for you, beside feeding <code class="docutils literal notranslate"><span class="pre">codetest</span></code>.</p>
<p>The parameters are:</p>
-<dl class="simple">
-<dt><code class="docutils literal notranslate"><span class="pre">MODULE</span></code></dt><dd><p>Specify the name of the module these tests are made for. Needs to be set,
+<dl class="docutils">
+<dt><code class="docutils literal notranslate"><span class="pre">MODULE</span></code></dt>
+<dd>Specify the name of the module these tests are made for. Needs to be set,
needs to be a single word. Ends up in <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">help</span></code> as a prefix, nothing
-will break if it does not match the name of any existing module.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">SOURCES</span></code></dt><dd><p>Describe a set of files hosting unit test code here. If its a wild mix of
+will break if it does not match the name of any existing module.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">SOURCES</span></code></dt>
+<dd>Describe a set of files hosting unit test code here. If its a wild mix of
C++ and Python files does not matter, CMake will sort this out for
you. But the programming language makes a difference for the <code class="docutils literal notranslate"><span class="pre">make</span></code>
targets produced. C++ files will all be gathered in a single
<code class="docutils literal notranslate"><span class="pre">test_suite_<MODULE>_run</span></code> target (there is also a <code class="docutils literal notranslate"><span class="pre">_xml</span></code> target but
this is for tools for automated testing). Python code works on a ‘one
target per file’ basis. So <code class="file docutils literal notranslate"><span class="pre">test_foo.py</span></code> will have own target
-<code class="docutils literal notranslate"><span class="pre">test_foo.py_run</span></code>.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">LINK</span></code></dt><dd><p>Add additional libraries and linker flags for C++ source files. Has no
-effect on Python tests.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">DATA</span></code></dt><dd><p>Define test data. Instead of giving data directories its own
+<code class="docutils literal notranslate"><span class="pre">test_foo.py_run</span></code>.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">LINK</span></code></dt>
+<dd>Add additional libraries and linker flags for C++ source files. Has no
+effect on Python tests.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">DATA</span></code></dt>
+<dd>Define test data. Instead of giving data directories its own
<code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code>, those files are added here. Usually located
somewhere in a dedicated <code class="file docutils literal notranslate"><span class="pre">data</span></code> subtree, files need to be given with
a path relative to this directory. That path will then be created in the
-build directory.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">TARGET</span></code></dt><dd><p>This defines an additional dependency for the unit test. That is, before
-running this unit test, this target will be built.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">BASE_TARGET</span></code></dt><dd><p>This defines an alternative base target to which to add this unit test.
+build directory.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">TARGET</span></code></dt>
+<dd>This defines an additional dependency for the unit test. That is, before
+running this unit test, this target will be built.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">BASE_TARGET</span></code></dt>
+<dd>This defines an alternative base target to which to add this unit test.
By default all unit tests are registered to be executed with the
-<code class="docutils literal notranslate"><span class="pre">codetest</span></code> target. This can be overridden by using this argument.</p>
-</dd>
+<code class="docutils literal notranslate"><span class="pre">codetest</span></code> target. This can be overridden by using this argument.</dd>
</dl>
</dd></dl>
@@ -232,7 +232,7 @@ By default all unit tests are registered to be executed with the
<h3>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h3>
<dl class="command">
<dt id="command:add_doc_source">
-<code class="sig-name descname">add_doc_source</code><a class="headerlink" href="#command:add_doc_source" title="Permalink to this definition">¶</a></dt>
+<code class="descname">add_doc_source</code><a class="headerlink" href="#command:add_doc_source" title="Permalink to this definition">¶</a></dt>
<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">add_doc_source(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">RST</span><span class="w"> </span><span class="nb">rst1</span><span class="w"> </span><span class="p">[</span><span class="nb">rst2...</span><span class="p">]</span><span class="nf">)</span><span class="w"></span>
</pre></div>
@@ -242,22 +242,22 @@ used in <code class="file docutils literal notranslate"><span class="pre">doc</s
module. This does not create any <code class="docutils literal notranslate"><span class="pre">make</span></code> targets. Lists filled here will all
be evaluated in the <code class="file docutils literal notranslate"><span class="pre">doc/CMakeLists.txt</span></code> of the repository root.</p>
<p>The parameters are:</p>
-<dl class="simple">
-<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt><dd><p>Specify the name of the module this branch of documentation belongs to.
+<dl class="docutils">
+<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt>
+<dd>Specify the name of the module this branch of documentation belongs to.
Needs to be set, needs to be a single word. Using module names is best
practice, while nothing will break if it does not refer to an existing one.
You will find a directory in <code class="file docutils literal notranslate"><span class="pre">doc/source</span></code> with that name in the build
-root.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">RST</span></code></dt><dd><p>Describe a set of files containing the documentation. Feed it a single file
-name or a CMake list.</p>
-</dd>
+root.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">RST</span></code></dt>
+<dd>Describe a set of files containing the documentation. Feed it a single file
+name or a CMake list.</dd>
</dl>
</dd></dl>
<dl class="command">
<dt id="command:add_doc_dependency">
-<code class="sig-name descname">add_doc_dependency</code><a class="headerlink" href="#command:add_doc_dependency" title="Permalink to this definition">¶</a></dt>
+<code class="descname">add_doc_dependency</code><a class="headerlink" href="#command:add_doc_dependency" title="Permalink to this definition">¶</a></dt>
<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">add_doc_dependency(</span><span class="no">NAME</span><span class="w"> </span><span class="nb">name</span><span class="w"></span>
<span class="w"> </span><span class="no">DEP</span><span class="w"> </span><span class="nb">dependency1</span><span class="w"> </span><span class="p">[</span><span class="nb">dependency2...</span><span class="p">]</span><span class="nf">)</span><span class="w"></span>
</pre></div>
@@ -265,17 +265,17 @@ name or a CMake list.</p>
<p>Add a dependency to the doc build system. For an existing name, add some
dependencies when it comes to building documentation. Mostly for internal use.</p>
<p>The parameters are:</p>
-<dl class="simple">
-<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt><dd><p>Specify a name the dependencies belong to. This name needs to be already
+<dl class="docutils">
+<dt><code class="docutils literal notranslate"><span class="pre">NAME</span></code></dt>
+<dd>Specify a name the dependencies belong to. This name needs to be already
known in the doc build system. Names of Python modules are good, otherwise
names introduced by <span class="target" id="index-0-command:add_doc_source"></span><a class="reference internal" href="#command:add_doc_source" title="add_doc_source"><code class="xref cmake cmake-command docutils literal notranslate"><span class="pre">add_doc_source()</span></code></a> work well. Dependencies
will be create for all reStructuredText files listed by
<span class="target" id="index-1-command:add_doc_source"></span><a class="reference internal" href="#command:add_doc_source" title="add_doc_source"><code class="xref cmake cmake-command docutils literal notranslate"><span class="pre">add_doc_source()</span></code></a> under this name and for all <code class="docutils literal notranslate"><span class="pre">make</span></code>
-targets related to the documentation.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">DEP</span></code></dt><dd><p>Hand over a dependency here or a CMake list. Files work, if given with
-absolute path.</p>
-</dd>
+targets related to the documentation.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">DEP</span></code></dt>
+<dd>Hand over a dependency here or a CMake list. Files work, if given with
+absolute path.</dd>
</dl>
</dd></dl>
@@ -284,7 +284,7 @@ absolute path.</p>
<h3>Actions<a class="headerlink" href="#actions" title="Permalink to this headline">¶</a></h3>
<dl class="command">
<dt id="command:pm_action">
-<code class="sig-name descname">pm_action</code><a class="headerlink" href="#command:pm_action" title="Permalink to this definition">¶</a></dt>
+<code class="descname">pm_action</code><a class="headerlink" href="#command:pm_action" title="Permalink to this definition">¶</a></dt>
<dd><div class="highlight-cmake notranslate"><div class="highlight"><pre><span></span><span class="nf">pm_action(</span><span class="no">ACTION</span><span class="w"> </span><span class="nb">action-script</span><span class="w"></span>
<span class="w"> </span><span class="no">TARGET</span><span class="w"> </span><span class="nb">target</span><span class="nf">)</span><span class="w"></span>
</pre></div>
@@ -295,14 +295,14 @@ Adding an action means connecting its file with the given target to be copied
to the <code class="file docutils literal notranslate"><span class="pre">libexec</span></code> directory. No dedicated <code class="docutils literal notranslate"><span class="pre">make</span></code> target will be
created.</p>
<p>The parameters are:</p>
-<dl class="simple">
-<dt><code class="docutils literal notranslate"><span class="pre">ACTION</span></code></dt><dd><p>Name of the action to be added. Should start with <code class="file docutils literal notranslate"><span class="pre">pm-</span></code>. Needs to be
+<dl class="docutils">
+<dt><code class="docutils literal notranslate"><span class="pre">ACTION</span></code></dt>
+<dd>Name of the action to be added. Should start with <code class="file docutils literal notranslate"><span class="pre">pm-</span></code>. Needs to be
an existing file in the same directory as the invoking
-<code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code>.</p>
-</dd>
-<dt><code class="docutils literal notranslate"><span class="pre">TARGET</span></code></dt><dd><p>Provide a <code class="docutils literal notranslate"><span class="pre">make</span></code> target to trigger copying the action’s script file. The
-target has to be created <strong>before</strong> any action may be attached to it.</p>
-</dd>
+<code class="file docutils literal notranslate"><span class="pre">CMakeLists.txt</span></code>.</dd>
+<dt><code class="docutils literal notranslate"><span class="pre">TARGET</span></code></dt>
+<dd>Provide a <code class="docutils literal notranslate"><span class="pre">make</span></code> target to trigger copying the action’s script file. The
+target has to be created <strong>before</strong> any action may be attached to it.</dd>
</dl>
</dd></dl>
@@ -312,7 +312,6 @@ target has to be created <strong>before</strong> any action may be attached to i
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -342,40 +341,34 @@ target has to be created <strong>before</strong> any action may be attached to i
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../developers.html">Documentation For Developers</a><ul>
- <li>Previous: <a href="../actions/index_dev.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">test_actions</span></code> - Testing Actions</a></li>
+ <li>Previous: <a href="../actions/index_dev.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">test_actions</span></code> - Testing Actions</a></li>
<li>Next: <a href="../portableIO.html" title="next chapter">Using Binary Files In ProMod3</a></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/cmake/index.rst.txt"
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
index 6156b9d2c9ba9ed6431261ddae3bc4cce325433c..efd454dae0676f9373d8fcb8a97239da4e4397d9 100644
--- a/doc/html/container/docker.html
+++ b/doc/html/container/docker.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Docker — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Docker — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="docker">
@@ -128,7 +127,6 @@ output when running a Python script with following code in the container:</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -149,12 +147,12 @@ output when running a Python script with following code in the container:</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2 current"><a class="reference internal" href="index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -180,33 +178,27 @@ output when running a Python script with following code in the container:</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
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<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/container/docker.rst.txt"
diff --git a/doc/html/container/index.html b/doc/html/container/index.html
index 8f18ef708af1893ddc04fea96707bd006e19ac2d..1cd6fb1b509d6a2aa6e8002a02d8a2d63b57c3af 100644
--- a/doc/html/container/index.html
+++ b/doc/html/container/index.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>ProMod3 and Containers — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>ProMod3 and Containers — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="project-and-containers">
@@ -49,7 +48,6 @@ some sugar on top.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -70,12 +68,12 @@ some sugar on top.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -99,33 +97,27 @@ some sugar on top.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
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-
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<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/container/index.rst.txt"
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
index c0ea15a885d5e61fdfdb2c388429c0a6be6c0924..61c1dc21108f9c9bc370ce4264333beb34a73f94 100644
--- a/doc/html/container/singularity.html
+++ b/doc/html/container/singularity.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Singularity — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Singularity — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="singularity">
@@ -44,15 +43,16 @@ Docker image.</p>
</div>
<div class="section" id="available-apps">
<h2>Available apps<a class="headerlink" href="#available-apps" title="Permalink to this headline">¶</a></h2>
-<dl class="simple">
-<dt>This container includes the following apps:</dt><dd><ul class="simple">
-<li><p><strong>OST</strong> - OpenStructure executable</p></li>
-<li><p><strong>PM</strong> - ProMod3 executable</p></li>
-<li><p><strong>IPython</strong> - OST/ProMod3-powered iPython shell</p></li>
-<li><p><strong>Notebook</strong> - A Jupyter notebook playground with OST, ProMod3 and nglview</p></li>
-<li><p><strong>lDDT</strong> - The Local Distance Difference Test</p></li>
-<li><p><strong>Molck</strong> - Molecular checker</p></li>
-<li><p><strong>ChemdictTool</strong> - Creating or update a compound library</p></li>
+<dl class="docutils">
+<dt>This container includes the following apps:</dt>
+<dd><ul class="first last simple">
+<li><strong>OST</strong> - OpenStructure executable</li>
+<li><strong>PM</strong> - ProMod3 executable</li>
+<li><strong>IPython</strong> - OST/ProMod3-powered iPython shell</li>
+<li><strong>Notebook</strong> - A Jupyter notebook playground with OST, ProMod3 and nglview</li>
+<li><strong>lDDT</strong> - The Local Distance Difference Test</li>
+<li><strong>Molck</strong> - Molecular checker</li>
+<li><strong>ChemdictTool</strong> - Creating or update a compound library</li>
</ul>
</dd>
</dl>
@@ -128,7 +128,6 @@ in the Docker documentation: <a class="reference internal" href="docker.html#doc
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -149,12 +148,12 @@ in the Docker documentation: <a class="reference internal" href="docker.html#doc
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2 current"><a class="reference internal" href="index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -173,40 +172,34 @@ in the Docker documentation: <a class="reference internal" href="docker.html#doc
<li><a href="../users.html">Documentation For Users</a><ul>
<li><a href="index.html">ProMod3 and Containers</a><ul>
<li>Previous: <a href="docker.html" title="previous chapter">Docker</a></li>
- <li>Next: <a href="../modelling/index.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+ <li>Next: <a href="../modelling/index.html" title="next chapter"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/container/singularity.rst.txt"
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 10ae1b3f0a57744e8807439af15d061638a5b985..9f612109a6e472105c26df477282cb25ce8cbf50 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Contributing — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Contributing — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="contributing">
@@ -372,13 +371,14 @@ documentation of <a class="reference internal" href="actions/index_dev.html#modu
explanations, it should be easy to go by examples from the <code class="file docutils literal notranslate"><span class="pre">actions</span></code>
directory. There are only two really important points:</p>
<ul>
-<li><p>No shebang line (<code class="docutils literal notranslate"><span class="pre">#!</span> <span class="pre">/usr/bin/python</span></code>) in your action! Also no
+<li><p class="first">No shebang line (<code class="docutils literal notranslate"><span class="pre">#!</span> <span class="pre">/usr/bin/python</span></code>) in your action! Also no
<code class="docutils literal notranslate"><span class="pre">#!</span> <span class="pre">/usr/bin/env</span> <span class="pre">python</span></code> or anything like this. This may lead to funny side
effects, like calling a Python interpreter from outside a virtual
environment or a different version OST. Basically it may mess up the
environment your action is running in. Actions are called by <code class="file docutils literal notranslate"><span class="pre">pm</span></code>,
-that’s enough to get everything just right.</p></li>
-<li><p>The action of your action happens in the <a class="reference external" href="https://docs.python.org/3.7/library/__main__.html"><code class="xref py py-attr docutils literal notranslate"><span class="pre">__main__</span></code></a> branch of the script.
+that’s enough to get everything just right.</p>
+</li>
+<li><p class="first">The action of your action happens in the <a class="reference external" href="https://docs.python.org/3.7/library/__main__.html"><code class="xref py py-attr docutils literal notranslate"><span class="pre">__main__</span></code></a> branch of the script.
Your action will have own function definitions, variables and all the bells
and whistles. Hiding behind <a class="reference external" href="https://docs.python.org/3.7/library/__main__.html"><code class="xref py py-attr docutils literal notranslate"><span class="pre">__main__</span></code></a> keeps everything separated and makes
things easier when it gets to debugging. So just after</p>
@@ -400,7 +400,7 @@ things easier when it gets to debugging. So just after</p>
add new scorers. As usual, you can use existing bits and pieces as examples and
try to be consistent with it. Here, we quickly give an overview of the separation of concerns:</p>
<ul>
-<li><p><a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>:
+<li><p class="first"><a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>:
Defines the scorer with all its parameters and energies and the functionality
to compute scores. Scorers are setup by the user (or loaded from disk) if
necessary.</p>
@@ -408,7 +408,7 @@ necessary.</p>
pointers to env. data kept and updated by the score env.. Also, they may be
linked to a score env. listener to handle specially organized data.</p>
</li>
-<li><p><a class="reference internal" href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>:
+<li><p class="first"><a class="reference internal" href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>:
Handles all model-specific data used by the scorers. The user sets up the
environment and updates it whenever something changes.</p>
<p>Residue-specific data is kept in arrays of fixed size (see <code class="xref py py-class docutils literal notranslate"><span class="pre">IdxHandler</span></code>
@@ -417,7 +417,7 @@ with “GetEnvSetData()” and used to determine whether env. data is available
for a certain residue. The list of sequences handled by the env. is fixed as
otherwise pointers into the data-storage would be invalidated.</p>
</li>
-<li><p><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnvListener</span></code>:
+<li><p class="first"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnvListener</span></code>:
Allows to have score-specific data to be extracted from the model-specific
data available in the score env. class. It is commonly used to define
spatially organized structures to quickly access other atoms within a given
@@ -428,31 +428,32 @@ listener. Listeners are not accessible by anyone outside of the scorers and
the score env. object responsible for it. Since the user doesn’t see them,
there is no Python API for them.</p>
</li>
-<li><p><code class="xref py py-class docutils literal notranslate"><span class="pre">IdxHandler</span></code>:
+<li><p class="first"><code class="xref py py-class docutils literal notranslate"><span class="pre">IdxHandler</span></code>:
This takes care of translating chain indices (range [0, GetNumChains()])
and residue numbers (range [1, GetChainSize(chain_idx)]) into the indexing
used internally by the score env. (range [0, GetNumResidues()]).
-The score env. takes care of this object and makes it accessible for scorers.</p></li>
+The score env. takes care of this object and makes it accessible for scorers.</p>
+</li>
</ul>
<p>As an example, let’s look at the <a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a>:</p>
<ul class="simple">
-<li><p>it contains score-specific parameters and energies which can be either
-set manually or loaded from disk</p></li>
-<li><p>it is linked to a score env. listener of type <code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaEnvListener</span></code>,
+<li>it contains score-specific parameters and energies which can be either
+set manually or loaded from disk</li>
+<li>it is linked to a score env. listener of type <code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaEnvListener</span></code>,
which provides a <code class="xref py py-meth docutils literal notranslate"><span class="pre">FindWithin()</span></code> function to quickly access neighboring
CB atoms (note that the same listener is also used by the
-<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a>)</p></li>
-<li><p>a pointer to the <code class="xref py py-class docutils literal notranslate"><span class="pre">IdxHandler</span></code> object of the score env. is extracted
+<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a>)</li>
+<li>a pointer to the <code class="xref py py-class docutils literal notranslate"><span class="pre">IdxHandler</span></code> object of the score env. is extracted
when the environment is attached and is used to get sequence-specific data
-when calculating the score</p></li>
+when calculating the score</li>
</ul>
<p>As a second example, look at the <a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer" title="promod3.scoring.PairwiseScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseScorer</span></code></a>:</p>
<ul class="simple">
-<li><p>it does not require any score-specific setup</p></li>
-<li><p>it is linked to residue-specific CA/CB positions and the pairwise functions
-defined in the score env.</p></li>
-<li><p>“GetEnvSetData()” of the score env. is used to determine if env. data is
-available for a given residue</p></li>
+<li>it does not require any score-specific setup</li>
+<li>it is linked to residue-specific CA/CB positions and the pairwise functions
+defined in the score env.</li>
+<li>“GetEnvSetData()” of the score env. is used to determine if env. data is
+available for a given residue</li>
</ul>
</div>
<div class="section" id="quick-testing-of-project-features">
@@ -485,28 +486,28 @@ tutorial on unit testing here. Again, have a look at how other modules treat
this topic and then there is quite a lot of educated material to be found on
the Internet. Nevertheless, here is a short list of most important advices:</p>
<ul class="simple">
-<li><p>Tests go into dedicated scripts/ source files in the <code class="file docutils literal notranslate"><span class="pre">tests</span></code> directory</p></li>
-<li><p>No external data dependencies, if tests need data, they find it in
-<code class="file docutils literal notranslate"><span class="pre">tests/data</span></code></p></li>
-<li><p>If ‘exotic’ Python modules are used, consider making the test aware of the
-possibility that the module is not available</p></li>
-<li><p>Tests do not fail on purpose</p></li>
-<li><p>No failing tests, that are considered ‘this does not affect anything’</p></li>
+<li>Tests go into dedicated scripts/ source files in the <code class="file docutils literal notranslate"><span class="pre">tests</span></code> directory</li>
+<li>No external data dependencies, if tests need data, they find it in
+<code class="file docutils literal notranslate"><span class="pre">tests/data</span></code></li>
+<li>If ‘exotic’ Python modules are used, consider making the test aware of the
+possibility that the module is not available</li>
+<li>Tests do not fail on purpose</li>
+<li>No failing tests, that are considered ‘this does not affect anything’</li>
</ul>
<p>To run the whole test suite, <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> is enough. This will also trigger
the <code class="docutils literal notranslate"><span class="pre">doctest</span></code> and <code class="docutils literal notranslate"><span class="pre">linkcheck</span></code> targets. Alternatively you can run:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">codetest</span></code> to run only unit tests from all modules in ProMod3.
+<li><code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">codetest</span></code> to run only unit tests from all modules in ProMod3.
Note that <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> does nothing more but invoking <code class="docutils literal notranslate"><span class="pre">doctest</span></code>,
-<code class="docutils literal notranslate"><span class="pre">linkcheck</span></code> and <code class="docutils literal notranslate"><span class="pre">codetest</span></code> as dependencies.</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check_xml</span></code> to run tests without stopping after each failure.
+<code class="docutils literal notranslate"><span class="pre">linkcheck</span></code> and <code class="docutils literal notranslate"><span class="pre">codetest</span></code> as dependencies.</li>
+<li><code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check_xml</span></code> to run tests without stopping after each failure.
Failures are shortly reported to the command line and the result of each test
is written in ‘PYTEST-<TestCaseName>.xml’ files in the ‘tests’ subfolders of
-your ‘build’ folder.</p></li>
-<li><p>Run single tests:
+your ‘build’ folder.</li>
+<li>Run single tests:
assuming you have <code class="file docutils literal notranslate"><span class="pre">your_module/tests/test_awesome_feature.py</span></code>, CMake
will provide you with a target <code class="docutils literal notranslate"><span class="pre">test_awesome_feature.py_run</span></code>. If your module
-has C++ tests, those will be available by <code class="docutils literal notranslate"><span class="pre">test_suite_your_module_run</span></code>.</p></li>
+has C++ tests, those will be available by <code class="docutils literal notranslate"><span class="pre">test_suite_your_module_run</span></code>.</li>
</ul>
</div>
<div class="section" id="writing-documentation">
@@ -549,10 +550,10 @@ test function. Usually, the codes are run and the return code is checked.
Command-line output or resulting files can also be checked (see existing test
codes for examples). A few more guidelines for example codes:</p>
<ul class="simple">
-<li><p>If it generates files as output, please delete them after checking them.</p></li>
-<li><p>If it requires external modules or binaries, check for their availablity. If
+<li>If it generates files as output, please delete them after checking them.</li>
+<li>If it requires external modules or binaries, check for their availablity. If
the external dependencies are not available, output a warning and skip the
-test.</p></li>
+test.</li>
</ul>
<p>A copy of the generated html documentation is kept in <code class="file docutils literal notranslate"><span class="pre">doc/html</span></code> so that
there is no need to compile ProMod3 to read it. Our policy is to keep that
@@ -570,11 +571,11 @@ folder in-sync with the latest documentation at least on the <code class="docuti
<p>For some tasks you may want to make use of third party contributions in your
module, for example</p>
<ul class="simple">
-<li><p>calling/ using the output of third party binaries</p></li>
-<li><p>external libraries</p></li>
-<li><p>smallish bits of source code included into the ProMod3 directory tree</p></li>
-<li><p>Python modules not distributed as part of the Python
-<a class="reference external" href="https://docs.python.org/3.7/library/">standard library</a></p></li>
+<li>calling/ using the output of third party binaries</li>
+<li>external libraries</li>
+<li>smallish bits of source code included into the ProMod3 directory tree</li>
+<li>Python modules not distributed as part of the Python
+<a class="reference external" href="https://docs.python.org/3.7/library/">standard library</a></li>
</ul>
<p>Modules from the Python standard library are covered by the Python
<a class="reference external" href="https://docs.python.org/3.6/license.html">license</a> and
@@ -598,7 +599,6 @@ contributions to web pages using ProMod3.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -629,39 +629,33 @@ contributions to web pages using ProMod3.</p>
<li><a href="index.html">Documentation overview</a><ul>
<li><a href="developers.html">Documentation For Developers</a><ul>
<li>Previous: <a href="dev_setup.html" title="previous chapter">ProMod3 Setup</a></li>
- <li>Next: <a href="actions/index_dev.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">test_actions</span></code> - Testing Actions</a></li>
+ <li>Next: <a href="actions/index_dev.html" title="next chapter"><code class="docutils literal notranslate"><span class="pre">test_actions</span></code> - Testing Actions</a></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
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-
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-
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</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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<a href="_sources/contributing.rst.txt"
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index e379e2db97aca62d73a13378197745c0ea22dd75..4db119f6e43fd07a28ca388d8630770c5f964dda 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Geometry functions — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Geometry functions — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,227 +30,267 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="geometry-functions">
<h1>Geometry functions<a class="headerlink" href="#geometry-functions" title="Permalink to this headline">¶</a></h1>
<dl class="function">
<dt id="promod3.core.EvaluateGromacsPosRule">
-<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">EvaluateGromacsPosRule</code><span class="sig-paren">(</span><em class="sig-param">rule</em>, <em class="sig-param">number</em>, <em class="sig-param">anchors</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.EvaluateGromacsPosRule" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.core.</code><code class="descname">EvaluateGromacsPosRule</code><span class="sig-paren">(</span><em>rule</em>, <em>number</em>, <em>anchors</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.EvaluateGromacsPosRule" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs <em>number</em> positions with the given Gromacs rule and anchor positions
(see Gromacs manual for details).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Gromacs rule</p></li>
-<li><p><strong>number</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Desired number of positions (max. 3)</p></li>
-<li><p><strong>anchors</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Gromacs rule</li>
+<li><strong>number</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Desired number of positions (max. 3)</li>
+<li><strong>anchors</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Constructed <em>number</em> positions.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Constructed <em>number</em> positions.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.core.ConstructCTerminalOxygens">
-<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">ConstructCTerminalOxygens</code><span class="sig-paren">(</span><em class="sig-param">c_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">n_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructCTerminalOxygens" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.core.</code><code class="descname">ConstructCTerminalOxygens</code><span class="sig-paren">(</span><em>c_pos</em>, <em>ca_pos</em>, <em>n_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructCTerminalOxygens" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs positions of O and OXT atoms for C terminal.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Positions of O and OXT atoms.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Positions of O and OXT atoms.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.core.ConstructAtomPos">
-<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">ConstructAtomPos</code><span class="sig-paren">(</span><em class="sig-param">A</em>, <em class="sig-param">B</em>, <em class="sig-param">C</em>, <em class="sig-param">bond_length</em>, <em class="sig-param">angle</em>, <em class="sig-param">dihedral</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructAtomPos" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.core.</code><code class="descname">ConstructAtomPos</code><span class="sig-paren">(</span><em>A</em>, <em>B</em>, <em>C</em>, <em>bond_length</em>, <em>angle</em>, <em>dihedral</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructAtomPos" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs position of atom “D” based on bond length (C-D), angle (B-C-D) and
dihedral (A-B-C-D).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom A</p></li>
-<li><p><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom B</p></li>
-<li><p><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</p></li>
-<li><p><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Bond length (C-D)</p></li>
-<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (B-C-D)</p></li>
-<li><p><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
+<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
+<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
+<li><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Bond length (C-D)</li>
+<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (B-C-D)</li>
+<li><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Position of atom D</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of atom D</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.core.ConstructCBetaPos">
-<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">ConstructCBetaPos</code><span class="sig-paren">(</span><em class="sig-param">n_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">c_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructCBetaPos" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.core.</code><code class="descname">ConstructCBetaPos</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>c_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.ConstructCBetaPos" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs position of C-beta atom given the positions of the backbone nitrogen,
C-alpha and C atoms.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Position of C-beta atom</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of C-beta atom</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.core.RotationAroundLine">
-<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">RotationAroundLine</code><span class="sig-paren">(</span><em class="sig-param">axis</em>, <em class="sig-param">anchor</em>, <em class="sig-param">angle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.RotationAroundLine" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.core.</code><code class="descname">RotationAroundLine</code><span class="sig-paren">(</span><em>axis</em>, <em>anchor</em>, <em>angle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.RotationAroundLine" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a geometric transform leading to a rotation with specified <cite>angle</cite>
around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
-<li><p><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</p></li>
-<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
+<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Transformation matrix</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Transformation matrix</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt>
-<code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">RotationAroundLine</code><span class="sig-paren">(</span><em class="sig-param">axis</em>, <em class="sig-param">angle</em><span class="sig-paren">)</span></dt>
+<code class="descclassname">promod3.core.</code><code class="descname">RotationAroundLine</code><span class="sig-paren">(</span><em>axis</em>, <em>angle</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a 3x3 matrix for a rotation by a specified <cite>angle</cite> around an <cite>axis</cite>
going through the origin.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
-<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Rotation matrix</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Rotation matrix</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="class">
<dt id="promod3.core.StemCoords">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">StemCoords</code><a class="headerlink" href="#promod3.core.StemCoords" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">StemCoords</code><a class="headerlink" href="#promod3.core.StemCoords" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">StemCoords</code><span class="sig-paren">(</span><em class="sig-param">res</em><span class="sig-paren">)</span></dt>
+<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">StemCoords</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span></dt>
<dd><p>Simple container class to store N, CA and C coordinates.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res</em> does not contain N, CA and C
-atoms.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res</em> does not contain N, CA and C
+atoms.</td>
+</tr>
+</tbody>
+</table>
<dl class="attribute">
<dt id="promod3.core.StemCoords.n_coord">
-<code class="sig-name descname">n_coord</code><a class="headerlink" href="#promod3.core.StemCoords.n_coord" title="Permalink to this definition">¶</a></dt>
+<code class="descname">n_coord</code><a class="headerlink" href="#promod3.core.StemCoords.n_coord" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.core.StemCoords.ca_coord">
-<code class="sig-name descname">ca_coord</code><a class="headerlink" href="#promod3.core.StemCoords.ca_coord" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ca_coord</code><a class="headerlink" href="#promod3.core.StemCoords.ca_coord" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.core.StemCoords.c_coord">
-<code class="sig-name descname">c_coord</code><a class="headerlink" href="#promod3.core.StemCoords.c_coord" title="Permalink to this definition">¶</a></dt>
+<code class="descname">c_coord</code><a class="headerlink" href="#promod3.core.StemCoords.c_coord" title="Permalink to this definition">¶</a></dt>
<dd><p>Position of nitrogen / alpha carbon / carbon atom.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.core.StemPairOrientation">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">StemPairOrientation</code><a class="headerlink" href="#promod3.core.StemPairOrientation" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">StemPairOrientation</code><a class="headerlink" href="#promod3.core.StemPairOrientation" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">StemPairOrientation</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em><span class="sig-paren">)</span></dt>
+<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">StemPairOrientation</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span></dt>
<dd><p>Relative orientation of a pair of stems. Can be used to define gaps with four
angles and one distance and is used in the fragment database for fast lookups.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference internal" href="#promod3.core.StemCoords" title="promod3.core.StemCoords"><code class="xref py py-class docutils literal notranslate"><span class="pre">StemCoords</span></code></a>) – Coordinates of stem A.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference internal" href="#promod3.core.StemCoords" title="promod3.core.StemCoords"><code class="xref py py-class docutils literal notranslate"><span class="pre">StemCoords</span></code></a>) – Coordinates of stem B.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_stem</strong> (<a class="reference internal" href="#promod3.core.StemCoords" title="promod3.core.StemCoords"><code class="xref py py-class docutils literal notranslate"><span class="pre">StemCoords</span></code></a>) – Coordinates of stem A.</li>
+<li><strong>c_stem</strong> (<a class="reference internal" href="#promod3.core.StemCoords" title="promod3.core.StemCoords"><code class="xref py py-class docutils literal notranslate"><span class="pre">StemCoords</span></code></a>) – Coordinates of stem B.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="attribute">
<dt id="promod3.core.StemPairOrientation.distance">
-<code class="sig-name descname">distance</code><a class="headerlink" href="#promod3.core.StemPairOrientation.distance" title="Permalink to this definition">¶</a></dt>
+<code class="descname">distance</code><a class="headerlink" href="#promod3.core.StemPairOrientation.distance" title="Permalink to this definition">¶</a></dt>
<dd><p>Distance of C atom of stem A to N atom of stem B.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.core.StemPairOrientation.angle_one">
-<code class="sig-name descname">angle_one</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_one" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angle_one</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_one" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.core.StemPairOrientation.angle_two">
-<code class="sig-name descname">angle_two</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_two" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angle_two</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Angles defining relative orientation of stem B with respect to stem A.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.core.StemPairOrientation.angle_three">
-<code class="sig-name descname">angle_three</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_three" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angle_three</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_three" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.core.StemPairOrientation.angle_four">
-<code class="sig-name descname">angle_four</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_four" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angle_four</code><a class="headerlink" href="#promod3.core.StemPairOrientation.angle_four" title="Permalink to this definition">¶</a></dt>
<dd><p>Angles defining relative orientation of stem A with respect to stem B.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -258,7 +299,6 @@ angles and one distance and is used in the fragment database for fast lookups.</
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -279,12 +319,12 @@ angles and one distance and is used in the fragment database for fast lookups.</
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -301,8 +341,8 @@ angles and one distance and is used in the fragment database for fast lookups.</
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
- <li>Previous: <a href="helper.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li>Previous: <a href="helper.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
<li>Next: <a href="runtime_profiling.html" title="next chapter">Runtime profiling</a></li>
</ul></li>
</ul></li>
@@ -310,33 +350,27 @@ angles and one distance and is used in the fragment database for fast lookups.</
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/geometry.rst.txt"
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index e3a5609a7a8cba0076dcb4fe4cf0753493ca3bf6..1d1d0b3a00098296d63b6421e6f39cdc5e26e41c 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Graph Minimizer — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Graph Minimizer — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="graph-minimizer">
@@ -44,130 +43,147 @@ a set <span class="math notranslate nohighlight">\(X=[x_1, x_2, ..., x_n]\)</spa
\[F(X)=\displaystyle\sum_iE_{self}(N_i[x_i]) +\displaystyle \sum_i \displaystyle \sum_{j>i}E_{pair}(N_i[x_i], N_j[x_j])\]</div>
<dl class="class">
<dt id="promod3.core.GraphMinimizer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">GraphMinimizer</code><a class="headerlink" href="#promod3.core.GraphMinimizer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">GraphMinimizer</code><a class="headerlink" href="#promod3.core.GraphMinimizer" title="Permalink to this definition">¶</a></dt>
<dd><dl class="method">
<dt id="promod3.core.GraphMinimizer.AddNode">
-<code class="sig-name descname">AddNode</code><span class="sig-paren">(</span><em class="sig-param">self_energies</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AddNode" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddNode</code><span class="sig-paren">(</span><em>self_energies</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AddNode" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds a node to the graph.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>self_energies</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Directly controls the number of possible solutions in that
-node and assigns the corresponding self energies</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The idx of the added node</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>self_energies</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Directly controls the number of possible solutions in that
+node and assigns the corresponding self energies</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The idx of the added node</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.AddEdge">
-<code class="sig-name descname">AddEdge</code><span class="sig-paren">(</span><em class="sig-param">node_idx_one</em>, <em class="sig-param">node_idx_two</em>, <em class="sig-param">pairwise_energies</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AddEdge" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddEdge</code><span class="sig-paren">(</span><em>node_idx_one</em>, <em>node_idx_two</em>, <em>pairwise_energies</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AddEdge" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds an edge between the specified nodes.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>node_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the first node</p></li>
-<li><p><strong>node_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the second node</p></li>
-<li><p><strong>pairwise_energies</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The pairwise energies that contribute to the
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>node_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the first node</li>
+<li><strong>node_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the second node</li>
+<li><strong>pairwise_energies</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The pairwise energies that contribute to the
overall energy function. There must be a list for
every possible solution in node one. All of those
lists must have exactly the length of possible
-solutions in node two.</p></li>
+solutions in node two.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The idx of the added edge</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>node_idx_one</em> or <em>node_idx_two</em>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The idx of the added edge</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>node_idx_one</em> or <em>node_idx_two</em>
specify non existent nodes or when <em>pairwise_energies</em> is
inconsistent with the number of solutions in the specified nodes.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.ApplyDEE">
-<code class="sig-name descname">ApplyDEE</code><span class="sig-paren">(</span><em class="sig-param">node_idx</em><span class="optional">[</span>, <em class="sig-param">e_cut=0.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyDEE" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplyDEE</code><span class="sig-paren">(</span><em>node_idx</em><span class="optional">[</span>, <em>e_cut=0.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyDEE" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies dead end elimination on one particular node and potentially
deactivates certain solutions. The goldstein criterion is described in
-<a class="reference internal" href="../references.html#goldstein1994" id="id1"><span>[goldstein1994]</span></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>node_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Node to apply dead end elimination</p></li>
-<li><p><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If set to
+<a class="reference internal" href="../references.html#goldstein1994" id="id1">[goldstein1994]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>node_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Node to apply dead end elimination</li>
+<li><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If set to
0.0, the default goldstein criterion is applied =>
a solution is removed if it’s dominated by all other
solutions in the same node. If you increase this value,
-a solution must be dominated by at least this <strong>e_cut</strong>.</p></li>
+a solution must be dominated by at least this <strong>e_cut</strong>.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> whether any solution has been deactivated.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> whether any solution has been deactivated.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.ApplyEdgeDecomposition">
-<code class="sig-name descname">ApplyEdgeDecomposition</code><span class="sig-paren">(</span><em class="sig-param">edge_idx</em>, <em class="sig-param">epsilon</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyEdgeDecomposition" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplyEdgeDecomposition</code><span class="sig-paren">(</span><em>edge_idx</em>, <em>epsilon</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyEdgeDecomposition" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies edge decomposition on one particular edge and potentially
deactivates it. The exact decomposition procedure is described in
-<a class="reference internal" href="../references.html#krivov2009" id="id2"><span>[krivov2009]</span></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>edge_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Edge to decompose.</p></li>
-<li><p><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</p></li>
+<a class="reference internal" href="../references.html#krivov2009" id="id2">[krivov2009]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>edge_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Edge to decompose.</li>
+<li><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> whether the edge has been decomposed and
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> whether the edge has been decomposed and
deactivated</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.Prune">
-<code class="sig-name descname">Prune</code><span class="sig-paren">(</span><em class="sig-param">epsilon</em><span class="optional">[</span>, <em class="sig-param">e_cut=0.0</em>, <em class="sig-param">consider_all_nodes=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.Prune" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Prune</code><span class="sig-paren">(</span><em>epsilon</em><span class="optional">[</span>, <em>e_cut=0.0</em>, <em>consider_all_nodes=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.Prune" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs edge decomposition followed by dead end elimination in an
iterative manner until no changes can be observed anymore given
<strong>epsilon</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</p></li>
-<li><p><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Parameter to control dead end elimination.</p></li>
-<li><p><strong>consider_all_nodes</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, wether the dead end elimination should be
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</li>
+<li><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Parameter to control dead end elimination.</li>
+<li><strong>consider_all_nodes</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, wether the dead end elimination should be
applied to all nodes, or only those who are
connected with an edge removed by edge
decomposition. This is useful if already a Prune
operation has been performed => only those nodes
connected to a removed edge have the chance for
-successful dead end elimination.</p></li>
+successful dead end elimination.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.Reset">
-<code class="sig-name descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.Reset" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.Reset" title="Permalink to this definition">¶</a></dt>
<dd><p>Resets the graph by undoing any pruning operation (DEE and edge decomposition)</p>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.TreeSolve">
-<code class="sig-name descname">TreeSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em class="sig-param">max_complexity=inf</em>, <em class="sig-param">initial_epsilon=0.02</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.TreeSolve" title="Permalink to this definition">¶</a></dt>
+<code class="descname">TreeSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em>max_complexity=inf</em>, <em>initial_epsilon=0.02</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.TreeSolve" title="Permalink to this definition">¶</a></dt>
<dd><p>The method solves a graph using a minimal width tree decomposition
approach in an iterative manner. In every iteration, the algorithm performs
a pruning step (DEE / Edge Decomposition) and subsequently tries to solve
@@ -177,29 +193,33 @@ particular connected component is is larger <strong>max_complexity</strong>,
this component is solved in a later iteration. The algorithm iterates until
all connected components are solved and steadily increases the epsilon value
resulting in a more and more agressive edge decomposition.
-Algorithm further descsribed in <a class="reference internal" href="../references.html#krivov2009" id="id3"><span>[krivov2009]</span></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max number of possible permutations, that have to
+Algorithm further descsribed in <a class="reference internal" href="../references.html#krivov2009" id="id3">[krivov2009]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max number of possible permutations, that have to
be enumerated in the resulting tree after tree
-decomposition.</p></li>
-<li><p><strong>initial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The initial energy threshold to perform edge
-decomposition.</p></li>
+decomposition.</li>
+<li><strong>initial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The initial energy threshold to perform edge
+decomposition.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A tuple with the first element being a list of indices
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of indices
representing the single solutions minimizing
the overall energy function.
The second element is the according energy value.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.AStarSolve">
-<code class="sig-name descname">AStarSolve</code><span class="sig-paren">(</span><em class="sig-param">e_thresh</em><span class="optional">[</span>, <em class="sig-param">max_n=100</em>, <em class="sig-param">max_visited_nodes=100000000</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AStarSolve" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AStarSolve</code><span class="sig-paren">(</span><em>e_thresh</em><span class="optional">[</span>, <em>max_n=100</em>, <em>max_visited_nodes=100000000</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AStarSolve" title="Permalink to this definition">¶</a></dt>
<dd><p>The method solves a graph using the A* algorithm. Besides creating the
minimal energy solution, the function produces a maximum of <strong>max_n</strong>
solutions sorted by energy. It aborts as soon as it sees the first solution
@@ -212,30 +232,34 @@ runtime or even hit the <strong>max_visited_nodes</strong> parameter that caps t
usage.
To have a valid solution you have to take care that you set the <strong>e_cut</strong>
parameter in the pruning function to <strong>e_tresh</strong>.
-Algorithm is described in <a class="reference internal" href="../references.html#leach1998" id="id4"><span>[leach1998]</span></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal energy difference of a solution to the
-optimal solution to be considered.</p></li>
-<li><p><strong>max_n</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The maximum number of solutions that will be generated.</p></li>
-<li><p><strong>max_visited_nodes</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Caps the memory usage of the algorithm. Besides
+Algorithm is described in <a class="reference internal" href="../references.html#leach1998" id="id4">[leach1998]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal energy difference of a solution to the
+optimal solution to be considered.</li>
+<li><strong>max_n</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The maximum number of solutions that will be generated.</li>
+<li><strong>max_visited_nodes</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Caps the memory usage of the algorithm. Besides
The memory used for pairwise energies and self
energies, the algorithm uses about
-<strong>max_visited_nodes</strong> * 20 bytes.</p></li>
+<strong>max_visited_nodes</strong> * 20 bytes.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A tuple with the first element being a list of
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of
solutions. The second element is a list
of energies for the according solutions.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.MCSolve">
-<code class="sig-name descname">MCSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em class="sig-param">n=100</em>, <em class="sig-param">mc_steps=100000</em>, <em class="sig-param">start_temperature=1000.0</em>, <em class="sig-param">change_frequency=1000</em>, <em class="sig-param">cooling_factor=0.9</em>, <em class="sig-param">seed=0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.MCSolve" title="Permalink to this definition">¶</a></dt>
+<code class="descname">MCSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em>n=100</em>, <em>mc_steps=100000</em>, <em>start_temperature=1000.0</em>, <em>change_frequency=1000</em>, <em>cooling_factor=0.9</em>, <em>seed=0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.MCSolve" title="Permalink to this definition">¶</a></dt>
<dd><p>Does a total of <strong>n</strong> Monte Carlo runs to find low energy solutions
of the graph. Each run starts with a random
configuration. At each of the <strong>mc_steps</strong> steps, a random node and
@@ -250,42 +274,49 @@ and is multiplied every <strong>change_frequency</strong> steps with <strong>coo
to achieve a simulated annealing effect.
There is no automatic pruning of the graph using DEE or edge decomposition,
you have to do that by yourself.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of Monte Carlo runs</p></li>
-<li><p><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of Monte Carlo steps per run</p></li>
-<li><p><strong>start_temperature</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Start temperature for the temperature dependent
-Metropolis criterion</p></li>
-<li><p><strong>change_frequency</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of steps the temperature stays the same</p></li>
-<li><p><strong>cooling_factor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor to multiply temperature each
-<strong>change_frequency</strong> steps</p></li>
-<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Seed for random number generator</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>n</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of Monte Carlo runs</li>
+<li><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of Monte Carlo steps per run</li>
+<li><strong>start_temperature</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Start temperature for the temperature dependent
+Metropolis criterion</li>
+<li><strong>change_frequency</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of steps the temperature stays the same</li>
+<li><strong>cooling_factor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor to multiply temperature each
+<strong>change_frequency</strong> steps</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Seed for random number generator</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A tuple with the first element being a list of
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of
solutions. The second element is a list
of energies for the according solutions.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.core.GraphMinimizer.NaiveSolve">
-<code class="sig-name descname">NaiveSolve</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.NaiveSolve" title="Permalink to this definition">¶</a></dt>
+<code class="descname">NaiveSolve</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.NaiveSolve" title="Permalink to this definition">¶</a></dt>
<dd><p>Don’t even think of using this… This function only exists for debug
purposes and does the full enumeration of the solution space.
It might become faster with the appropriate
<a class="reference external" href="https://www.youtube.com/watch?v=fQGbXmkSArs">techniques</a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>A tuple with the first element being a list of indices
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A tuple with the first element being a list of indices
representing the single solutions minimizing
the overall energy function.
-The second element is the according energy value.</p>
-</dd>
-</dl>
+The second element is the according energy value.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -294,7 +325,6 @@ The second element is the according energy value.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -315,12 +345,12 @@ The second element is the according energy value.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
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-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -337,42 +367,36 @@ The second element is the according energy value.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
<li>Previous: <a href="runtime_profiling.html" title="previous chapter">Runtime profiling</a></li>
- <li>Next: <a href="setcompoundschemlib.html" title="next chapter"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+ <li>Next: <a href="setcompoundschemlib.html" title="next chapter"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
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-
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</div>
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- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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<a href="../_sources/core/graph_minimizer.rst.txt"
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index acf81f09fe5d27a9609f33bce5d22cfccca0ef21..6abb2303e27b455c68ba34793f62d6acebf77093 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>helper - Shared Functionality For the Everything — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>helper - Shared Functionality For the Everything — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="module-promod3.core.helper">
@@ -49,21 +48,25 @@ rather empty modules left alone.</p>
</div>
<dl class="function">
<dt id="promod3.core.helper.MsgErrorAndExit">
-<code class="sig-prename descclassname">promod3.core.helper.</code><code class="sig-name descname">MsgErrorAndExit</code><span class="sig-paren">(</span><em class="sig-param">msg</em>, <em class="sig-param">exit_status</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.MsgErrorAndExit" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.core.helper.</code><code class="descname">MsgErrorAndExit</code><span class="sig-paren">(</span><em>msg</em>, <em>exit_status</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.MsgErrorAndExit" title="Permalink to this definition">¶</a></dt>
<dd><p>Send a messages to the OST <a class="reference external" href="https://www.openstructure.org/docs/base/logging/">error log</a> and
exit the Python interpreter.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>msg</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The message.</p></li>
-<li><p><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code, ends up in <code class="docutils literal notranslate"><span class="pre">$?</span></code> in the shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is
-traditionally reserved to successful commands.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>msg</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The message.</li>
+<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code, ends up in <code class="docutils literal notranslate"><span class="pre">$?</span></code> in the shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is
+traditionally reserved to successful commands.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>No return value, exits script with value <code class="docutils literal notranslate"><span class="pre">exit_status</span></code>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">No return value, exits script with value <code class="docutils literal notranslate"><span class="pre">exit_status</span></code>.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -89,29 +92,33 @@ a file name and checks whether it is a <code class="docutils literal notranslate
</div>
<dl class="function">
<dt id="promod3.core.helper.FileExists">
-<code class="sig-prename descclassname">promod3.core.helper.</code><code class="sig-name descname">FileExists</code><span class="sig-paren">(</span><em class="sig-param">prefix</em>, <em class="sig-param">exit_status</em>, <em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileExists" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.core.helper.</code><code class="descname">FileExists</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileExists" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks if a file exists, terminates if not. The error message displayed is
fixed and only needs a <em>prefix</em> describing the specimen of file.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
-“file does not exist: <code class="docutils literal notranslate"><span class="pre">file</span></code>”.</p></li>
-<li><p><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal notranslate"><span class="pre">$?</span></code> in the
-shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is traditionally reserved to successful commands.</p></li>
-<li><p><strong>file</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path including file name to be checked.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
+“file does not exist: <code class="docutils literal notranslate"><span class="pre">file</span></code>”.</li>
+<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal notranslate"><span class="pre">$?</span></code> in the
+shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is traditionally reserved to successful commands.</li>
+<li><strong>file</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path including file name to be checked.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>No return value, exits script with value <code class="docutils literal notranslate"><span class="pre">exit_status</span></code> if file
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">No return value, exits script with value <code class="docutils literal notranslate"><span class="pre">exit_status</span></code> if file
is missing.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.core.helper.FileExtension">
-<code class="sig-prename descclassname">promod3.core.helper.</code><code class="sig-name descname">FileExtension</code><span class="sig-paren">(</span><em class="sig-param">prefix</em>, <em class="sig-param">exit_status</em>, <em class="sig-param">filename</em>, <em class="sig-param">extensions</em>, <em class="sig-param">gzip=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileExtension" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.core.helper.</code><code class="descname">FileExtension</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>filename</em>, <em>extensions</em>, <em>gzip=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileExtension" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks a file to carry a known extension given by a list of strings. Since
files are very often compressed these days, an additional “gz” suffix can be
tracked automatically by this function. Thus, the list of <em>extensions</em> only
@@ -122,51 +129,59 @@ extension, its extension and a Boolean to tell whether the file carries the
gzip extension or not. If <em>gzip</em> detection is turned of, only a tuple is
returned: file name and extension. If the tested file name has an
unrecognised extension, this function terminates the script.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
-“file extension not supported: <code class="docutils literal notranslate"><span class="pre">filename</span></code>”.</p></li>
-<li><p><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal notranslate"><span class="pre">$?</span></code> in the
-shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is traditionally reserved to successful commands.</p></li>
-<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path including file name to be checked.</p></li>
-<li><p><strong>extensions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of strings without a leading “.”.</p></li>
-<li><p><strong>gzip</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Indicates whether to check for an additional “gz” extension.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
+“file extension not supported: <code class="docutils literal notranslate"><span class="pre">filename</span></code>”.</li>
+<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal notranslate"><span class="pre">$?</span></code> in the
+shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is traditionally reserved to successful commands.</li>
+<li><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path including file name to be checked.</li>
+<li><strong>extensions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of strings without a leading “.”.</li>
+<li><strong>gzip</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Indicates whether to check for an additional “gz” extension.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>(base name of <code class="docutils literal notranslate"><span class="pre">filename</span></code> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>), extension of file
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">(base name of <code class="docutils literal notranslate"><span class="pre">filename</span></code> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>), extension of file
without a “.gz” (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>), flag to indicate an additional
“.gz” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>)) <strong>if</strong> <code class="docutils literal notranslate"><span class="pre">gzip</span></code> is set, (base name of
<code class="docutils literal notranslate"><span class="pre">filename</span></code> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>), extension of file) <strong>if not</strong>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.core.helper.FileGzip">
-<code class="sig-prename descclassname">promod3.core.helper.</code><code class="sig-name descname">FileGzip</code><span class="sig-paren">(</span><em class="sig-param">prefix</em>, <em class="sig-param">exit_status</em>, <em class="sig-param">filename</em>, <em class="sig-param">allowed=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileGzip" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.core.helper.</code><code class="descname">FileGzip</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>filename</em>, <em>allowed=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.helper.FileGzip" title="Permalink to this definition">¶</a></dt>
<dd><p>See if a file is gzipped or not. This is basically done by checking for a
“gz” suffix. May also be used to verify that a file is not compressed where
it does not apply. That is where <em>allowed</em> comes in. If “gz” is not allowed,
terminates the script on gzip files.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – String to put in front of the failure-message where gzip
-files are not allowed.</p></li>
-<li><p><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code on gzip files to be avoided, ends up in
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – String to put in front of the failure-message where gzip
+files are not allowed.</li>
+<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Exit code on gzip files to be avoided, ends up in
<code class="docutils literal notranslate"><span class="pre">$?</span></code> in the shell. <code class="docutils literal notranslate"><span class="pre">0</span></code> is traditionally reserved to
-successful commands.</p></li>
-<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path including file name to be checked.</p></li>
-<li><p><strong>allowed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Set to <code class="docutils literal notranslate"><span class="pre">False</span></code> if gzipped files are not allowed. Then the
-script will terminate if a gzip file is found.</p></li>
+successful commands.</li>
+<li><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path including file name to be checked.</li>
+<li><strong>allowed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Set to <code class="docutils literal notranslate"><span class="pre">False</span></code> if gzipped files are not allowed. Then the
+script will terminate if a gzip file is found.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Flag to indicate if file is gzipped (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>).</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Flag to indicate if file is gzipped (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>).</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -174,7 +189,6 @@ script will terminate if a gzip file is found.</p></li>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -195,12 +209,12 @@ script will terminate if a gzip file is found.</p></li>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -217,8 +231,8 @@ script will terminate if a gzip file is found.</p></li>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
- <li>Previous: <a href="pm3argparse.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li>Previous: <a href="pm3argparse.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
<li>Next: <a href="geometry.html" title="next chapter">Geometry functions</a></li>
</ul></li>
</ul></li>
@@ -226,33 +240,27 @@ script will terminate if a gzip file is found.</p></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/helper.rst.txt"
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 1684e67ea84430a56d7fa9beb69d517c65b820bc..551c891176d54176d2663a43965cb80a1a739b21 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>core - ProMod3 Core Functionality — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>core - ProMod3 Core Functionality — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="module-promod3.core">
@@ -40,12 +39,12 @@ modeling per se but cover standard programming issues.</p>
<p>Contents:</p>
<div class="toctree-wrapper compound">
<ul>
-<li class="toctree-l1"><a class="reference internal" href="pm3argparse.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="pm3argparse.html"><code class="docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a><ul>
<li class="toctree-l2"><a class="reference internal" href="pm3argparse.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="pm3argparse.html#argument-parser">Argument Parser</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="helper.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="helper.html"><code class="docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a><ul>
<li class="toctree-l2"><a class="reference internal" href="helper.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="helper.html#messages">Messages</a></li>
<li class="toctree-l2"><a class="reference internal" href="helper.html#file-tests">File Tests</a></li>
@@ -60,7 +59,6 @@ modeling per se but cover standard programming issues.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -81,12 +79,12 @@ modeling per se but cover standard programming issues.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -104,39 +102,33 @@ modeling per se but cover standard programming issues.</p>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
<li>Previous: <a href="../loop/load_loop_objects.html" title="previous chapter">Loading Precomputed Objects</a></li>
- <li>Next: <a href="pm3argparse.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
+ <li>Next: <a href="pm3argparse.html" title="next chapter"><code class="docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/index.rst.txt"
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index 0cbcfccb1194e13f1628445e9fa7241b6250f7b8..ad588482c05bbd2192e5f094c543e73abc327ccb 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>pm3argparse - Parsing Command Lines — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>pm3argparse - Parsing Command Lines — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="module-promod3.core.pm3argparse">
@@ -72,7 +71,7 @@ docstring in your script.</p>
<h2>Argument Parser<a class="headerlink" href="#argument-parser" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.core.pm3argparse.</code><code class="sig-name descname">PM3ArgumentParser</code><span class="sig-paren">(</span><em class="sig-param">description</em>, <em class="sig-param">action=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.core.pm3argparse.</code><code class="descname">PM3ArgumentParser</code><span class="sig-paren">(</span><em>description</em>, <em>action=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser" title="Permalink to this definition">¶</a></dt>
<dd><p>This class is a child of <a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a>. It provides a set
of standard arguments which can be activated with <code class="xref py py-meth docutils literal notranslate"><span class="pre">Add*()</span></code> methods and
then assembled with <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AssembleParser()</span></code></a>. This helps keeping up a common
@@ -83,106 +82,116 @@ instance is possible here.</p>
<p>Attributes beyond <a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a>:</p>
<dl class="attribute">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.action">
-<code class="sig-name descname">action</code><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.action" title="Permalink to this definition">¶</a></dt>
+<code class="descname">action</code><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.action" title="Permalink to this definition">¶</a></dt>
<dd><p>Indicates if the calling script is a ProMod3 action.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.__init__">
-<code class="sig-name descname">__init__</code><span class="sig-paren">(</span><em class="sig-param">description</em>, <em class="sig-param">action=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.__init__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__init__</code><span class="sig-paren">(</span><em>description</em>, <em>action=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.__init__" title="Permalink to this definition">¶</a></dt>
<dd><p>Create a new instance of <code class="xref py py-class docutils literal notranslate"><span class="pre">PM3ArgumentParser</span></code>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>description</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Help text for this script, handed down to
-<a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#description"><code class="xref py py-attr docutils literal notranslate"><span class="pre">description</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">argparse.ArgumentParser.__init__()</span></code></a>.</p></li>
-<li><p><strong>action</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Indicates if the calling script is a ProMod3 action.
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>description</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Help text for this script, handed down to
+<a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#description"><code class="xref py py-attr docutils literal notranslate"><span class="pre">description</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">argparse.ArgumentParser.__init__()</span></code></a>.</li>
+<li><strong>action</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Indicates if the calling script is a ProMod3 action.
This influences <a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#prog"><code class="xref py py-attr docutils literal notranslate"><span class="pre">prog</span></code></a> of
<a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArgumentParser</span></code></a> by clipping of the
first 3 characters of the file name of the script. If
<code class="docutils literal notranslate"><span class="pre">False</span></code>, default behaviour of
-<a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArgumentParser</span></code></a> kicks in.</p></li>
+<a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ArgumentParser</span></code></a> kicks in.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a>.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment">
-<code class="sig-name descname">AddAlignment</code><span class="sig-paren">(</span><em class="sig-param">allow_multitemplate=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddAlignment</code><span class="sig-paren">(</span><em>allow_multitemplate=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment" title="Permalink to this definition">¶</a></dt>
<dd><p>Commandline options for alignments.</p>
<p>Activate everything needed to load alignments to the argument parser.
Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AssembleParser()</span></code></a> and the
input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>allow_multitemplate</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – enable support for multitemplate alignments</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>allow_multitemplate</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – enable support for multitemplate alignments</td>
+</tr>
+</tbody>
+</table>
<p>Options/arguments added:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">-f/--fasta</span> <span class="pre"><FILE></span></code> - Target-template alignment in FASTA format.
+<li><code class="docutils literal notranslate"><span class="pre">-f/--fasta</span> <span class="pre"><FILE></span></code> - Target-template alignment in FASTA format.
Target sequence is either named “trg” or “target” or the first
-sequence is used. File can be plain or gzipped.</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">-c/--clustal</span> <span class="pre"><FILE></span></code> - Target-template alignment in CLUSTAL format.
+sequence is used. File can be plain or gzipped.</li>
+<li><code class="docutils literal notranslate"><span class="pre">-c/--clustal</span> <span class="pre"><FILE></span></code> - Target-template alignment in CLUSTAL format.
Target sequence is either named “trg” or “target” or the first
-sequence is used. File can be plain or gzipped.</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">-j/--json</span> <span class="pre"><OBJECT>|<FILE></span></code> - Alignments provided as JSON
-file/object. File can be plain or gzipped.</p></li>
+sequence is used. File can be plain or gzipped.</li>
+<li><code class="docutils literal notranslate"><span class="pre">-j/--json</span> <span class="pre"><OBJECT>|<FILE></span></code> - Alignments provided as JSON
+file/object. File can be plain or gzipped.</li>
</ul>
<p>See <a class="reference internal" href="../actions/index.html#promod-build-model"><span class="std std-ref">here</span></a> for details on the file formats.</p>
<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">fasta</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--fasta</span></code> option, a
-<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</p></li>
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">clustal</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--clustal</span></code> option, a
-<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</p></li>
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">json</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--json</span></code> option, a
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">fasta</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--fasta</span></code> option, a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</li>
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">clustal</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--clustal</span></code> option, a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</li>
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">json</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--json</span></code> option, a
<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, where each string may be a filename
-or a JSON object string.</p></li>
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">alignments</span></code> - <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.AlignmentList</span></code>, same order as given.
+or a JSON object string.</li>
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">alignments</span></code> - <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.AlignmentList</span></code>, same order as given.
First sequence of the alignment is the target sequence, if in doubt,
-check for sequence roles <code class="docutils literal notranslate"><span class="pre">TARGET</span></code> or <code class="docutils literal notranslate"><span class="pre">TEMPLATE</span></code></p></li>
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">aln_sources</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> with the original
-source(s) of the alignment: may be filename(s) or JSON strings.</p></li>
+check for sequence roles <code class="docutils literal notranslate"><span class="pre">TARGET</span></code> or <code class="docutils literal notranslate"><span class="pre">TEMPLATE</span></code></li>
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">aln_sources</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> with the original
+source(s) of the alignment: may be filename(s) or JSON strings.</li>
</ul>
<p>Exit codes related to alignment input:</p>
<ul class="simple">
-<li><p>12 - a given alignment file does not exist</p></li>
-<li><p>13 - never raised (parameter for checking gzip files)</p></li>
-<li><p>14 - gzip file cannot be opened</p></li>
-<li><p>15 - found an empty alignment file</p></li>
-<li><p>16 - unsupported number of sequences in alignment: only 1 sequence or
-(unless <em>allow_multitemplate</em> = True) more than 2 sequences</p></li>
-<li><p>17 - mutliple target sequences found in alignment</p></li>
-<li><p>18 - error when reading fasta/clustal file</p></li>
-<li><p>19 - problem with a JSON formatted file handed over to <code class="docutils literal notranslate"><span class="pre">--json</span></code></p></li>
-<li><p>20 - JSON file could not be decoded into a JSON object</p></li>
-<li><p>21 - JSON object has no ‘alignmentlist’ key</p></li>
-<li><p>22 - JSON object has no ‘target’/’template’ in the ‘alignmentlist’</p></li>
-<li><p>23 - JSON string could not be decoded</p></li>
-<li><p>24 - JSON object ‘alignmentlist’ does not point to a list</p></li>
-<li><p>25 - JSON object ‘alignmentlist’ member is not a dictionary</p></li>
-<li><p>26 - JSON object ‘alignmentlist’ ‘target’/’template’ does not point
-to a dictionary</p></li>
-<li><p>27 - JSON object ‘alignmentlist’ ‘target’/’template’ does not have
-a needed key</p></li>
-<li><p>28 - JSON object ‘alignmentlist’ ‘target’/’template’ has a value of
-wrong type</p></li>
+<li>12 - a given alignment file does not exist</li>
+<li>13 - never raised (parameter for checking gzip files)</li>
+<li>14 - gzip file cannot be opened</li>
+<li>15 - found an empty alignment file</li>
+<li>16 - unsupported number of sequences in alignment: only 1 sequence or
+(unless <em>allow_multitemplate</em> = True) more than 2 sequences</li>
+<li>17 - mutliple target sequences found in alignment</li>
+<li>18 - error when reading fasta/clustal file</li>
+<li>19 - problem with a JSON formatted file handed over to <code class="docutils literal notranslate"><span class="pre">--json</span></code></li>
+<li>20 - JSON file could not be decoded into a JSON object</li>
+<li>21 - JSON object has no ‘alignmentlist’ key</li>
+<li>22 - JSON object has no ‘target’/’template’ in the ‘alignmentlist’</li>
+<li>23 - JSON string could not be decoded</li>
+<li>24 - JSON object ‘alignmentlist’ does not point to a list</li>
+<li>25 - JSON object ‘alignmentlist’ member is not a dictionary</li>
+<li>26 - JSON object ‘alignmentlist’ ‘target’/’template’ does not point
+to a dictionary</li>
+<li>27 - JSON object ‘alignmentlist’ ‘target’/’template’ does not have
+a needed key</li>
+<li>28 - JSON object ‘alignmentlist’ ‘target’/’template’ has a value of
+wrong type</li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddFragments">
-<code class="sig-name descname">AddFragments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddFragments" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddFragments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddFragments" title="Permalink to this definition">¶</a></dt>
<dd><p>Commandline option for usage of Fragments</p>
<p>Activate everything needed to setup
<a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a> objects in the argument parser.
@@ -190,135 +199,138 @@ Command line arguments are then added in <a class="reference internal" href="#pr
input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>.</p>
<p>Options/arguments added:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">-r/--use-fragments</span></code> - Boolean flag whether to setup fragger handles.</p></li>
+<li><code class="docutils literal notranslate"><span class="pre">-r/--use-fragments</span></code> - Boolean flag whether to setup fragger handles.</li>
</ul>
<p>Notes:</p>
<ul class="simple">
-<li><p>Fragger handles are setup to identify fragments in a
-<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.StructureDB</span></code></a>.</p></li>
-<li><p>If no profiles are provided as additional argument
+<li>Fragger handles are setup to identify fragments in a
+<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.StructureDB</span></code></a>.</li>
+<li>If no profiles are provided as additional argument
(<code class="docutils literal notranslate"><span class="pre">-s/--seqprof</span> <span class="pre"><FILE></span></code>), fragments are identified based on BLOSUM62
-sequence similarity.</p></li>
-<li><p>If you provide profiles that are not in hhm format, fragments are
+sequence similarity.</li>
+<li>If you provide profiles that are not in hhm format, fragments are
identified based on BLOSUM62 sequence similarity, sequence profile
-scoring and structural profile scoring.</p></li>
-<li><p>If you provide profiles in hhm format (optimal case), psipred
+scoring and structural profile scoring.</li>
+<li>If you provide profiles in hhm format (optimal case), psipred
predictions are fetched from there and fragments are identified based
on secondary structure agreement, secondary structure dependent
torsion probabilities, sequence profile scoring and structure
-profile scoring.</p></li>
+profile scoring.</li>
</ul>
<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">fragger_handles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">fragger_handles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
<a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>, ordered to match the target
-sequences.</p></li>
+sequences.</li>
</ul>
<p>Exit codes related to fragments input:</p>
<ul class="simple">
-<li><p>56 - cannot read psipred prediction from hhm file</p></li>
+<li>56 - cannot read psipred prediction from hhm file</li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddProfile">
-<code class="sig-name descname">AddProfile</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddProfile</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Commandline options for profiles</p>
<p>Activate everything needed to load profiles to the argument parser.
Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AssembleParser()</span></code></a> and the
input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>.</p>
<p>Options/arguments added:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">-s/--seqprof</span> <span class="pre"><FILE></span></code> - Sequence profile in any format readable
+<li><code class="docutils literal notranslate"><span class="pre">-s/--seqprof</span> <span class="pre"><FILE></span></code> - Sequence profile in any format readable
by the <code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.io.LoadSequenceProfile()</span></code> method. Format is chosen by
file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm,
.pssm.gz. Consider to use
<code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code> if you have a file
-in a3m format at hand.</p></li>
+in a3m format at hand.</li>
</ul>
<p>Notes:</p>
<ul class="simple">
-<li><p>the profiles are mapped based on exact matches towards the gapless
+<li>the profiles are mapped based on exact matches towards the gapless
target sequences, i.e. one profile is mapped to several chains in
-case of homo-oligomers</p></li>
-<li><p>every profile must have a unique sequence to avoid ambiguities</p></li>
-<li><p>all or nothing - you cannot provide profiles for only a subset of
-target sequences</p></li>
+case of homo-oligomers</li>
+<li>every profile must have a unique sequence to avoid ambiguities</li>
+<li>all or nothing - you cannot provide profiles for only a subset of
+target sequences</li>
</ul>
<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
-ordered to match the target sequences.</p></li>
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
+ordered to match the target sequences.</li>
</ul>
<p>Exit codes related to profile input:</p>
<ul class="simple">
-<li><p>51 - a given profile file does not exist</p></li>
-<li><p>52 - failure to read a given profile file</p></li>
-<li><p>53 - a profile cannot be mapped to any target sequence</p></li>
-<li><p>54 - profile sequences are not unique</p></li>
-<li><p>55 - only subset of target sequences is covered by profile</p></li>
+<li>51 - a given profile file does not exist</li>
+<li>52 - failure to read a given profile file</li>
+<li>53 - a profile cannot be mapped to any target sequence</li>
+<li>54 - profile sequences are not unique</li>
+<li>55 - only subset of target sequences is covered by profile</li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AddStructure">
-<code class="sig-name descname">AddStructure</code><span class="sig-paren">(</span><em class="sig-param">attach_views=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddStructure</code><span class="sig-paren">(</span><em>attach_views=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure" title="Permalink to this definition">¶</a></dt>
<dd><p>Commandline options for structures.</p>
<p>Activate everything needed to load structures to the argument parser.
Command line arguments are then added in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AssembleParser()</span></code></a> and the
input is post processed and checked in <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>attach_views</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True: attach views to alignments. Requires call
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>attach_views</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True: attach views to alignments. Requires call
to <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment" title="promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddAlignment()</span></code></a>. Chains for each sequence
are identified based on the sequence name of the
templates in the alignments (see
-<a class="reference internal" href="../actions/index.html#promod-build-model"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<a class="reference internal" href="../actions/index.html#promod-build-model"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
<p>Options/arguments added:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">-p/--pdb</span> <span class="pre"><FILE></span></code> - Structure in PDB format. File can be plain or
-gzipped.</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">-e/--entity</span> <span class="pre"><FILE></span></code> - Structure in any format readable by the
+<li><code class="docutils literal notranslate"><span class="pre">-p/--pdb</span> <span class="pre"><FILE></span></code> - Structure in PDB format. File can be plain or
+gzipped.</li>
+<li><code class="docutils literal notranslate"><span class="pre">-e/--entity</span> <span class="pre"><FILE></span></code> - Structure in any format readable by the
<code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code> method. Format is chosen by file ending.
-Recognized File Extensions: .ent, .pdb, .ent.gz, .pdb.gz, .cif, .cif.gz.</p></li>
+Recognized File Extensions: .ent, .pdb, .ent.gz, .pdb.gz, .cif, .cif.gz.</li>
</ul>
<p>Notes:</p>
<ul class="simple">
-<li><p>one of the inputs must be given and only one type of input acceptable</p></li>
-<li><p>callable multiple times (structures appended in given order)</p></li>
+<li>one of the inputs must be given and only one type of input acceptable</li>
+<li>callable multiple times (structures appended in given order)</li>
</ul>
<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">pdb</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--pdb</span></code> option, a
-<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</p></li>
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">entity</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--entity</span></code> option, a
-<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</p></li>
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">structures</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.EntityHandle</span></code>, same
-order as given.</p></li>
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">structure_sources</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> with the
-original filenames of the structures.</p></li>
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">pdb</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--pdb</span></code> option, a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</li>
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">entity</span></code> - filled with the input of the <code class="docutils literal notranslate"><span class="pre">--entity</span></code> option, a
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> (filenames).</li>
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">structures</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.EntityHandle</span></code>, same
+order as given.</li>
+<li><code class="xref py py-attr docutils literal notranslate"><span class="pre">structure_sources</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> with the
+original filenames of the structures.</li>
</ul>
<p>Exit codes related to alignment input:</p>
<ul class="simple">
-<li><p>32 - a given structure file does not exist</p></li>
-<li><p>33 - failure to read a given structure file</p></li>
-<li><p>34 - file ending is not a supported format</p></li>
+<li>32 - a given structure file does not exist</li>
+<li>33 - failure to read a given structure file</li>
+<li>34 - file ending is not a supported format</li>
</ul>
<p>Exit codes if <em>attach_views</em> = True:</p>
<ul class="simple">
-<li><p>41 - attach_views used without adding alignments</p></li>
-<li><p>42 - inconsistent offsets between seq. name and seq. in alignment</p></li>
-<li><p>43 - non-integer offset defined in seq. name</p></li>
-<li><p>44 - too many “|” in seq. name</p></li>
-<li><p>45 - chain to attach to sequence could not be identified</p></li>
+<li>41 - attach_views used without adding alignments</li>
+<li>42 - inconsistent offsets between seq. name and seq. in alignment</li>
+<li>43 - non-integer offset defined in seq. name</li>
+<li>44 - too many “|” in seq. name</li>
+<li>45 - chain to attach to sequence could not be identified</li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser">
-<code class="sig-name descname">AssembleParser</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AssembleParser</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser" title="Permalink to this definition">¶</a></dt>
<dd><p>When adding options via the <code class="xref py py-meth docutils literal notranslate"><span class="pre">Add*()</span></code> methods, call this after you
are done. Everything before just tells the parser that it should
contain those option sets but does not actually add anything.
@@ -328,22 +340,24 @@ and with the right constraints.</p>
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.Parse">
-<code class="sig-name descname">Parse</code><span class="sig-paren">(</span><em class="sig-param">args=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Parse</code><span class="sig-paren">(</span><em>args=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="Permalink to this definition">¶</a></dt>
<dd><p>Parse an argument string. See <code class="xref py py-meth docutils literal notranslate"><span class="pre">Add*()</span></code> methods.</p>
<p>Options/arguments added by default: <code class="docutils literal notranslate"><span class="pre">-h/--help</span></code> shows usage.</p>
<p>General exit codes:</p>
<ul class="simple">
-<li><p>1 - an unhandled exception was raised</p></li>
-<li><p>2 - arguments cannot be parsed or required arguments are missing</p></li>
+<li>1 - an unhandled exception was raised</li>
+<li>2 - arguments cannot be parsed or required arguments are missing</li>
</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>args</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – The argument string. As default <a class="reference external" href="https://docs.python.org/3.7/library/sys.html#sys.argv"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sys.argv</span></code></a> is used.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Namespace filled with attributes (see <code class="xref py py-meth docutils literal notranslate"><span class="pre">Add*()</span></code> methods).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>args</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – The argument string. As default <a class="reference external" href="https://docs.python.org/3.7/library/sys.html#sys.argv"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sys.argv</span></code></a> is used.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Namespace filled with attributes (see <code class="xref py py-meth docutils literal notranslate"><span class="pre">Add*()</span></code> methods).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -353,7 +367,6 @@ and with the right constraints.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -374,12 +387,12 @@ and with the right constraints.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -396,42 +409,36 @@ and with the right constraints.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
- <li>Next: <a href="helper.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+ <li>Next: <a href="helper.html" title="next chapter"><code class="docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
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- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/pm3argparse.rst.txt"
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index aa9651473d8c7dbe31a910ab31729f28accd08f8..795b6c9fad6daab07814879961cac843f5caba8e 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Runtime profiling — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Runtime profiling — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,15 +30,13 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="runtime-profiling">
<h1>Runtime profiling<a class="headerlink" href="#runtime-profiling" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="promod3.core.StaticRuntimeProfiler">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.core.</code><code class="sig-name descname">StaticRuntimeProfiler</code><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">StaticRuntimeProfiler</code><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler" title="Permalink to this definition">¶</a></dt>
<dd><p>Defines functionality for runtime profiling.</p>
<p>All profiling is completely turned off by default and must be activated at
compile-time by adding <code class="docutils literal notranslate"><span class="pre">-DPM3_RUNTIME_PROFILING_LEVEL=N</span></code> to your CMake
@@ -51,83 +50,99 @@ generated considering the number of timings and the total runtime for that
timer. If a timer within another timed entity, the outer timer is paused,
while the inner one is running. Hence, the sum of all timers will be the
total time spent in any timer (nothing is counted twice!).</p>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.core.StaticRuntimeProfiler.Start">
-<em class="property">static </em><code class="sig-name descname">Start</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Start" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Start</code><span class="sig-paren">(</span><em>id</em>, <em>level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Start" title="Permalink to this definition">¶</a></dt>
<dd><p>Start a timer for the given <cite>id</cite>. This pauses any other currently running
timer.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Identifier for this timer.</p></li>
-<li><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Timer only started if level <= <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Identifier for this timer.</li>
+<li><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Timer only started if level <= <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.core.StaticRuntimeProfiler.StartScoped">
-<em class="property">static </em><code class="sig-name descname">StartScoped</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.StartScoped" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">StartScoped</code><span class="sig-paren">(</span><em>id</em>, <em>level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.StartScoped" title="Permalink to this definition">¶</a></dt>
<dd><p>Start a timer for the given <cite>id</cite> as in <a class="reference internal" href="#promod3.core.StaticRuntimeProfiler.Start" title="promod3.core.StaticRuntimeProfiler.Start"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Start()</span></code></a>, but this will stop it
automatically when the returned variable goes out of scope.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Identifier for this timer.</p></li>
-<li><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Timer only started if level <= <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Identifier for this timer.</li>
+<li><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Timer only started if level <= <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Object that will call <a class="reference internal" href="#promod3.core.StaticRuntimeProfiler.Stop" title="promod3.core.StaticRuntimeProfiler.Stop"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Stop()</span></code></a> when it goes out of scope</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Object that will call <a class="reference internal" href="#promod3.core.StaticRuntimeProfiler.Stop" title="promod3.core.StaticRuntimeProfiler.Stop"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Stop()</span></code></a> when it goes out of scope</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.core.StaticRuntimeProfiler.Stop">
-<em class="property">static </em><code class="sig-name descname">Stop</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Stop" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Stop</code><span class="sig-paren">(</span><em>id</em>, <em>level=1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Stop" title="Permalink to this definition">¶</a></dt>
<dd><p>Stop the currently running timer. If a timer was paused when starting this
timer, it will be resumed now. Note that there is no error checking here, so
this will fail miserably if no timer is currently running.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Timer only stopped if level <= <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Timer only stopped if level <= <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.core.StaticRuntimeProfiler.PrintSummary">
-<em class="property">static </em><code class="sig-name descname">PrintSummary</code><span class="sig-paren">(</span><em class="sig-param">max_to_show=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.PrintSummary" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">PrintSummary</code><span class="sig-paren">(</span><em>max_to_show=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.PrintSummary" title="Permalink to this definition">¶</a></dt>
<dd><p>Display a summary of all timed entities. The timers are collected by id and
sorted by total runtime. If more than 10 entries are shown and the used id’s
have the form “GROUP::NAME”, an additional summary is shown with the total
times spent in each “GROUP”.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>max_to_show</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – if >= 0, show only top <cite>max_to_show</cite> entries.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>max_to_show</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – if >= 0, show only top <cite>max_to_show</cite> entries.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.core.StaticRuntimeProfiler.IsEnabled">
-<em class="property">static </em><code class="sig-name descname">IsEnabled</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.IsEnabled" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code> > 0. Otherwise, profiling
-is completely turned off.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">IsEnabled</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.IsEnabled" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if <code class="docutils literal notranslate"><span class="pre">PM3_RUNTIME_PROFILING_LEVEL</span></code> > 0. Otherwise, profiling
+is completely turned off.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.core.StaticRuntimeProfiler.Clear">
-<em class="property">static </em><code class="sig-name descname">Clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Clear" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.StaticRuntimeProfiler.Clear" title="Permalink to this definition">¶</a></dt>
<dd><p>Clears all timed entries. Note that there is no error checking here, so this
will fail miserably if timers are currently running.</p>
</dd></dl>
@@ -138,7 +153,6 @@ will fail miserably if timers are currently running.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -159,12 +173,12 @@ will fail miserably if timers are currently running.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -181,7 +195,7 @@ will fail miserably if timers are currently running.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
<li>Previous: <a href="geometry.html" title="previous chapter">Geometry functions</a></li>
<li>Next: <a href="graph_minimizer.html" title="next chapter">Graph Minimizer</a></li>
</ul></li>
@@ -190,33 +204,27 @@ will fail miserably if timers are currently running.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/runtime_profiling.rst.txt"
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index cabf318b8994fff813783df478b5cfc4dcc4189a..f6cbb73e8d60cf848b57bb6bf6609d49473eb9d2 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>SetCompoundsChemlib() — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>SetCompoundsChemlib() — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="setcompoundschemlib">
@@ -44,21 +43,23 @@ need to call this function, only if you want to load a different chemical
components dictionary.</p>
<dl class="function">
<dt id="promod3.SetCompoundsChemlib">
-<code class="sig-prename descclassname">promod3.</code><code class="sig-name descname">SetCompoundsChemlib</code><span class="sig-paren">(</span><em class="sig-param">path_to_chemlib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.SetCompoundsChemlib" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.</code><code class="descname">SetCompoundsChemlib</code><span class="sig-paren">(</span><em>path_to_chemlib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.SetCompoundsChemlib" title="Permalink to this definition">¶</a></dt>
<dd><p>Load a compounds library. Does not return anything, the library is just
enabled globally.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>path_to_chemlib</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Points to the file to be loaded.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>path_to_chemlib</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Points to the file to be loaded.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -79,12 +80,12 @@ enabled globally.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -108,33 +109,27 @@ enabled globally.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/setcompoundschemlib.rst.txt"
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index 5d173da4203c8e761982eb05bc75ab63ff3d49ad..2a060c73826e7fe234a7ce2a43e024b9755ff058 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>ProMod3 Setup — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>ProMod3 Setup — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="project-setup">
@@ -59,11 +58,11 @@ whole projects extending ProMod3 and see that they work seamlessly together
with the rest of the system. There do exist a couple of rather strict rules for
what goes into this branch:</p>
<ul class="simple">
-<li><p>Your code must have been (briefly) reviewed by others</p></li>
-<li><p>There have to be unit tests</p></li>
-<li><p>It needs to pass <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> <strong>including</strong> <code class="docutils literal notranslate"><span class="pre">doctest</span></code> & <code class="docutils literal notranslate"><span class="pre">linkcheck</span></code></p></li>
-<li><p>Your project needs documentation</p></li>
-<li><p>It must not break the ability of out-of-source builds</p></li>
+<li>Your code must have been (briefly) reviewed by others</li>
+<li>There have to be unit tests</li>
+<li>It needs to pass <code class="docutils literal notranslate"><span class="pre">make</span> <span class="pre">check</span></code> <strong>including</strong> <code class="docutils literal notranslate"><span class="pre">doctest</span></code> & <code class="docutils literal notranslate"><span class="pre">linkcheck</span></code></li>
+<li>Your project needs documentation</li>
+<li>It must not break the ability of out-of-source builds</li>
</ul>
<p>The reason to be a bit restrictive on branches which end up in actual releases,
should be mostly obvious: ProMod3 is used by productive services as a third
@@ -197,17 +196,17 @@ repository root. The directory structure of your module should look like this:</
</div>
<p>Additionally to the module directories there are a few extra folders:</p>
<ul class="simple">
-<li><p><code class="file docutils literal notranslate"><span class="pre">actions</span></code>: Scripts callable as <code class="docutils literal notranslate"><span class="pre">pm</span> <span class="pre"><ACTION_NAME></span></code>.
-See <a class="reference internal" href="contributing.html#how-to-start-your-own-action"><span class="std std-ref">here</span></a> for details.</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">cmake_support</span></code>: Helper functions for CMake.
-See <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span class="std std-ref">here</span></a> for details.</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">doc</span></code>: High-level documentation, test scripts (<code class="file docutils literal notranslate"><span class="pre">doc/tests</span></code>) and a
+<li><code class="file docutils literal notranslate"><span class="pre">actions</span></code>: Scripts callable as <code class="docutils literal notranslate"><span class="pre">pm</span> <span class="pre"><ACTION_NAME></span></code>.
+See <a class="reference internal" href="contributing.html#how-to-start-your-own-action"><span class="std std-ref">here</span></a> for details.</li>
+<li><code class="file docutils literal notranslate"><span class="pre">cmake_support</span></code>: Helper functions for CMake.
+See <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span class="std std-ref">here</span></a> for details.</li>
+<li><code class="file docutils literal notranslate"><span class="pre">doc</span></code>: High-level documentation, test scripts (<code class="file docutils literal notranslate"><span class="pre">doc/tests</span></code>) and a
copy of the generated html documentation (<code class="file docutils literal notranslate"><span class="pre">doc/html</span></code>). The latter must
be kept up-to-date at least on the <code class="docutils literal notranslate"><span class="pre">master</span></code> branch.
-See <a class="reference internal" href="contributing.html#writing-documentation"><span class="std std-ref">here</span></a> for details.</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">extras</span></code>: Extra data and information that doesn’t fit anywhere
-else (e.g. Git hooks or scripts to recreate the binary files).</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">scripts</span></code>: Input for scripts that end up in <code class="file docutils literal notranslate"><span class="pre">stage/bin</span></code></p></li>
+See <a class="reference internal" href="contributing.html#writing-documentation"><span class="std std-ref">here</span></a> for details.</li>
+<li><code class="file docutils literal notranslate"><span class="pre">extras</span></code>: Extra data and information that doesn’t fit anywhere
+else (e.g. Git hooks or scripts to recreate the binary files).</li>
+<li><code class="file docutils literal notranslate"><span class="pre">scripts</span></code>: Input for scripts that end up in <code class="file docutils literal notranslate"><span class="pre">stage/bin</span></code></li>
</ul>
</div>
<div class="section" id="cmake">
@@ -236,7 +235,6 @@ modules from there, use the binaries from <code class="file docutils literal not
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -273,33 +271,27 @@ modules from there, use the binaries from <code class="file docutils literal not
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/dev_setup.rst.txt"
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 40fba96583f81dcf40fe8b37169ff05ef060119f..7084fedebc67848cc80f6bd2f5f058fe931016ed 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Documentation For Developers — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Documentation For Developers — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="documentation-for-developers">
@@ -60,7 +59,7 @@ new features.</p>
<li class="toctree-l2"><a class="reference internal" href="contributing.html#third-party-contributions-license-issues">Third Party Contributions (License Issues)</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="actions/index_dev.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">test_actions</span></code> - Testing Actions</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="actions/index_dev.html"><code class="docutils literal notranslate"><span class="pre">test_actions</span></code> - Testing Actions</a><ul>
<li class="toctree-l2"><a class="reference internal" href="actions/index_dev.html#creating-an-action-unit-test-script">Creating an Action Unit Test Script</a></li>
<li class="toctree-l2"><a class="reference internal" href="actions/index_dev.html#unit-test-actions-api">Unit Test Actions API</a></li>
</ul>
@@ -83,7 +82,6 @@ new features.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -118,33 +116,27 @@ new features.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/developers.rst.txt"
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index f18ed2b4690f6241a3b4224e93eb75afbf7b54a7..5ef68c4bd5228d4b81369271fa83fc79b7cf5f62 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -1,11 +1,13 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Index — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Index — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -19,7 +21,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -28,8 +29,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
@@ -2257,7 +2256,6 @@
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -2290,33 +2288,27 @@
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index 20ff1b4fa4b46126008093a01b22123b95d630cd..80a23c32bac0dd7b3a391415c5fe91aa5ffc6e88 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Getting Started — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Getting Started — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="getting-started">
@@ -39,17 +38,20 @@
<h2>Get and Run ProMod3<a class="headerlink" href="#get-and-run-project" title="Permalink to this headline">¶</a></h2>
<p>Either utilize <a class="reference internal" href="container/index.html#container"><span class="std std-ref">containers</span></a> or start from source code:</p>
<ol class="arabic">
-<li><p>Fetch the source code from <a class="reference external" href="https://git.scicore.unibas.ch/schwede/ProMod3.git">https://git.scicore.unibas.ch/schwede/ProMod3.git</a>.
+<li><p class="first">Fetch the source code from <a class="reference external" href="https://git.scicore.unibas.ch/schwede/ProMod3.git">https://git.scicore.unibas.ch/schwede/ProMod3.git</a>.
Or directly pull it with git:</p>
<div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> git clone https://git.scicore.unibas.ch/schwede/ProMod3.git <DIR>
</pre></div>
</div>
</li>
-<li><p>Obtain all dependencies and compile ProMod3 with <code class="docutils literal notranslate"><span class="pre">cmake</span></code> and <code class="docutils literal notranslate"><span class="pre">make</span></code>
-(see <a class="reference internal" href="buildsystem.html#building-promod"><span class="std std-ref">here</span></a>).</p></li>
-<li><p>Ensure that you have a <code class="docutils literal notranslate"><span class="pre">stage/bin</span></code> folder which includes a <code class="docutils literal notranslate"><span class="pre">pm</span></code> executable.
-For convenience, add the folder to your <code class="docutils literal notranslate"><span class="pre">PATH</span></code> env. variable.</p></li>
-<li><p>You can now execute ProMod3 by running the following in your terminal:</p></li>
+<li><p class="first">Obtain all dependencies and compile ProMod3 with <code class="docutils literal notranslate"><span class="pre">cmake</span></code> and <code class="docutils literal notranslate"><span class="pre">make</span></code>
+(see <a class="reference internal" href="buildsystem.html#building-promod"><span class="std std-ref">here</span></a>).</p>
+</li>
+<li><p class="first">Ensure that you have a <code class="docutils literal notranslate"><span class="pre">stage/bin</span></code> folder which includes a <code class="docutils literal notranslate"><span class="pre">pm</span></code> executable.
+For convenience, add the folder to your <code class="docutils literal notranslate"><span class="pre">PATH</span></code> env. variable.</p>
+</li>
+<li><p class="first">You can now execute ProMod3 by running the following in your terminal:</p>
+</li>
</ol>
<blockquote>
<div><div class="highlight-console notranslate"><div class="highlight"><pre><span></span><span class="gp">$</span> pm <COMMAND>
@@ -57,8 +59,9 @@ For convenience, add the folder to your <code class="docutils literal notranslat
</div>
<p>Here <code class="docutils literal notranslate"><span class="pre"><COMMAND></span></code> can be:</p>
<ul>
-<li><p>a predefined “action” (see <a class="reference internal" href="actions/index.html#promod-actions"><span class="std std-ref">here</span></a>)</p></li>
-<li><p>the path to a python script, such as the following example:</p>
+<li><p class="first">a predefined “action” (see <a class="reference internal" href="actions/index.html#promod-actions"><span class="std std-ref">here</span></a>)</p>
+</li>
+<li><p class="first">the path to a python script, such as the following example:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
@@ -80,12 +83,12 @@ can visualize with any pdb reader (e.g. <code class="docutils literal notranslat
Commonly, your input is a template structure and an alignment of the template to
the desired target sequence. The modelling steps then are:</p>
<ul class="simple">
-<li><p>Build a raw model from a template by copying the part of the template which
-is conserved</p></li>
-<li><p>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code></a> module)</p></li>
-<li><p>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code></a> module)</p></li>
-<li><p>Minimize energy of final model using molecular mechanics
-(using <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</p></li>
+<li>Build a raw model from a template by copying the part of the template which
+is conserved</li>
+<li>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code></a> module)</li>
+<li>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code></a> module)</li>
+<li>Minimize energy of final model using molecular mechanics
+(using <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
</ul>
<p>Since a good amount of time is spent in OpenMM routines to minimize energy, we
try to use the fast and multi-threaded “CPU” platform of OpenMM (should be
@@ -99,7 +102,6 @@ not set, 1 thread will be used by default.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -120,12 +122,12 @@ not set, 1 thread will be used by default.</p>
<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -149,33 +151,27 @@ not set, 1 thread will be used by default.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
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</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/gettingstarted.rst.txt"
diff --git a/doc/html/index.html b/doc/html/index.html
index 54aac08070a269cd5e98cd508a5c2fa2828a04f6..48736a0c783604f8b6d4ffc81ebfacd942b36dd3 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>ProMod3 — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>ProMod3 — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -19,7 +21,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -28,13 +29,11 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="promod3">
<h1>ProMod3<a class="headerlink" href="#promod3" title="Permalink to this headline">¶</a></h1>
-<p>ProMod3 is a modelling engine based on the <a class="reference external" href="https://openstructure.org">OpenStructure</a> <a class="reference internal" href="references.html#biasini2013" id="id1"><span>[biasini2013]</span></a>
+<p>ProMod3 is a modelling engine based on the <a class="reference external" href="https://openstructure.org">OpenStructure</a> <a class="reference internal" href="references.html#biasini2013" id="id1">[biasini2013]</a>
computational structural biology framework that can perform all steps required
to generate a protein model by homology. Its modular design aims at
implementing flexible modelling pipelines and fast prototyping of novel
@@ -50,12 +49,12 @@ algorithms.</p>
<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -73,7 +72,6 @@ algorithms.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -107,33 +105,27 @@ algorithms.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
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-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/index.rst.txt"
diff --git a/doc/html/license.html b/doc/html/license.html
index 63f69948957f005fda4e9602f3788ed4fbe5b2f5..2fa7eaf1e51cfcc2ccd9a981b902d1ebfdb7e3f8 100644
--- a/doc/html/license.html
+++ b/doc/html/license.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>License — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>License — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="license">
@@ -251,7 +250,6 @@ doc/Copyright_cmake.py.txt
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -286,33 +284,27 @@ doc/Copyright_cmake.py.txt
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
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<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/license.rst.txt"
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index 606df70990b579ae9dc000f6eeca585cc72d47cf..f27b4188bdce492b5a6be0d1175442ff9542ba6a 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Handling All Atom Positions — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Handling All Atom Positions — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="handling-all-atom-positions">
@@ -72,147 +71,168 @@ handle changes during loop modelling.</p>
<h2>The AllAtomEnv class<a class="headerlink" href="#the-allatomenv-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.AllAtomEnv">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AllAtomEnv</code><span class="sig-paren">(</span><em class="sig-param">seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AllAtomEnv</code><span class="sig-paren">(</span><em>seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv" title="Permalink to this definition">¶</a></dt>
<dd><p>The all atom environment contains and handles positions of all atoms during
loop modelling. It is linked to a (list of) seqres (one per chain) at
construction. The idea is to initialize it at the beginning of the modelling
process with all known positions and then update the environment whenever a
new loop is being added.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
-chain). Whenever setting structural data, consistency with this SEQRES is enforced.</p>
-</dd>
-</dl>
+chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
+</tr>
+</tbody>
+</table>
<p>Indexing to access parts of the environment:</p>
<ul class="simple">
-<li><p><em>chain_idx</em>: Index of chain as it occurs in <em>seqres</em> (0 for single sequence)</p></li>
-<li><p><em>start_resnum</em>: Residue number defining the position in the SEQRES of chain
+<li><em>chain_idx</em>: Index of chain as it occurs in <em>seqres</em> (0 for single sequence)</li>
+<li><em>start_resnum</em>: Residue number defining the position in the SEQRES of chain
with index <em>chain_idx</em>. <strong>The numbering starts for every chain with the
-value 1</strong>.</p></li>
-<li><p>internal residue indexing: all residues of all chains are simply
-concatenated one after each other (indexing starts at 0)</p></li>
+value 1</strong>.</li>
+<li>internal residue indexing: all residues of all chains are simply
+concatenated one after each other (indexing starts at 0)</li>
</ul>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.SetInitialEnvironment">
-<code class="sig-name descname">SetInitialEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env_structure</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.SetInitialEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetInitialEnvironment</code><span class="sig-paren">(</span><em>env_structure</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.SetInitialEnvironment" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets full environment. Existing data is cleared first.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
-order as the SEQRES items provided in constructor.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>env</em> is inconsistent with
+order as the SEQRES items provided in constructor.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>env</em> is inconsistent with
SEQRES set in constructor. This can be because of corrupt residue
-numbers or sequence mismatches.</p>
-</dd>
-</dl>
+numbers or sequence mismatches.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.SetEnvironment">
-<code class="sig-name descname">SetEnvironment</code><span class="sig-paren">(</span><em class="sig-param">new_env_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.SetEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetEnvironment</code><span class="sig-paren">(</span><em>new_env_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.SetEnvironment" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">SetEnvironment</code><span class="sig-paren">(</span><em class="sig-param">new_pos</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">SetEnvironment</code><span class="sig-paren">(</span><em>new_pos</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="sig-name descname">SetEnvironment</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">SetEnvironment</code><span class="sig-paren">(</span><em>bb_list</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
<dd><p>Add/update atom positions in environment. In the end, all residues covered
in <em>new_env_pos</em> / <em>new_pos</em> / <em>bb_list</em> will be set as defined there. This
means, that positions in the env. may be reset, newly set or cleared.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</p></li>
-<li><p><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</p></li>
-<li><p><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</li>
+<li><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</li>
+<li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>new_pos</em> / <em>new_env_pos</em> /
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>new_pos</em> / <em>new_env_pos</em> /
<em>bb_list</em> is inconsistent with SEQRES set in constructor or when
either <em>start_resnum</em> or <em>chain_idx</em> point to invalid positions in
the SEQRES.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.ClearEnvironment">
-<code class="sig-name descname">ClearEnvironment</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.ClearEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ClearEnvironment</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.ClearEnvironment" title="Permalink to this definition">¶</a></dt>
<dd><p>Clears a stretch of length <em>num_residues</em> in the environment in chain
with idx <em>chain_idx</em> starting from residue number <em>start_resnum</em></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start of stretch to clear</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of stretch to clear</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start of stretch to clear</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of stretch to clear</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
<em>chain_idx</em> point to invalid positions in the SEQRES.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.GetEnvironment">
-<code class="sig-name descname">GetEnvironment</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetEnvironment" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Copy of stretch of structural data in environment. Useful to store
+<code class="descname">GetEnvironment</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetEnvironment" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Copy of stretch of structural data in environment. Useful to store
a loop to reset later with <a class="reference internal" href="#promod3.loop.AllAtomEnv.SetEnvironment" title="promod3.loop.AllAtomEnv.SetEnvironment"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnvironment()</span></code></a>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start of stretch to store</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of stretch to store</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start of stretch to store</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of stretch to store</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
<em>chain_idx</em> point to invalid positions in the SEQRES.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.GetSeqres">
-<code class="sig-name descname">GetSeqres</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetSeqres" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>SEQRES that was set in constructor (one sequence per chain).</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetSeqres</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetSeqres" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomEnv.GetAllAtomPositions">
-<code class="sig-name descname">GetAllAtomPositions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetAllAtomPositions" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Reference (use with caution!) to the internal storage of all atom
+<code class="descname">GetAllAtomPositions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomEnv.GetAllAtomPositions" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Reference (use with caution!) to the internal storage of all atom
positions for the environment. All residues of all chains are
stored continuously in there. To get a copy of some positions use
-<a class="reference internal" href="#promod3.loop.AllAtomEnv.GetEnvironment" title="promod3.loop.AllAtomEnv.GetEnvironment"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetEnvironment()</span></code></a>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
-</dd>
-</dl>
+<a class="reference internal" href="#promod3.loop.AllAtomEnv.GetEnvironment" title="promod3.loop.AllAtomEnv.GetEnvironment"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetEnvironment()</span></code></a>.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -222,557 +242,621 @@ stored continuously in there. To get a copy of some positions use
<h2>The AllAtomPositions class<a class="headerlink" href="#the-allatompositions-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.AllAtomPositions">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AllAtomPositions</code><a class="headerlink" href="#promod3.loop.AllAtomPositions" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AllAtomPositions</code><a class="headerlink" href="#promod3.loop.AllAtomPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Container for the positions of all heavy atoms of an arbitrary amino acid sequence. This is tailored for fast operations within C++ codes. The Python export described here, is mainly meant for debugging or to initialize the object and feed it to other classes using it.</p>
<p>Indexing of positions and residues:</p>
<ul class="simple">
-<li><p>residue indexing is in the range [0, <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetNumResidues" title="promod3.loop.AllAtomPositions.GetNumResidues"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumResidues()</span></code></a>-1] and is in the
-order of the sequence used to initialize the object</p></li>
-<li><p>indexing of single atoms is in the range [0, <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetNumAtoms" title="promod3.loop.AllAtomPositions.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>-1]. For
+<li>residue indexing is in the range [0, <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetNumResidues" title="promod3.loop.AllAtomPositions.GetNumResidues"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumResidues()</span></code></a>-1] and is in the
+order of the sequence used to initialize the object</li>
+<li>indexing of single atoms is in the range [0, <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetNumAtoms" title="promod3.loop.AllAtomPositions.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>-1]. For
each residue you can find the bounds with <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetFirstIndex" title="promod3.loop.AllAtomPositions.GetFirstIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetFirstIndex()</span></code></a> and
-<a class="reference internal" href="#promod3.loop.AllAtomPositions.GetLastIndex" title="promod3.loop.AllAtomPositions.GetLastIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLastIndex()</span></code></a> or find a single atom with <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetIndex" title="promod3.loop.AllAtomPositions.GetIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetIndex()</span></code></a></p></li>
+<a class="reference internal" href="#promod3.loop.AllAtomPositions.GetLastIndex" title="promod3.loop.AllAtomPositions.GetLastIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLastIndex()</span></code></a> or find a single atom with <a class="reference internal" href="#promod3.loop.AllAtomPositions.GetIndex" title="promod3.loop.AllAtomPositions.GetIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetIndex()</span></code></a></li>
</ul>
<p>Each atom position is initially unset (unless a list of residues is passed
when constructing it) and can only be set with calls to <a class="reference internal" href="#promod3.loop.AllAtomPositions.SetPos" title="promod3.loop.AllAtomPositions.SetPos"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetPos()</span></code></a> or
<a class="reference internal" href="#promod3.loop.AllAtomPositions.SetResidue" title="promod3.loop.AllAtomPositions.SetResidue"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetResidue()</span></code></a>.</p>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.AllAtomPositions">
-<code class="sig-name descname">AllAtomPositions</code><span class="sig-paren">(</span><em class="sig-param">sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.AllAtomPositions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AllAtomPositions</code><span class="sig-paren">(</span><em>sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.AllAtomPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a container for the given <em>sequence</em> with all positions unset.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of amino acid one letter codes.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
-code which is not one of the 20 default amino acids.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of amino acid one letter codes.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+code which is not one of the 20 default amino acids.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">AllAtomPositions</code><span class="sig-paren">(</span><em class="sig-param">residues</em><span class="sig-paren">)</span></dt>
+<code class="descname">AllAtomPositions</code><span class="sig-paren">(</span><em>residues</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a container for the given <em>residues</em>. Both sequence and positions
are extracted from the given residues.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>residues</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandleList</span></code>) – List of residues</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any residue has a one letter
-code which is not one of the 20 default amino acids.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>residues</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandleList</span></code>) – List of residues</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any residue has a one letter
+code which is not one of the 20 default amino acids.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">AllAtomPositions</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">residues</em><span class="sig-paren">)</span></dt>
+<code class="descname">AllAtomPositions</code><span class="sig-paren">(</span><em>sequence</em>, <em>residues</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a container for the given <em>sequence</em> and extracts positions from
<em>residues</em>. The residues may be different amino acids than the given
<em>sequence</em> (see <a class="reference internal" href="#promod3.loop.AllAtomPositions.SetResidue" title="promod3.loop.AllAtomPositions.SetResidue"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetResidue()</span></code></a>).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of amino acid one letter codes.</p></li>
-<li><p><strong>residues</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandleList</span></code>) – List of residues from which positions are extracted.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of amino acid one letter codes.</li>
+<li><strong>residues</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandleList</span></code>) – List of residues from which positions are extracted.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
code which is not one of the 20 default amino acids or if
<em>sequence</em> and <em>residues</em> are inconsistent in size.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">AllAtomPositions</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span></dt>
+<code class="descname">AllAtomPositions</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a container for the given backbone. Both sequence and backbone
positions are extracted from the given residues.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Backbone list of residues</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any residue has a one letter
-code which is not one of the 20 default amino acids.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Backbone list of residues</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any residue has a one letter
+code which is not one of the 20 default amino acids.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.SetResidue">
-<code class="sig-name descname">SetResidue</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.SetResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetResidue</code><span class="sig-paren">(</span><em>res_index</em>, <em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.SetResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Set positions for residue at index <em>res_index</em> given the atoms in <em>res</em>.
For each expected heavy atom, we search for an atom of that name in <em>res</em>
and if found set the corresponding position, otherwise we unset it.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">SetResidue</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">other</em>, <em class="sig-param">other_res_index</em><span class="sig-paren">)</span></dt>
+<code class="descname">SetResidue</code><span class="sig-paren">(</span><em>res_index</em>, <em>other</em>, <em>other_res_index</em><span class="sig-paren">)</span></dt>
<dd><p>Set positions for residue at index <em>res_index</em> given the positions of
residue at index <em>other_res_index</em> in <em>other</em> position container. Each
position is set or cleared according to the data in <em>other</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Position container from which we take data</p></li>
-<li><p><strong>other_res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index in <em>other</em></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
+<li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Position container from which we take data</li>
+<li><strong>other_res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index in <em>other</em></li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> or <em>other_res_index</em>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> or <em>other_res_index</em>
out of bounds or if residues in the two containers are inconsistent
(different amino acids).</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.SetPos">
-<code class="sig-name descname">SetPos</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.SetPos" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Set position at that index.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</p></li>
+<code class="descname">SetPos</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.SetPos" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Set position at that index.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.ClearPos">
-<code class="sig-name descname">ClearPos</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ClearPos" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Unset position at that index.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">ClearPos</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ClearPos" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Unset position at that index.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.ClearResidue">
-<code class="sig-name descname">ClearResidue</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ClearResidue" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Unset all positions for residue at that index.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">ClearResidue</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ClearResidue" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Unset all positions for residue at that index.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetPos">
-<code class="sig-name descname">GetPos</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPos" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Position at given index.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom position index.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">GetPos</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPos" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position at given index.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom position index.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.IsSet">
-<code class="sig-name descname">IsSet</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsSet" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if the position at that index is currently set.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom position index.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">IsSet</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsSet" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if the position at that index is currently set.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom position index.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetIndex">
-<code class="sig-name descname">GetIndex</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetIndex" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Atom position index for atom named <em>atom_name</em> (standard PDB
+<code class="descname">GetIndex</code><span class="sig-paren">(</span><em>res_index</em>, <em>atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetIndex" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Atom position index for atom named <em>atom_name</em> (standard PDB
naming) for residue at index <em>res_index</em>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds or
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds or
if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetFirstIndex">
-<code class="sig-name descname">GetFirstIndex</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetFirstIndex" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>First atom position index for residue at index <em>res_index</em>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">GetFirstIndex</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetFirstIndex" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">First atom position index for residue at index <em>res_index</em>.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetLastIndex">
-<code class="sig-name descname">GetLastIndex</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetLastIndex" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Last atom position index for residue at index <em>res_index</em>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">GetLastIndex</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetLastIndex" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Last atom position index for residue at index <em>res_index</em>.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetAA">
-<code class="sig-name descname">GetAA</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetAA" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Amino acid type of residue at index <em>res_index</em>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">GetAA</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetAA" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of residue at index <em>res_index</em>.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.IsAnySet">
-<code class="sig-name descname">IsAnySet</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsAnySet" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if any atom position of residue at index <em>res_index</em> is set.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">IsAnySet</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsAnySet" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if any atom position of residue at index <em>res_index</em> is set.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.IsAllSet">
-<code class="sig-name descname">IsAllSet</code><span class="sig-paren">(</span><em class="sig-param">res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsAllSet" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if all atom positions of residue at index <em>res_index</em> are set.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">IsAllSet</code><span class="sig-paren">(</span><em>res_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.IsAllSet" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if all atom positions of residue at index <em>res_index</em> are set.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetPhiTorsion">
-<code class="sig-name descname">GetPhiTorsion</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">def_angle=-1.0472</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPhiTorsion" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Phi torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
+<code class="descname">GetPhiTorsion</code><span class="sig-paren">(</span><em>res_index</em>, <em>def_angle=-1.0472</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPhiTorsion" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Phi torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
if required atom positions (C-N-CA-C) are not set.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Default phi angle.</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
+<li><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Default phi angle.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> - 1 or <em>res_index</em>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> - 1 or <em>res_index</em>
out of bounds.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetPsiTorsion">
-<code class="sig-name descname">GetPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">def_angle=-0.7854</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPsiTorsion" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Psi torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
+<code class="descname">GetPsiTorsion</code><span class="sig-paren">(</span><em>res_index</em>, <em>def_angle=-0.7854</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Psi torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
if required atom positions (N-CA-C-N) are not set.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Default psi angle.</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
+<li><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Default psi angle.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> or <em>res_index</em> + 1
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> or <em>res_index</em> + 1
out of bounds.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetOmegaTorsion">
-<code class="sig-name descname">GetOmegaTorsion</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">def_angle=3.14159</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetOmegaTorsion" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Omega torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
+<code class="descname">GetOmegaTorsion</code><span class="sig-paren">(</span><em>res_index</em>, <em>def_angle=3.14159</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetOmegaTorsion" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Omega torsion angle of residue at index <em>res_index</em> or <em>def_angle</em>
if required atom positions (CA-C-N-CA) are not set.
Here, we use CA-C of residue <em>res_index</em> - 1 and N-CA of residue
<em>res_index</em> (consistent with OST’s
<code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code>).</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Default omega angle.</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
+<li><strong>def_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Default omega angle.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> - 1 or <em>res_index</em>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> - 1 or <em>res_index</em>
out of bounds.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetNumAtoms">
-<code class="sig-name descname">GetNumAtoms</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of atom positions stored in this container.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetNumAtoms</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of atom positions stored in this container.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetNumResidues">
-<code class="sig-name descname">GetNumResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetNumResidues" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of residues stored in this container.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetNumResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetNumResidues" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of residues stored in this container.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.GetSequence">
-<code class="sig-name descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetSequence" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Sequence of one letter codes of all residues stored here.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.GetSequence" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Sequence of one letter codes of all residues stored here.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.Copy">
-<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.Copy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Full copy of this object.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.Copy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Full copy of this object.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.Extract">
-<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">from</em>, <em class="sig-param">to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.Extract" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Container with residues with indices in range [<em>from</em>, <em>to</em>-1].</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue index</p></li>
-<li><p><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – One after last residue index</p></li>
+<code class="descname">Extract</code><span class="sig-paren">(</span><em>from</em>, <em>to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.Extract" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Container with residues with indices in range [<em>from</em>, <em>to</em>-1].</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue index</li>
+<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – One after last residue index</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>from</em> >= <em>to</em> or if any residue
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>from</em> >= <em>to</em> or if any residue
index is out of bounds.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">res_indices</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Container with residues with indices in <em>res_indices</em>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – List of residue index</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any residue index is out of
-bounds.</p>
-</dd>
-</dl>
+<code class="descname">Extract</code><span class="sig-paren">(</span><em>res_indices</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Container with residues with indices in <em>res_indices</em>.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – List of residue index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any residue index is out of
+bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.ExtractBackbone">
-<code class="sig-name descname">ExtractBackbone</code><span class="sig-paren">(</span><em class="sig-param">from</em>, <em class="sig-param">to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ExtractBackbone" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Backbone list of residues with indices in range [<em>from</em>, <em>to</em>-1].
+<code class="descname">ExtractBackbone</code><span class="sig-paren">(</span><em>from</em>, <em>to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ExtractBackbone" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Backbone list of residues with indices in range [<em>from</em>, <em>to</em>-1].
CB atoms are reconstructed if unset.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue index</p></li>
-<li><p><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – One after last residue index</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue index</li>
+<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – One after last residue index</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>from</em> >= <em>to</em>, if any residue
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>from</em> >= <em>to</em>, if any residue
index is out of bounds or if any residue has any unset backbone
atom (N, CA, C, O).</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.ToEntity">
-<code class="sig-name descname">ToEntity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ToEntity" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>All residues packed in a single chain as an OST entity.
-Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">ToEntity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.ToEntity" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">All residues packed in a single chain as an OST entity.
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.AllAtomPositions.InsertInto">
-<code class="sig-name descname">InsertInto</code><span class="sig-paren">(</span><em class="sig-param">res_index</em>, <em class="sig-param">chain</em>, <em class="sig-param">res_num</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.InsertInto" title="Permalink to this definition">¶</a></dt>
+<code class="descname">InsertInto</code><span class="sig-paren">(</span><em>res_index</em>, <em>chain</em>, <em>res_num</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AllAtomPositions.InsertInto" title="Permalink to this definition">¶</a></dt>
<dd><p>Insert a single residue (taken from given index) into the <em>chain</em> (with
given res. number). Existing data is replaced and atoms are (re)connected
according to the default connectivity of that amino acid. Peptide links to
neighboring residues are set according to residue numbering. To make this
function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds, if
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_index</em> out of bounds, if
<em>chain</em> is invalid or if not all backbone atoms (N, C, CA) set.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -782,32 +866,38 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
<h2>The AllAtomEnvPositions class<a class="headerlink" href="#the-allatomenvpositions-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.AllAtomEnvPositions">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AllAtomEnvPositions</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AllAtomEnvPositions</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>To link the arbitrary amino acid sequence defined in <a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>
and the SEQRES of <a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>, we provide a helper class containing
structural data as well as a mapping to the internal residue indices of
<a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>.</p>
<dl class="attribute">
<dt id="promod3.loop.AllAtomEnvPositions.all_pos">
-<code class="sig-name descname">all_pos</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions.all_pos" title="Permalink to this definition">¶</a></dt>
+<code class="descname">all_pos</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions.all_pos" title="Permalink to this definition">¶</a></dt>
<dd><p>Container for the positions of all heavy atoms of some residues.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.AllAtomEnvPositions.res_indices">
-<code class="sig-name descname">res_indices</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions.res_indices" title="Permalink to this definition">¶</a></dt>
+<code class="descname">res_indices</code><a class="headerlink" href="#promod3.loop.AllAtomEnvPositions.res_indices" title="Permalink to this definition">¶</a></dt>
<dd><p>Residue indices to be used by <a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for each residue defined
in <em>all_pos</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -817,7 +907,7 @@ in <em>all_pos</em>.</p>
<h2>Distinguishing amino acid atoms<a class="headerlink" href="#distinguishing-amino-acid-atoms" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.AminoAcidAtom">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AminoAcidAtom</code><a class="headerlink" href="#promod3.loop.AminoAcidAtom" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidAtom</code><a class="headerlink" href="#promod3.loop.AminoAcidAtom" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates all heavy atoms of all amino acids. The naming scheme is TLC_AN,
where TLC is the standard three letter code of the amino acid and AN is the
atom name (standard PDB naming) of the heavy atom. Examples: <em>ALA_CB</em>,
@@ -831,7 +921,7 @@ integer in the range [0, <em>XXX_NUM_ATOMS</em>-1].</p>
<dl class="class">
<dt id="promod3.loop.AminoAcidHydrogen">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AminoAcidHydrogen</code><a class="headerlink" href="#promod3.loop.AminoAcidHydrogen" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidHydrogen</code><a class="headerlink" href="#promod3.loop.AminoAcidHydrogen" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates all hydrogens of all amino acids. The naming scheme is TLC_AN,
where TLC is the standard three letter code of the amino acid and AN is the
atom name (standard PDB naming) of the hydrogen. Examples: <em>ALA_H</em>,
@@ -848,310 +938,343 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
<dl class="class">
<dt id="promod3.loop.AminoAcidLookup">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
<dd><p>Collection of static methods to lookup properties of amino acid types
(<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) and
hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>).</p>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetOLC">
-<em class="property">static </em><code class="sig-name descname">GetOLC</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetOLC" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>One letter code for the given amino acid</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetOLC</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetOLC" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">One letter code for the given amino acid</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetAAA">
-<em class="property">static </em><code class="sig-name descname">GetAAA</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAAA" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetAAA</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAAA" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="sig-name descname">GetAAA</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Heavy atom type for the given amino acid and atom.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
-<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumAtoms(aa)-1])</p></li>
-<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
+<em class="property">static </em><code class="descname">GetAAA</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_name</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Heavy atom type for the given amino acid and atom.</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumAtoms(aa)-1])</li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_idx</em> out of bounds or if
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_idx</em> out of bounds or if
<em>atom_name</em> is not one of the heavy atoms of <em>aa</em>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetAAH">
-<em class="property">static </em><code class="sig-name descname">GetAAH</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAAH" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetAAH</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAAH" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="sig-name descname">GetAAH</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Hydrogen type for the given amino acid and atom.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
-<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumHydrogens(aa)-1])</p></li>
-<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
+<em class="property">static </em><code class="descname">GetAAH</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_name</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Hydrogen type for the given amino acid and atom.</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumHydrogens(aa)-1])</li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_idx</em> out of bounds or if
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_idx</em> out of bounds or if
<em>atom_name</em> is not one of the hydrogens of <em>aa</em>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetIndex">
-<em class="property">static </em><code class="sig-name descname">GetIndex</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetIndex" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Atom index (in [0, GetNumAtoms(aa)-1]) for the given amino acid and
+<em class="property">static </em><code class="descname">GetIndex</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetIndex" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Atom index (in [0, GetNumAtoms(aa)-1]) for the given amino acid and
atom.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
-<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_name</em> is not one of the
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_name</em> is not one of the
heavy atoms of <em>aa</em>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetHydrogenIndex">
-<em class="property">static </em><code class="sig-name descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetHydrogenIndex" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Atom index (in [0, GetNumHydrogens(aa)-1]) for the given amino acid
+<em class="property">static </em><code class="descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em>aa</em>, <em>atom_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetHydrogenIndex" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Atom index (in [0, GetNumHydrogens(aa)-1]) for the given amino acid
and atom.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
-<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_name</em> is not one of the
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>atom_name</em> is not one of the
hydrogens of <em>aa</em>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetNumAtoms">
-<em class="property">static </em><code class="sig-name descname">GetNumAtoms</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of heavy atoms of the given amino acid</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetNumAtoms</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of heavy atoms of the given amino acid</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetMaxNumAtoms">
-<em class="property">static </em><code class="sig-name descname">GetMaxNumAtoms</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetMaxNumAtoms" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Max. number of heavy atoms for any amino acid</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetMaxNumAtoms</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetMaxNumAtoms" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Max. number of heavy atoms for any amino acid</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetNumHydrogens">
-<em class="property">static </em><code class="sig-name descname">GetNumHydrogens</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetNumHydrogens" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of hydrogens of the given amino acid</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetNumHydrogens</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetNumHydrogens" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of hydrogens of the given amino acid</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetMaxNumHydrogens">
-<em class="property">static </em><code class="sig-name descname">GetMaxNumHydrogens</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetMaxNumHydrogens" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Max. number of hydrogens for any amino acid</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetMaxNumHydrogens</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetMaxNumHydrogens" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Max. number of hydrogens for any amino acid</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetAA">
-<em class="property">static </em><code class="sig-name descname">GetAA</code><span class="sig-paren">(</span><em class="sig-param">aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAA" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetAA</code><span class="sig-paren">(</span><em>aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAA" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="sig-name descname">GetAA</code><span class="sig-paren">(</span><em class="sig-param">aah</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Amino acid type of the given heavy atom type</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</p></li>
-<li><p><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</p></li>
+<em class="property">static </em><code class="descname">GetAA</code><span class="sig-paren">(</span><em>aah</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Amino acid type of the given heavy atom type</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</li>
+<li><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetAtomName">
-<em class="property">static </em><code class="sig-name descname">GetAtomName</code><span class="sig-paren">(</span><em class="sig-param">aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomName" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetAtomName</code><span class="sig-paren">(</span><em>aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomName" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="sig-name descname">GetAtomName</code><span class="sig-paren">(</span><em class="sig-param">aah</em><span class="sig-paren">)</span></dt>
+<em class="property">static </em><code class="descname">GetAtomName</code><span class="sig-paren">(</span><em>aah</em><span class="sig-paren">)</span></dt>
<dt id="promod3.loop.AminoAcidLookup.GetAtomNameCharmm">
-<em class="property">static </em><code class="sig-name descname">GetAtomNameCharmm</code><span class="sig-paren">(</span><em class="sig-param">aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomNameCharmm" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetAtomNameCharmm</code><span class="sig-paren">(</span><em>aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomNameCharmm" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="sig-name descname">GetAtomNameCharmm</code><span class="sig-paren">(</span><em class="sig-param">aah</em><span class="sig-paren">)</span></dt>
+<em class="property">static </em><code class="descname">GetAtomNameCharmm</code><span class="sig-paren">(</span><em>aah</em><span class="sig-paren">)</span></dt>
<dt id="promod3.loop.AminoAcidLookup.GetAtomNameAmber">
-<em class="property">static </em><code class="sig-name descname">GetAtomNameAmber</code><span class="sig-paren">(</span><em class="sig-param">aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomNameAmber" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetAtomNameAmber</code><span class="sig-paren">(</span><em>aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAtomNameAmber" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="sig-name descname">GetAtomNameAmber</code><span class="sig-paren">(</span><em class="sig-param">aah</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Atom name of the given heavy atom type according to PDB (default),
+<em class="property">static </em><code class="descname">GetAtomNameAmber</code><span class="sig-paren">(</span><em>aah</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Atom name of the given heavy atom type according to PDB (default),
CHARMM or AMBER naming.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</p></li>
-<li><p><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</li>
+<li><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetElement">
-<em class="property">static </em><code class="sig-name descname">GetElement</code><span class="sig-paren">(</span><em class="sig-param">aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetElement" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Chemical element of the given heavy atom type</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetElement</code><span class="sig-paren">(</span><em>aaa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetElement" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Chemical element of the given heavy atom type</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aaa</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetAnchorAtomIndex">
-<em class="property">static </em><code class="sig-name descname">GetAnchorAtomIndex</code><span class="sig-paren">(</span><em class="sig-param">aah</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAnchorAtomIndex" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Atom index (in [0, GetNumAtoms(GetAA(aah))-1]) of the anchor to
-which the given hydrogen is attached.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetAnchorAtomIndex</code><span class="sig-paren">(</span><em>aah</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetAnchorAtomIndex" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Atom index (in [0, GetNumAtoms(GetAA(aah))-1]) of the anchor to
+which the given hydrogen is attached.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aah</strong> (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>) – Hydrogen type</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetHNIndex">
-<em class="property">static </em><code class="sig-name descname">GetHNIndex</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetHNIndex" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Atom index (in [0, GetNumHydrogens(aa)-1]) of H atom attached to N
-when residue is peptide bound.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. PRO)</p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetHNIndex</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetHNIndex" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Atom index (in [0, GetNumHydrogens(aa)-1]) of H atom attached to N
+when residue is peptide bound.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. PRO)</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetH1Index">
-<em class="property">static </em><code class="sig-name descname">GetH1Index</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH1Index" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetH1Index</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH1Index" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.AminoAcidLookup.GetH2Index">
-<em class="property">static </em><code class="sig-name descname">GetH2Index</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH2Index" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetH2Index</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH2Index" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.AminoAcidLookup.GetH3Index">
-<em class="property">static </em><code class="sig-name descname">GetH3Index</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH3Index" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Atom index (in [0, GetNumHydrogens(aa)-1]) of H atom attached to N
-when residue is N terminal.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. H3 for PRO)</p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetH3Index</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.AminoAcidLookup.GetH3Index" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Atom index (in [0, GetNumHydrogens(aa)-1]) of H atom attached to N
+when residue is N terminal.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. H3 for PRO)</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -1161,7 +1284,6 @@ when residue is N terminal.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -1182,12 +1304,12 @@ when residue is N terminal.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -1204,42 +1326,36 @@ when residue is N terminal.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li>Previous: <a href="structure_db.html" title="previous chapter">Structural Data</a></li>
- <li>Next: <a href="mm_system_creation.html" title="next chapter">Generate <code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a></li>
+ <li>Next: <a href="mm_system_creation.html" title="next chapter">Generate <code class="docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
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- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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<a href="../_sources/loop/all_atom.rst.txt"
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index f8d64017e6e5f84a550406d6af13dd62434f3ce4..bc203c9950665a139f17eae99ff48700adbec51c 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Representing Loops — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Representing Loops — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="representing-loops">
@@ -78,7 +77,7 @@ converted from, to, or inserted to a <a class="reference external" href="https:/
<h2>The BackboneList class<a class="headerlink" href="#the-backbonelist-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.BackboneList">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">BackboneList</code><a class="headerlink" href="#promod3.loop.BackboneList" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">BackboneList</code><a class="headerlink" href="#promod3.loop.BackboneList" title="Permalink to this definition">¶</a></dt>
<dd><p>Container for the positions of the backbone atoms (nitrogen (N), alpha carbon
(CA), beta carbon (CB), carbon (C), oxygen (O)), the one letter codes and
amino acid types of a segment. This object allows to get, set or modify the
@@ -91,672 +90,778 @@ of residue <em>i</em> and N-CA of residue <em>i+1</em> (this is shifted by 1 res
compared to OST’s <code class="xref py py-meth docutils literal notranslate"><span class="pre">GetOmegaTorsion()</span></code>).</p>
<dl class="method">
<dt id="promod3.loop.BackboneList.BackboneList">
-<code class="sig-name descname">BackboneList</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.BackboneList" title="Permalink to this definition">¶</a></dt>
+<code class="descname">BackboneList</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.BackboneList" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates empty BackboneList</p>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">BackboneList</code><span class="sig-paren">(</span><em class="sig-param">sequence</em><span class="sig-paren">)</span></dt>
+<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>sequence</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a helical BackboneList from given sequence</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
-code which is not one of the 20 default amino acids.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+code which is not one of the 20 default amino acids.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">BackboneList</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">dihedral_angles</em><span class="sig-paren">)</span></dt>
+<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>sequence</em>, <em>dihedral_angles</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a BackboneList from given <em>sequence</em> and <em>dihedral_angles</em></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</p></li>
-<li><p><strong>dihedral_angles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> objects defining the backbone
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</li>
+<li><strong>dihedral_angles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> objects defining the backbone
dihedral angles of created BackboneList. Every
<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> must either have two or three
elements. Two elements are considered to define the
phi and psi angles, leading to an idealized omega
angle of 180 degrees. In case of three elements, all
-angles are defined.</p></li>
+angles are defined.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
code which is not one of the 20 default amino acids or if
<em>sequence</em> and <em>dihedral_angles</em> are inconsistent in size.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">BackboneList</code><span class="sig-paren">(</span><em class="sig-param">residues</em><span class="sig-paren">)</span></dt>
+<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>residues</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a BackboneList with positions and sequence extracted from
<em>residues</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
which the backbone positions and one letter codes
-are extracted.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if a residue in <em>residues</em>
+are extracted.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if a residue in <em>residues</em>
contains a one letter code which is not one of the 20 default
amino acids or when there is a residue not providing all
-required positions.</p>
-</dd>
-</dl>
+required positions.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">BackboneList</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">residues</em><span class="sig-paren">)</span></dt>
+<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>sequence</em>, <em>residues</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a BackboneList from given <em>sequence</em> and positions extracted from
<em>residues</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</p></li>
-<li><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
-which the backbone positions are extracted.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</li>
+<li><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+which the backbone positions are extracted.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
code which is not one of the 20 default amino acids or if
<em>sequence</em> and <em>residues</em> are inconsistent in size or when there is
a residue not providing all necessary positions.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ToDensity">
-<code class="sig-name descname">ToDensity</code><span class="sig-paren">(</span><em class="sig-param">padding=10.0</em>, <em class="sig-param">sampling=Vec3(1.0</em>, <em class="sig-param">1.0</em>, <em class="sig-param">1.0)</em>, <em class="sig-param">resolution=3.0</em>, <em class="sig-param">high_resolution=false</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ToDensity" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The whole backbone list converted to a density map.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></p>
-</dd>
-</dl>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
-<li><p><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </p></li>
-<li><p><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
-<li><p><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p></li>
+<code class="descname">ToDensity</code><span class="sig-paren">(</span><em>padding=10.0</em>, <em>sampling=Vec3(1.0</em>, <em>1.0</em>, <em>1.0)</em>, <em>resolution=3.0</em>, <em>high_resolution=false</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ToDensity" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to a density map.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></td>
+</tr>
+</tbody>
+</table>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </li>
+<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </li>
+<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </li>
+<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ToEntity">
-<code class="sig-name descname">ToEntity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ToEntity" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The whole backbone list converted to an OST entity.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">ToEntity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ToEntity" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to an OST entity.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.InsertInto">
-<code class="sig-name descname">InsertInto</code><span class="sig-paren">(</span><em class="sig-param">chain</em>, <em class="sig-param">start_resnum</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.InsertInto" title="Permalink to this definition">¶</a></dt>
+<code class="descname">InsertInto</code><span class="sig-paren">(</span><em>chain</em>, <em>start_resnum</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.InsertInto" title="Permalink to this definition">¶</a></dt>
<dd><p>Inserts the backbone list into the <em>chain</em>. If the residues corresponding
to the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> are already present in the entity, they will
be replaced, otherwise they will be added to the entity.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">InsertInto</code><span class="sig-paren">(</span><em class="sig-param">map</em>, <em class="sig-param">resolution=3.0</em>, <em class="sig-param">high_resolution=false</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </p></li>
-<li><p><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
-<li><p><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p></li>
+<code class="descname">InsertInto</code><span class="sig-paren">(</span><em>map</em>, <em>resolution=3.0</em>, <em>high_resolution=false</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
+<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </li>
+<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetBounds">
-<code class="sig-name descname">GetBounds</code><span class="sig-paren">(</span><em class="sig-param">all_atom=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetBounds" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p></p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p>
-</dd>
-</dl>
+<code class="descname">GetBounds</code><span class="sig-paren">(</span><em>all_atom=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetBounds" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetSequence">
-<code class="sig-name descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetSequence" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The amino acid sequence.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetSequence" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The amino acid sequence.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetSequence">
-<code class="sig-name descname">SetSequence</code><span class="sig-paren">(</span><em class="sig-param">sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetSequence" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Set amino acid sequence to this.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
+<code class="descname">SetSequence</code><span class="sig-paren">(</span><em>sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetSequence" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Set amino acid sequence to this.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sequence</em> contains a one letter
code which is not one of the 20 default amino acids or size of
-<em>sequence</em> does not match.</p>
-</dd>
-</dl>
+<em>sequence</em> does not match.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.Extract">
-<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">from</em>, <em class="sig-param">to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Extract" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Items with indices <em>from</em>, …, <em>to</em>-1 of this list.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">Extract</code><span class="sig-paren">(</span><em>from</em>, <em>to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Extract" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Items with indices <em>from</em>, …, <em>to</em>-1 of this list.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ReplaceFragment">
-<code class="sig-name descname">ReplaceFragment</code><span class="sig-paren">(</span><em class="sig-param">sub_fragment</em>, <em class="sig-param">index</em>, <em class="sig-param">superpose_stems</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReplaceFragment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ReplaceFragment</code><span class="sig-paren">(</span><em>sub_fragment</em>, <em>index</em>, <em>superpose_stems</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReplaceFragment" title="Permalink to this definition">¶</a></dt>
<dd><p>Replaces a fragment of the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> starting at position
<em>index</em> by the <em>sub_fragment</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sub_fragment</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The fragment to be inserted</p></li>
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The position at which the fragment
-replacement will begin</p></li>
-<li><p><strong>superpose_stems</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to false, the function will simply
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>sub_fragment</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The fragment to be inserted</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The position at which the fragment
+replacement will begin</li>
+<li><strong>superpose_stems</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to false, the function will simply
replace the according
<code class="xref py py-class docutils literal notranslate"><span class="pre">Backbone</span></code> objects. If set to True,
the n-terminal and c-terminal tails are superposed onto the <em>sub_fragment</em>
stems using the positions at <em>index</em> and
-<em>index</em> + len( <em>sub_fragment</em> )-1.</p></li>
+<em>index</em> + len( <em>sub_fragment</em> )-1.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if
<em>sub_fragment</em> does not fully fit into
actual fragment at specified <em>index</em></p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetN">
-<code class="sig-name descname">GetN</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetN" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetN</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetN" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetCA">
-<code class="sig-name descname">GetCA</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetCA" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetCA</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetCA" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetCB">
-<code class="sig-name descname">GetCB</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetCB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetCB</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetCB" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetC">
-<code class="sig-name descname">GetC</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetC" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetC</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetC" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetO">
-<code class="sig-name descname">GetO</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetO" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
-atom for residue at given index.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
-</dd>
-</dl>
+<code class="descname">GetO</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetO" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
+atom for residue at given index.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetN">
-<code class="sig-name descname">SetN</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetN" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetN</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetN" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetCA">
-<code class="sig-name descname">SetCA</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetCA" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetCA</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetCA" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetCB">
-<code class="sig-name descname">SetCB</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetCB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetCB</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetCB" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetC">
-<code class="sig-name descname">SetC</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetC" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetC</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetC" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetO">
-<code class="sig-name descname">SetO</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetO" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
-/ oxygen atom to this.</p></li>
+<code class="descname">SetO</code><span class="sig-paren">(</span><em>index</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetO" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
+/ oxygen atom to this.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetOLC">
-<code class="sig-name descname">GetOLC</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetOLC" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>One letter code of the residue at given index.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
-</dd>
-</dl>
+<code class="descname">GetOLC</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetOLC" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">One letter code of the residue at given index.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetOLC">
-<code class="sig-name descname">SetOLC</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetOLC" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</p></li>
+<code class="descname">SetOLC</code><span class="sig-paren">(</span><em>index</em>, <em>olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetOLC" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
+<li><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetAA">
-<code class="sig-name descname">GetAA</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetAA" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Amino acid type of the residue at given index.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
-</dd>
-</dl>
+<code class="descname">GetAA</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetAA" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of the residue at given index.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetAA">
-<code class="sig-name descname">SetAA</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAA" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</p></li>
+<code class="descname">SetAA</code><span class="sig-paren">(</span><em>index</em>, <em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAA" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>aa</em> == ost.conop.XXX.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>aa</em> == ost.conop.XXX.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.Set">
-<code class="sig-name descname">Set</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">n_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">cb_pos</em>, <em class="sig-param">c_pos</em>, <em class="sig-param">o_pos</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Set" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Set</code><span class="sig-paren">(</span><em>index</em>, <em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>c_pos</em>, <em>o_pos</em>, <em>olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Set" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">Set</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">n_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">c_pos</em>, <em class="sig-param">o_pos</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span></dt>
+<code class="descname">Set</code><span class="sig-paren">(</span><em>index</em>, <em>n_pos</em>, <em>ca_pos</em>, <em>c_pos</em>, <em>o_pos</em>, <em>olc</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="sig-name descname">Set</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">res</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span></dt>
+<code class="descname">Set</code><span class="sig-paren">(</span><em>index</em>, <em>res</em>, <em>olc</em><span class="sig-paren">)</span></dt>
<dd><p>Set all backbone informations. This will reconstruct CB positions if needed
and set the amino acid type according to the given one letter code.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
-<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
-<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
-<li><p><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
+<li><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.__len__">
-<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of residues in this backbone list.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of residues in this backbone list.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.resize">
-<code class="sig-name descname">resize</code><span class="sig-paren">(</span><em class="sig-param">new_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.resize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>new_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Resize backbone list to contain this number of residues.
+<code class="descname">resize</code><span class="sig-paren">(</span><em>new_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.resize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>new_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Resize backbone list to contain this number of residues.
If new residues are added, their properties will not be
initialized. Existing residues are untouched unless the
-list is shrinked (in that case extra residues are deleted).</p>
-</dd>
-</dl>
+list is shrinked (in that case extra residues are deleted).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.empty">
-<code class="sig-name descname">empty</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.empty" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True if the list is empty (i.e. size 0).</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">empty</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.empty" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True if the list is empty (i.e. size 0).</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.append">
-<code class="sig-name descname">append</code><span class="sig-paren">(</span><em class="sig-param">n_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">cb_pos</em>, <em class="sig-param">c_pos</em>, <em class="sig-param">o_pos</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.append" title="Permalink to this definition">¶</a></dt>
+<code class="descname">append</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>c_pos</em>, <em>o_pos</em>, <em>olc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.append" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">append</code><span class="sig-paren">(</span><em class="sig-param">n_pos</em>, <em class="sig-param">ca_pos</em>, <em class="sig-param">c_pos</em>, <em class="sig-param">o_pos</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span></dt>
+<code class="descname">append</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>c_pos</em>, <em>o_pos</em>, <em>olc</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="sig-name descname">append</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">olc</em><span class="sig-paren">)</span></dt>
+<code class="descname">append</code><span class="sig-paren">(</span><em>res</em>, <em>olc</em><span class="sig-paren">)</span></dt>
<dd><p>Appends a new residue at the end of the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>. This will
reconstruct CB positions if needed and set the amino acid type according
to the given one letter code.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
-<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
-<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
-<li><p><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
+<li><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.clear">
-<code class="sig-name descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.clear" title="Permalink to this definition">¶</a></dt>
+<code class="descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.clear" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove all residues from this list.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.Copy">
-<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Copy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.Copy" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates and returns a deep copy of this <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>. This can be
useful, since Python uses reference assignments.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ReconstructCBetaPositions">
-<code class="sig-name descname">ReconstructCBetaPositions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructCBetaPositions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ReconstructCBetaPositions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructCBetaPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Does a simple reconstruction of all CB positions based on the current
N, CA and C positions.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ReconstructOxygenPositions">
-<code class="sig-name descname">ReconstructOxygenPositions</code><span class="sig-paren">(</span><em class="sig-param">last_psi=-0.78540</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructOxygenPositions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ReconstructOxygenPositions</code><span class="sig-paren">(</span><em>last_psi=-0.78540</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructOxygenPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Does a simple reconstruction of all oxygen positions based on the actual
N, CA and C positions. The position of the last oxygen depends on the next
residue, an additional parameter is therefore required.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>last_psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi angle of the last BackboneList residue,
-the default value corresponds to a typical alpha-helix.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>last_psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi angle of the last BackboneList residue,
+the default value corresponds to a typical alpha-helix.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ReconstructCStemOxygen">
-<code class="sig-name descname">ReconstructCStemOxygen</code><span class="sig-paren">(</span><em class="sig-param">after_c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructCStemOxygen" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ReconstructCStemOxygen</code><span class="sig-paren">(</span><em>after_c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ReconstructCStemOxygen" title="Permalink to this definition">¶</a></dt>
<dd><p>Reconstructs the last oxygen of this backbone list. The oxygen position
depends on the residue following the C stem. The position is only
reconstructed if the residue handle is valid.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
-element of this backbone list)</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
+element of this backbone list)</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.ApplyTransform">
-<code class="sig-name descname">ApplyTransform</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">transform</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ApplyTransform" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplyTransform</code><span class="sig-paren">(</span><em>index</em>, <em>transform</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ApplyTransform" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies a transformation to the positions of a single residue.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">ApplyTransform</code><span class="sig-paren">(</span><em class="sig-param">from</em>, <em class="sig-param">to</em>, <em class="sig-param">transform</em><span class="sig-paren">)</span></dt>
+<code class="descname">ApplyTransform</code><span class="sig-paren">(</span><em>from</em>, <em>to</em>, <em>transform</em><span class="sig-paren">)</span></dt>
<dd><p>Applies a transformation to the positions of the residues with indices
<em>from</em>, …, <em>to</em>-1 of this list.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start index.</p></li>
-<li><p><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – End index (one past last residue to transform).</p></li>
-<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start index.</li>
+<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – End index (one past last residue to transform).</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">ApplyTransform</code><span class="sig-paren">(</span><em class="sig-param">transform</em><span class="sig-paren">)</span></dt>
+<code class="descname">ApplyTransform</code><span class="sig-paren">(</span><em>transform</em><span class="sig-paren">)</span></dt>
<dd><p>Applies a transformation to all positions of this list.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>transform</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetTransform">
-<code class="sig-name descname">GetTransform</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetTransform" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetTransform</code><span class="sig-paren">(</span><em>index</em>, <em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetTransform" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetTransform</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">other</em>, <em class="sig-param">other_index</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Minimum RMSD transformation of residue <em>index</em> onto <em>res</em> or
+<code class="descname">GetTransform</code><span class="sig-paren">(</span><em>index</em>, <em>other</em>, <em>other_index</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Minimum RMSD transformation of residue <em>index</em> onto <em>res</em> or
residue <em>other_index</em> of <em>other</em> backbone list considering the
positions of the N, CA and C atoms.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</p></li>
-<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p></li>
-<li><p><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
+<li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</li>
+<li><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">GetTransform</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Get minimum RMSD transformation of CA positions of this backbone
-list onto CA positions of <em>other</em> backbone list.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p>
-</dd>
-</dl>
+<code class="descname">GetTransform</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Get minimum RMSD transformation of CA positions of this backbone
+list onto CA positions of <em>other</em> backbone list.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SuperposeOnto">
-<code class="sig-name descname">SuperposeOnto</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SuperposeOnto" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SuperposeOnto</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SuperposeOnto" title="Permalink to this definition">¶</a></dt>
<dd><p>Superposes this backbone list onto another one using CA positions.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.RotateAroundPhiTorsion">
-<code class="sig-name descname">RotateAroundPhiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPhiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="descname">RotateAroundPhiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPhiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.RotateAroundPsiTorsion">
-<code class="sig-name descname">RotateAroundPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">psi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="descname">RotateAroundPsiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>psi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPsiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.RotateAroundOmegaTorsion">
-<code class="sig-name descname">RotateAroundOmegaTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">omega</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundOmegaTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="descname">RotateAroundOmegaTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>omega</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundOmegaTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.RotateAroundPhiPsiTorsion">
-<code class="sig-name descname">RotateAroundPhiPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPhiPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="descname">RotateAroundPhiPsiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>psi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPhiPsiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetAroundPhiTorsion">
-<code class="sig-name descname">SetAroundPhiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPhiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetAroundPhiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPhiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetAroundPsiTorsion">
-<code class="sig-name descname">SetAroundPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">psi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetAroundPsiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>psi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPsiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetAroundOmegaTorsion">
-<code class="sig-name descname">SetAroundOmegaTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">omega</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundOmegaTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetAroundOmegaTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>omega</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundOmegaTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.SetAroundPhiPsiTorsion">
-<code class="sig-name descname">SetAroundPhiPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em>, <em class="sig-param">sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPhiPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetAroundPhiPsiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>psi</em>, <em>sequential=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetAroundPhiPsiTorsion" title="Permalink to this definition">¶</a></dt>
<dd><p>Rotates/sets the phi/psi/omega torsion angle of the backbone at position
<em>index</em> in the backbone list by/to the given angle(s).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle by which to rotate phi torsion.</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle by which to rotate psi torsion.</p></li>
-<li><p><strong>omega</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle by which to rotate omega torsion.</p></li>
-<li><p><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle by which to rotate phi torsion.</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle by which to rotate psi torsion.</li>
+<li><strong>omega</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle by which to rotate omega torsion.</li>
+<li><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all
residues after the one with <em>index</em>. Otherwise, it will
be propagated in the direction where it will affect the
-least number of residues.</p></li>
+least number of residues.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.GetPhiTorsion">
-<code class="sig-name descname">GetPhiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetPhiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetPhiTorsion</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetPhiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetPsiTorsion">
-<code class="sig-name descname">GetPsiTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetPsiTorsion</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetPsiTorsion" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.GetOmegaTorsion">
-<code class="sig-name descname">GetOmegaTorsion</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetOmegaTorsion" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The phi/psi/omega torsion angle for residue at given index.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
-</dd>
-</dl>
+<code class="descname">GetOmegaTorsion</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.GetOmegaTorsion" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The phi/psi/omega torsion angle for residue at given index.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.TransOmegaTorsions">
-<code class="sig-name descname">TransOmegaTorsions</code><span class="sig-paren">(</span><em class="sig-param">thresh=20/180*pi</em>, <em class="sig-param">allow_prepro_cis=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.TransOmegaTorsions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">TransOmegaTorsions</code><span class="sig-paren">(</span><em>thresh=20/180*pi</em>, <em>allow_prepro_cis=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.TransOmegaTorsions" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks whether this backbone list only contains trans omega torsion angles.
Usually, you would want this to be the case, but it can fail if you have any
unfavorable omega torsion angle in your backbone.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Allowed deviation from ideal trans angle (pi)</p></li>
-<li><p><strong>allow_prepro_cis</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether cis-omega torsions should be
-allowed in case of a subsequent proline.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Allowed deviation from ideal trans angle (pi)</li>
+<li><strong>allow_prepro_cis</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether cis-omega torsions should be
+allowed in case of a subsequent proline.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>whether <em>bb_list</em> only contains trans-omega torsions.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if size of this backbone list is
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">whether <em>bb_list</em> only contains trans-omega torsions.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if size of this backbone list is
smaller than 3.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.SetBackrub">
-<code class="sig-name descname">SetBackrub</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">primary_rot_angle</em>, <em class="sig-param">flanking_rot_angle_one</em>, <em class="sig-param">flanking_rot_angle_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetBackrub" title="Permalink to this definition">¶</a></dt>
-<dd><p>Applies a backrub motion <a class="reference internal" href="../references.html#davis2006" id="id1"><span>[davis2006]</span></a> at residue defined by <strong>index</strong>.
+<code class="descname">SetBackrub</code><span class="sig-paren">(</span><em>index</em>, <em>primary_rot_angle</em>, <em>flanking_rot_angle_one</em>, <em>flanking_rot_angle_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetBackrub" title="Permalink to this definition">¶</a></dt>
+<dd><p>Applies a backrub motion <a class="reference internal" href="../references.html#davis2006" id="id1">[davis2006]</a> at residue defined by <strong>index</strong>.
The first rotation axis is defined by the CA positions from residues at
<strong>index</strong> -1 and <strong>index</strong> +1. All atoms in between get rotated around this
axis by <strong>primary_rot_angle</strong>. To restore the the hydrogen bond network
@@ -767,83 +872,96 @@ position with an angle of <strong>flanking_rot_angle_one</strong>. The second ro
around the axis from the transformed central CA position to the CA position
from residue at position <strong>index</strong> +1 with an angle of
<strong>flanking_rot_angle_two</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Position of central residue of the backrub motion</p></li>
-<li><p><strong>primary_rot_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the first rotation in radians</p></li>
-<li><p><strong>flanking_rot_angle_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the first compensatory rotation
-in radians</p></li>
-<li><p><strong>flanking_rot_angle_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the second compensatory rotation
-in radians</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Position of central residue of the backrub motion</li>
+<li><strong>primary_rot_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the first rotation in radians</li>
+<li><strong>flanking_rot_angle_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the first compensatory rotation
+in radians</li>
+<li><strong>flanking_rot_angle_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the second compensatory rotation
+in radians</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is smaller 1 or
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is smaller 1 or
larger size of BackboneList - 2</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">SetBackrub</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">primary_rot_angle</em><span class="optional">[</span>, <em class="sig-param">scaling=1.0</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="descname">SetBackrub</code><span class="sig-paren">(</span><em>index</em>, <em>primary_rot_angle</em><span class="optional">[</span>, <em>scaling=1.0</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>Applies the backrub motion described above but calculates the ideal angles
for the compensatory rotations in a way, that the new oxygen positions are
as close as possible to the original ones. The ideal angles can be scaled
down by <strong>scaling</strong> to make them less extreme.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Position of central residue of the backrub motion</p></li>
-<li><p><strong>primary_rot_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the first rotation in radians</p></li>
-<li><p><strong>scaling</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The ideal angles for the compensatory rotations will
-be scaled by this value.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Position of central residue of the backrub motion</li>
+<li><strong>primary_rot_angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle of the first rotation in radians</li>
+<li><strong>scaling</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The ideal angles for the compensatory rotations will
+be scaled by this value.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is smaller 1 or
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is smaller 1 or
larger size of BackboneList - 2</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.MinCADistance">
-<code class="sig-name descname">MinCADistance</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.MinCADistance" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Minimal pairwise CA-distance between this and the <em>other</em>
-backbone list.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p>
-</dd>
-</dl>
+<code class="descname">MinCADistance</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.MinCADistance" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Minimal pairwise CA-distance between this and the <em>other</em>
+backbone list.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.BackboneList.RMSD">
-<code class="sig-name descname">RMSD</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RMSD" title="Permalink to this definition">¶</a></dt>
+<code class="descname">RMSD</code><span class="sig-paren">(</span><em>other</em>, <em>superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RMSD" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.BackboneList.CARMSD">
-<code class="sig-name descname">CARMSD</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.CARMSD" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>RMSD / C-alpha RMSD between this and the <em>other</em> backbone list.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p></li>
-<li><p><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to superpose before calculating the RMSD.</p></li>
+<code class="descname">CARMSD</code><span class="sig-paren">(</span><em>other</em>, <em>superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.CARMSD" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">RMSD / C-alpha RMSD between this and the <em>other</em> backbone list.</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</li>
+<li><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to superpose before calculating the RMSD.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -853,7 +971,6 @@ backbone list.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -874,12 +991,12 @@ backbone list.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -896,8 +1013,8 @@ backbone list.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
<li>Next: <a href="torsion_sampler.html" title="next chapter">Sampling Dihedral Angles</a></li>
</ul></li>
</ul></li>
@@ -905,33 +1022,27 @@ backbone list.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/backbone.rst.txt"
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 0ec568e810b7056234b8ed36fa586907e744b477..5ea7d7d40d1528fe32dde6b8137749297f3b63e4 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>loop - Loop Handling — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>loop - Loop Handling — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="module-promod3.loop">
@@ -106,7 +105,7 @@ loops. The following example should give you an idea of what can be done:</p>
<li class="toctree-l2"><a class="reference internal" href="all_atom.html#distinguishing-amino-acid-atoms">Distinguishing amino acid atoms</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="mm_system_creation.html">Generate <code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="mm_system_creation.html">Generate <code class="docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a><ul>
<li class="toctree-l2"><a class="reference internal" href="mm_system_creation.html#create-mm-systems-for-loops">Create MM systems for loops</a></li>
<li class="toctree-l2"><a class="reference internal" href="mm_system_creation.html#forcefield-lookup-for-amino-acids">Forcefield lookup for amino acids</a></li>
</ul>
@@ -118,7 +117,6 @@ loops. The following example should give you an idea of what can be done:</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -139,12 +137,12 @@ loops. The following example should give you an idea of what can be done:</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -168,33 +166,27 @@ loops. The following example should give you an idea of what can be done:</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/index.rst.txt"
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index 8564b0a91585176ba7ed6416e434cb0fca56c2d5..3d5bd43d253ffba41578c413e00a7ba26a6c8b0e 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Loading Precomputed Objects — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Loading Precomputed Objects — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="loading-precomputed-objects">
@@ -39,117 +38,124 @@
ProMod3 offers to load precomputed instances for direct usage.</p>
<dl class="method">
<dt id="promod3.loop.LoadTorsionSampler">
-<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadTorsionSampler</code><span class="sig-paren">(</span><em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSampler" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSampler</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by <a class="reference internal" href="../references.html#solis2006" id="id1"><span>[solis2006]</span></a> that has been trained on
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id1">[solis2006]</a> that has been trained on
non-redundant protein structures.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The torsion sampler</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The torsion sampler</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.LoadTorsionSamplerCoil">
-<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadTorsionSamplerCoil</code><span class="sig-paren">(</span><em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerCoil" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerCoil</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerCoil" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by <a class="reference internal" href="../references.html#solis2006" id="id2"><span>[solis2006]</span></a> that has been trained on coil
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id2">[solis2006]</a> that has been trained on coil
residues of non-redundant protein structures.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The torsion sampler</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The torsion sampler</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.LoadTorsionSamplerHelical">
-<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadTorsionSamplerHelical</code><span class="sig-paren">(</span><em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerHelical" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerHelical</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerHelical" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by <a class="reference internal" href="../references.html#solis2006" id="id3"><span>[solis2006]</span></a> that has been trained on helical
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id3">[solis2006]</a> that has been trained on helical
residues of non-redundant protein structures.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The torsion sampler</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The torsion sampler</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.LoadTorsionSamplerExtended">
-<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadTorsionSamplerExtended</code><span class="sig-paren">(</span><em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerExtended" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.loop.</code><code class="descname">LoadTorsionSamplerExtended</code><span class="sig-paren">(</span><em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadTorsionSamplerExtended" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a torsion sampler with an amino acid grouping
-as defined by <a class="reference internal" href="../references.html#solis2006" id="id4"><span>[solis2006]</span></a> that has been trained on extended
+as defined by <a class="reference internal" href="../references.html#solis2006" id="id4">[solis2006]</a> that has been trained on extended
residues of non-redundant protein structures.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The torsion sampler</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The torsion sampler</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.LoadStructureDB">
-<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadStructureDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadStructureDB" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.loop.</code><code class="descname">LoadStructureDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadStructureDB" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a structure db containing roughly 21000 chains form the
PDB with seqid redundancy cutoff of 60%</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The structure db</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The structure db</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.LoadFragDB">
-<code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">LoadFragDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadFragDB" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.loop.</code><code class="descname">LoadFragDB</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoadFragDB" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads and returns a FragDB containing fragments up to the length of 14,
therefore capable of bridging gaps up to the length of 12. The returned
databases contains the location of fragments in the <a class="reference internal" href="structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>
returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" title="promod3.loop.LoadStructureDB"><code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadStructureDB()</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The Fragment database</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Fragment database</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -170,12 +176,12 @@ returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" t
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -192,42 +198,36 @@ returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" t
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
- <li>Previous: <a href="mm_system_creation.html" title="previous chapter">Generate <code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a></li>
- <li>Next: <a href="../core/index.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li>Previous: <a href="mm_system_creation.html" title="previous chapter">Generate <code class="docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a></li>
+ <li>Next: <a href="../core/index.html" title="next chapter"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
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- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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<a href="../_sources/loop/load_loop_objects.rst.txt"
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index e3fd0c60adc0127c59ee9e992a79bb02fceb47ea..5110342b60f1cb3c51960fa24cbda974c559bf5c 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Generate ost.mol.mm systems — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Generate ost.mol.mm systems — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="generate-ost-mol-mm-systems">
@@ -80,8 +79,8 @@ specialized forcefield lookup for amino acids (<a class="reference internal" hre
</pre></div>
</div>
<div class="admonition note">
-<p class="admonition-title">Note</p>
-<p>To simplify use when sidechains may be missing and the region of interest for
+<p class="first admonition-title">Note</p>
+<p class="last">To simplify use when sidechains may be missing and the region of interest for
the MM system has to be determined, it might be better to use the simpler
<a class="reference internal" href="../modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.SidechainReconstructor</span></code></a> and
<a class="reference internal" href="../modelling/loop_closing.html#promod3.modelling.AllAtomRelaxer" title="promod3.modelling.AllAtomRelaxer"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.AllAtomRelaxer</span></code></a> classes. Even if all the sidechains
@@ -92,59 +91,67 @@ sidechains without reconstructing them is minimal.</p>
<h2>Create MM systems for loops<a class="headerlink" href="#create-mm-systems-for-loops" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.MmSystemCreator">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">MmSystemCreator</code><span class="sig-paren">(</span><em class="sig-param">ff_lookup</em>, <em class="sig-param">fix_surrounding_hydrogens=True</em>, <em class="sig-param">kill_electrostatics=False</em>, <em class="sig-param">nonbonded_cutoff=8</em>, <em class="sig-param">inaccurate_pot_energy=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">MmSystemCreator</code><span class="sig-paren">(</span><em>ff_lookup</em>, <em>fix_surrounding_hydrogens=True</em>, <em>kill_electrostatics=False</em>, <em>nonbonded_cutoff=8</em>, <em>inaccurate_pot_energy=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup a system creator for a specific forcefield. The constructor only stores
the settings. Most setup work is done by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>.</p>
<p>The idea is to have a set of movable loop residues and a set of fixed
surrounding residues which interact with the loop.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_lookup</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>) – Forcefield to use with this system creator.</p></li>
-<li><p><strong>fix_surrounding_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If False, the hydrogens of the surrounding
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_lookup</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>) – Forcefield to use with this system creator.</li>
+<li><strong>fix_surrounding_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If False, the hydrogens of the surrounding
residues can move to improve H-bond building
(True by default as it only has a minor
impact on the result and a big one on
-performance).</p></li>
-<li><p><strong>kill_electrostatics</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, all charges are removed from the system.
+performance).</li>
+<li><strong>kill_electrostatics</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, all charges are removed from the system.
This is good for H-bond building, but may be bad
-if residues in the surrounding are missing (gaps).</p></li>
-<li><p><strong>nonbonded_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Defines cutoff to set for non bonded interactions.
+if residues in the surrounding are missing (gaps).</li>
+<li><strong>nonbonded_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Defines cutoff to set for non bonded interactions.
Recommended values: 5 if kill_electrostatics = True,
-8 otherwise. Negative value means no cutoff.</p></li>
-<li><p><strong>inaccurate_pot_energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, we do not set correct non-bonded
+8 otherwise. Negative value means no cutoff.</li>
+<li><strong>inaccurate_pot_energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, we do not set correct non-bonded
interactions between fixed atoms. This leads
to inaccurate pot. energies but it is faster and
has no effect on simulation runs (e.g. ApplySD)
-otherwise.</p></li>
+otherwise.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetDisulfidBridges">
-<code class="sig-name descname">GetDisulfidBridges</code><span class="sig-paren">(</span><em class="sig-param">all_pos</em>, <em class="sig-param">res_indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetDisulfidBridges" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Pairs of indices (i,j), where res_indices[i] and res_indices[j] are
+<code class="descname">GetDisulfidBridges</code><span class="sig-paren">(</span><em>all_pos</em>, <em>res_indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetDisulfidBridges" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Pairs of indices (i,j), where res_indices[i] and res_indices[j] are
assumed to have a disulfid bridge (CYS-SG pairs within 2.5 A).</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</p></li>
-<li><p><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</li>
+<li><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.SetupSystem">
-<code class="sig-name descname">SetupSystem</code><span class="sig-paren">(</span><em class="sig-param">all_pos</em>, <em class="sig-param">res_indices</em>, <em class="sig-param">loop_length</em>, <em class="sig-param">is_n_ter</em>, <em class="sig-param">is_c_ter</em>, <em class="sig-param">disulfid_bridges</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.SetupSystem" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetupSystem</code><span class="sig-paren">(</span><em>all_pos</em>, <em>res_indices</em>, <em>loop_length</em>, <em>is_n_ter</em>, <em>is_c_ter</em>, <em>disulfid_bridges</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.SetupSystem" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">SetupSystem</code><span class="sig-paren">(</span><em class="sig-param">all_pos</em>, <em class="sig-param">res_indices</em>, <em class="sig-param">loop_start_indices</em>, <em class="sig-param">loop_lengths</em>, <em class="sig-param">is_n_ter</em>, <em class="sig-param">is_c_ter</em>, <em class="sig-param">disulfid_bridges</em><span class="sig-paren">)</span></dt>
+<code class="descname">SetupSystem</code><span class="sig-paren">(</span><em>all_pos</em>, <em>res_indices</em>, <em>loop_start_indices</em>, <em>loop_lengths</em>, <em>is_n_ter</em>, <em>is_c_ter</em>, <em>disulfid_bridges</em><span class="sig-paren">)</span></dt>
<dd><p>Setup a new system for the loop / surrounding defined by <em>all_pos</em> and
<em>res_indices</em>. Positions are taken from <em>all_pos[res_indices[i]]</em> and each
of them must have all heavy atoms defined. Residue <em>all_pos[i]</em> is assumed
@@ -167,59 +174,67 @@ loop length is defined.</p>
<p>If possible, this uses the “CPU” platform in OpenMM using the env. variable
<code class="docutils literal notranslate"><span class="pre">PM3_OPENMM_CPU_THREADS</span></code> to define the number of desired threads (1 thread
is used if variable is undefined).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</p></li>
-<li><p><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</p></li>
-<li><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of single loop (incl. stems).</p></li>
-<li><p><strong>loop_start_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start indices of loops.</p></li>
-<li><p><strong>loop_lengths</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Lengths of loops (incl. stems).</p></li>
-<li><p><strong>is_n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – For each <em>res_indices[i]</em>, <em>is_n_ter[i]</em> defines whether
-that residue is N-terminal.</p></li>
-<li><p><strong>is_c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – For each <em>res_indices[i]</em>, <em>is_c_ter[i]</em> defines whether
-that residue is C-terminal.</p></li>
-<li><p><strong>disulfid_bridges</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with two
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</li>
+<li><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</li>
+<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of single loop (incl. stems).</li>
+<li><strong>loop_start_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start indices of loops.</li>
+<li><strong>loop_lengths</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Lengths of loops (incl. stems).</li>
+<li><strong>is_n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – For each <em>res_indices[i]</em>, <em>is_n_ter[i]</em> defines whether
+that residue is N-terminal.</li>
+<li><strong>is_c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – For each <em>res_indices[i]</em>, <em>is_c_ter[i]</em> defines whether
+that residue is C-terminal.</li>
+<li><strong>disulfid_bridges</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with two
<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Pairs of indices (i,j), where res_indices[i] and
res_indices[j] form a disulfid bridge (see
-<a class="reference internal" href="#promod3.loop.MmSystemCreator.GetDisulfidBridges" title="promod3.loop.MmSystemCreator.GetDisulfidBridges"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetDisulfidBridges()</span></code></a>)</p></li>
+<a class="reference internal" href="#promod3.loop.MmSystemCreator.GetDisulfidBridges" title="promod3.loop.MmSystemCreator.GetDisulfidBridges"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetDisulfidBridges()</span></code></a>)</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if loops out of bounds with respect
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if loops out of bounds with respect
to <em>res_indices</em>, <em>loop_start_indices</em> / <em>loop_lengths</em> or
<em>res_indices</em> / <em>is_n_ter</em> / <em>is_c_ter</em> have inconsistent lengths,
or if any <em>all_pos[res_indices[i]]</em> is invalid or has unset heavy
atoms.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.UpdatePositions">
-<code class="sig-name descname">UpdatePositions</code><span class="sig-paren">(</span><em class="sig-param">all_pos</em>, <em class="sig-param">res_indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.UpdatePositions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">UpdatePositions</code><span class="sig-paren">(</span><em>all_pos</em>, <em>res_indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.UpdatePositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Updates the positions in the system. Even though <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> is
already very fast, this can speed up resetting a simulation. The data must
be consistent with the data used in the last <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> call.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</p></li>
-<li><p><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>all_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Provides positions for each <em>res_indices[i]</em>.</li>
+<li><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>all_pos</em>.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if data is inconsistent with last
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if data is inconsistent with last
<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> call (same number of residues, same AA).</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.ExtractLoopPositions">
-<code class="sig-name descname">ExtractLoopPositions</code><span class="sig-paren">(</span><em class="sig-param">loop_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.ExtractLoopPositions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ExtractLoopPositions</code><span class="sig-paren">(</span><em>loop_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.ExtractLoopPositions" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">ExtractLoopPositions</code><span class="sig-paren">(</span><em class="sig-param">out_pos</em>, <em class="sig-param">res_indices</em><span class="sig-paren">)</span></dt>
+<code class="descname">ExtractLoopPositions</code><span class="sig-paren">(</span><em>out_pos</em>, <em>res_indices</em><span class="sig-paren">)</span></dt>
<dd><p>Extracts loop positions from the current simulation. If the simulation was
run (via <a class="reference internal" href="#promod3.loop.MmSystemCreator.GetSimulation" title="promod3.loop.MmSystemCreator.GetSimulation"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetSimulation()</span></code></a>), we internally have new positions for the
residues corresponding to <em>all_pos[res_indices[i]]</em> passed in
@@ -235,146 +250,169 @@ matching amino acid types with respect to the loop residues passed as
acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]</em> of
<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>. Only loop residues with <em>i</em> in the ranges defined by
<a class="reference internal" href="#promod3.loop.MmSystemCreator.GetLoopStartIndices" title="promod3.loop.MmSystemCreator.GetLoopStartIndices"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLoopStartIndices()</span></code></a> / <a class="reference internal" href="#promod3.loop.MmSystemCreator.GetLoopLengths" title="promod3.loop.MmSystemCreator.GetLoopLengths"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLoopLengths()</span></code></a> are touched.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>loop_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Reduced storage only covering loop positions.</p></li>
-<li><p><strong>out_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Storage for loop positions linked to <em>res_indices</em>.</p></li>
-<li><p><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>out_pos</em>.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>loop_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Reduced storage only covering loop positions.</li>
+<li><strong>out_pos</strong> (<a class="reference internal" href="all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Storage for loop positions linked to <em>res_indices</em>.</li>
+<li><strong>res_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue indices into <em>out_pos</em>.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if data is inconsistent with last
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if data is inconsistent with last
<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> call (big enough and matching AA).</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetSimulation">
-<code class="sig-name descname">GetSimulation</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetSimulation" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Simulation object setup by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>. Use this to run
-MM simulations.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetSimulation</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetSimulation" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Simulation object setup by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>. Use this to run
+MM simulations.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetNumResidues">
-<code class="sig-name descname">GetNumResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetNumResidues" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of residues of current simulation setup.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetNumResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetNumResidues" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of residues of current simulation setup.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetNumLoopResidues">
-<code class="sig-name descname">GetNumLoopResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetNumLoopResidues" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of loop residues (incl. stems) of current simulation setup.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetNumLoopResidues</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetNumLoopResidues" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of loop residues (incl. stems) of current simulation setup.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetLoopStartIndices">
-<code class="sig-name descname">GetLoopStartIndices</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetLoopStartIndices" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Start indices of loops (see <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>).</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetLoopStartIndices</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetLoopStartIndices" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Start indices of loops (see <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>).</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetLoopLengths">
-<code class="sig-name descname">GetLoopLengths</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetLoopLengths" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Lengths of loops (see <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>).</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetLoopLengths</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetLoopLengths" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Lengths of loops (see <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a>).</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetForcefieldAminoAcids">
-<code class="sig-name descname">GetForcefieldAminoAcids</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetForcefieldAminoAcids" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Forcefield-specific amino acid type for each residue of last
-<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> call.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetForcefieldAminoAcids</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetForcefieldAminoAcids" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Forcefield-specific amino acid type for each residue of last
+<a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetupSystem()</span></code></a> call.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetIndexing">
-<code class="sig-name descname">GetIndexing</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetIndexing" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetIndexing</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetIndexing" title="Permalink to this definition">¶</a></dt>
<dd><p>The atoms of residue <em>i</em> are stored from <em>idx[i]</em> to <em>idx[i+1]-1</em>, where
<em>idx</em> is the list returned by this function. The atoms themselves are
ordered according to the indexing defined by <a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Indexing to positions vector used by the simulation object.
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Indexing to positions vector used by the simulation object.
The last item of the list contains the number of atoms in the
-system.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+system.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.GetCpuPlatformSupport">
-<code class="sig-name descname">GetCpuPlatformSupport</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetCpuPlatformSupport" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if we will use OpenMM’s “CPU” platform (enabled by default
-if platform is available). False, if we use “Reference” platform.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetCpuPlatformSupport</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.GetCpuPlatformSupport" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if we will use OpenMM’s “CPU” platform (enabled by default
+if platform is available). False, if we use “Reference” platform.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.MmSystemCreator.SetCpuPlatformSupport">
-<code class="sig-name descname">SetCpuPlatformSupport</code><span class="sig-paren">(</span><em class="sig-param">cpu_platform_support</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.SetCpuPlatformSupport" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetCpuPlatformSupport</code><span class="sig-paren">(</span><em>cpu_platform_support</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.MmSystemCreator.SetCpuPlatformSupport" title="Permalink to this definition">¶</a></dt>
<dd><p>Override “CPU” platform support setting. Useful to force the use of the
OpenMM’s “Reference” platform for testing (by default we use “CPU” if it is
available).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>cpu_platform_support</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if “CPU” platform desired (ignored if
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cpu_platform_support</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if “CPU” platform desired (ignored if
platform not available). False, if “Reference”
-platform desired.</p>
-</dd>
-</dl>
+platform desired.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -387,421 +425,477 @@ FF specific data for amino acids in a protein. We distinguish amino acid types
(and a few variants thereof) which may all be N- and/or C-terminal.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldLookup">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
<ul class="simple">
-<li><p>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
+<li>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
<em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
-residue is terminal)</p></li>
-<li><p>extract masses, charges and LJ-parameters for each atom (list of length <em>N</em>)</p></li>
-<li><p>extract connectivities (<a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a>), which include all
-possible bonds, angles, dihedrals, impropers and LJ pairs</p></li>
+residue is terminal)</li>
+<li>extract masses, charges and LJ-parameters for each atom (list of length <em>N</em>)</li>
+<li>extract connectivities (<a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a>), which include all
+possible bonds, angles, dihedrals, impropers and LJ pairs</li>
</ul>
<p>There is functionality to adapt the lookup and store it as needed or you can
load a predefined one with <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetDefault" title="promod3.loop.ForcefieldLookup.GetDefault"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetDefault()</span></code></a> or <a class="reference internal" href="#promod3.loop.ForcefieldLookup.LoadCHARMM" title="promod3.loop.ForcefieldLookup.LoadCHARMM"><code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadCHARMM()</span></code></a>.</p>
<p>The atom indexing and <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetAA" title="promod3.loop.ForcefieldLookup.GetAA"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetAA()</span></code></a> are independent of the loaded file.</p>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.ForcefieldLookup.GetDefault">
-<em class="property">static </em><code class="sig-name descname">GetDefault</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetDefault" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>A default singleton instance (shared throughout the Python process)
+<em class="property">static </em><code class="descname">GetDefault</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetDefault" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A default singleton instance (shared throughout the Python process)
of this class with all data defined. Using this instance has the
-advantage that the object is only loaded once!</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a></p>
-</dd>
-</dl>
+advantage that the object is only loaded once!</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.ForcefieldLookup.SetDefault">
-<em class="property">static </em><code class="sig-name descname">SetDefault</code><span class="sig-paren">(</span><em class="sig-param">new_default</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetDefault" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">SetDefault</code><span class="sig-paren">(</span><em>new_default</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetDefault" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets default singleton instance for all future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetDefault" title="promod3.loop.ForcefieldLookup.GetDefault"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetDefault()</span></code></a> calls.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>new_default</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>) – Lookup object to use as the new default.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>new_default</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>) – Lookup object to use as the new default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.ForcefieldLookup.LoadCHARMM">
-<em class="property">static </em><code class="sig-name descname">LoadCHARMM</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.LoadCHARMM" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Predefined lookup object extracted from a CHARMM forcefield
-(loaded from disk)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a></p>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="method">
+<em class="property">static </em><code class="descname">LoadCHARMM</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.LoadCHARMM" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Predefined lookup object extracted from a CHARMM forcefield
+(loaded from disk)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
<dt id="promod3.loop.ForcefieldLookup.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.ForcefieldLookup.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.ForcefieldLookup.Save" title="promod3.loop.ForcefieldLookup.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.loop.ForcefieldLookup.SavePortable" title="promod3.loop.ForcefieldLookup.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded lookup object</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded lookup object</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.ForcefieldLookup.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetAA">
-<code class="sig-name descname">GetAA</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetAA" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Amino acid type for given <em>ff_aa</em></p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p>
-</dd>
-</dl>
+<code class="descname">GetAA</code><span class="sig-paren">(</span><em>ff_aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetAA" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type for given <em>ff_aa</em></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetNumAtoms">
-<code class="sig-name descname">GetNumAtoms</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of atoms for given input.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
-<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
-<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
+<code class="descname">GetNumAtoms</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Number of atoms for given input.</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
+<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
+<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetHeavyIndex">
-<code class="sig-name descname">GetHeavyIndex</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetHeavyIndex" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetHeavyIndex</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetHeavyIndex" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetHeavyIndex</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Internal index for given heavy atom in [0, <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>]</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
-<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index as returned by <a class="reference internal" href="all_atom.html#promod3.loop.AminoAcidLookup.GetIndex" title="promod3.loop.AminoAcidLookup.GetIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AminoAcidLookup.GetIndex()</span></code></a></p></li>
-<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
+<code class="descname">GetHeavyIndex</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>atom_name</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Internal index for given heavy atom in [0, <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>]</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
+<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index as returned by <a class="reference internal" href="all_atom.html#promod3.loop.AminoAcidLookup.GetIndex" title="promod3.loop.AminoAcidLookup.GetIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AminoAcidLookup.GetIndex()</span></code></a></li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetHydrogenIndex">
-<code class="sig-name descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetHydrogenIndex" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>atom_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetHydrogenIndex" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">atom_name</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Internal index for given hydrogen atom in [0, <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>]</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
-<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index as returned by
-<a class="reference internal" href="all_atom.html#promod3.loop.AminoAcidLookup.GetHydrogenIndex" title="promod3.loop.AminoAcidLookup.GetHydrogenIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AminoAcidLookup.GetHydrogenIndex()</span></code></a></p></li>
-<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
+<code class="descname">GetHydrogenIndex</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>atom_name</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Internal index for given hydrogen atom in [0, <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>]</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
+<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index as returned by
+<a class="reference internal" href="all_atom.html#promod3.loop.AminoAcidLookup.GetHydrogenIndex" title="promod3.loop.AminoAcidLookup.GetHydrogenIndex"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AminoAcidLookup.GetHydrogenIndex()</span></code></a></li>
+<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetOXTIndex">
-<code class="sig-name descname">GetOXTIndex</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetOXTIndex" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Internal index of OXT atom for C-terminal residue</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
-<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
+<code class="descname">GetOXTIndex</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetOXTIndex" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Internal index of OXT atom for C-terminal residue</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
+<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetFudgeLJ">
-<code class="sig-name descname">GetFudgeLJ</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetFudgeLJ" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Dampening factor for LJ 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetFudgeLJ</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetFudgeLJ" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for LJ 1,4 interactions (see
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetFudgeQQ">
-<code class="sig-name descname">GetFudgeQQ</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetFudgeQQ" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Dampening factor for electrostatic 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetFudgeQQ</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetFudgeQQ" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for electrostatic 1,4 interactions (see
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetMasses">
-<code class="sig-name descname">GetMasses</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetMasses" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
-<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
-<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
+<code class="descname">GetMasses</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetMasses" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
+<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
+<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetCharges">
-<code class="sig-name descname">GetCharges</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetCharges" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
-<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
-<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
+<code class="descname">GetCharges</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetCharges" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
+<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
+<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetSigmas">
-<code class="sig-name descname">GetSigmas</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetSigmas" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Sigma in nm for each atom
+<code class="descname">GetSigmas</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetSigmas" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Sigma in nm for each atom
(see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
-<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
-<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
+<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
+<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetEpsilons">
-<code class="sig-name descname">GetEpsilons</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetEpsilons" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Epsilon in kJ/mol for each atom
+<code class="descname">GetEpsilons</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetEpsilons" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Epsilon in kJ/mol for each atom
(see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
-<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
-<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
+<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
+<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetInternalConnectivity">
-<code class="sig-name descname">GetInternalConnectivity</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Internal connectivity of a residue</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p></li>
-<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</p></li>
-<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</p></li>
+<code class="descname">GetInternalConnectivity</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Internal connectivity of a residue</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</li>
+<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if N-terminal variant desired</li>
+<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if C-terminal variant desired</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity">
-<code class="sig-name descname">GetPeptideBoundConnectivity</code><span class="sig-paren">(</span><em class="sig-param">ff_aa_one</em>, <em class="sig-param">ff_aa_two</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>All connectivity which include peptide bond between two residues
+<code class="descname">GetPeptideBoundConnectivity</code><span class="sig-paren">(</span><em>ff_aa_one</em>, <em>ff_aa_two</em>, <em>is_nter</em>, <em>is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">All connectivity which include peptide bond between two residues
(additional to <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="promod3.loop.ForcefieldLookup.GetInternalConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetInternalConnectivity()</span></code></a>)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ff_aa_one</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type of first residue</p></li>
-<li><p><strong>ff_aa_two</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type of second residue</p></li>
-<li><p><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if first residue is N-terminal</p></li>
-<li><p><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if second residue is C-terminal</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ff_aa_one</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type of first residue</li>
+<li><strong>ff_aa_two</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type of second residue</li>
+<li><strong>is_nter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if first residue is N-terminal</li>
+<li><strong>is_cter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True if second residue is C-terminal</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.GetDisulfidConnectivity">
-<code class="sig-name descname">GetDisulfidConnectivity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetDisulfidConnectivity" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>All connectivity which include disulfid bridge between two cysteins
-(additional to <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="promod3.loop.ForcefieldLookup.GetInternalConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetInternalConnectivity()</span></code></a>)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetDisulfidConnectivity</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetDisulfidConnectivity" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">All connectivity which include disulfid bridge between two cysteins
+(additional to <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="promod3.loop.ForcefieldLookup.GetInternalConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetInternalConnectivity()</span></code></a>)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.ForcefieldConnectivity" title="promod3.loop.ForcefieldConnectivity"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldConnectivity</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetFudgeLJ">
-<code class="sig-name descname">SetFudgeLJ</code><span class="sig-paren">(</span><em class="sig-param">fudge</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetFudgeLJ" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetFudgeLJ</code><span class="sig-paren">(</span><em>fudge</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetFudgeLJ" title="Permalink to this definition">¶</a></dt>
<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetFudgeLJ" title="promod3.loop.ForcefieldLookup.GetFudgeLJ"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetFudgeLJ()</span></code></a> calls to <em>fudge</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetFudgeQQ">
-<code class="sig-name descname">SetFudgeQQ</code><span class="sig-paren">(</span><em class="sig-param">fudge</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetFudgeQQ" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetFudgeQQ</code><span class="sig-paren">(</span><em>fudge</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetFudgeQQ" title="Permalink to this definition">¶</a></dt>
<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetFudgeQQ" title="promod3.loop.ForcefieldLookup.GetFudgeQQ"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetFudgeQQ()</span></code></a> calls to <em>fudge</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetMasses">
-<code class="sig-name descname">SetMasses</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">masses</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetMasses" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetMasses</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em>, <em>masses</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetMasses" title="Permalink to this definition">¶</a></dt>
<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetMasses" title="promod3.loop.ForcefieldLookup.GetMasses"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetMasses()</span></code></a> calls to <em>masses</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetCharges">
-<code class="sig-name descname">SetCharges</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">charges</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetCharges" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetCharges</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em>, <em>charges</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetCharges" title="Permalink to this definition">¶</a></dt>
<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetCharges" title="promod3.loop.ForcefieldLookup.GetCharges"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetCharges()</span></code></a> calls to <em>charges</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetSigmas">
-<code class="sig-name descname">SetSigmas</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">sigmas</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetSigmas" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetSigmas</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em>, <em>sigmas</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetSigmas" title="Permalink to this definition">¶</a></dt>
<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetSigmas" title="promod3.loop.ForcefieldLookup.GetSigmas"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetSigmas()</span></code></a> calls to <em>sigmas</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetEpsilons">
-<code class="sig-name descname">SetEpsilons</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">epsilons</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetEpsilons" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetEpsilons</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em>, <em>epsilons</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetEpsilons" title="Permalink to this definition">¶</a></dt>
<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetEpsilons" title="promod3.loop.ForcefieldLookup.GetEpsilons"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetEpsilons()</span></code></a> calls to <em>epsilons</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetInternalConnectivity">
-<code class="sig-name descname">SetInternalConnectivity</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetInternalConnectivity" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetInternalConnectivity</code><span class="sig-paren">(</span><em>ff_aa</em>, <em>is_nter</em>, <em>is_cter</em>, <em>connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetInternalConnectivity" title="Permalink to this definition">¶</a></dt>
<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetInternalConnectivity" title="promod3.loop.ForcefieldLookup.GetInternalConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetInternalConnectivity()</span></code></a> calls to
<em>connectivity</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity">
-<code class="sig-name descname">SetPeptideBoundConnectivity</code><span class="sig-paren">(</span><em class="sig-param">ff_aa_one</em>, <em class="sig-param">ff_aa_two</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em>, <em class="sig-param">connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetPeptideBoundConnectivity</code><span class="sig-paren">(</span><em>ff_aa_one</em>, <em>ff_aa_two</em>, <em>is_nter</em>, <em>is_cter</em>, <em>connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity" title="Permalink to this definition">¶</a></dt>
<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity" title="promod3.loop.ForcefieldLookup.GetPeptideBoundConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetPeptideBoundConnectivity()</span></code></a> calls to
<em>connectivity</em>.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.ForcefieldLookup.SetDisulfidConnectivity">
-<code class="sig-name descname">SetDisulfidConnectivity</code><span class="sig-paren">(</span><em class="sig-param">connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetDisulfidConnectivity" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetDisulfidConnectivity</code><span class="sig-paren">(</span><em>connectivity</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SetDisulfidConnectivity" title="Permalink to this definition">¶</a></dt>
<dd><p>Set value for future <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetDisulfidConnectivity" title="promod3.loop.ForcefieldLookup.GetDisulfidConnectivity"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetDisulfidConnectivity()</span></code></a> calls to
<em>connectivity</em>.</p>
</dd></dl>
@@ -810,23 +904,22 @@ for details.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldAminoAcid">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the amino acid types for forcefields. The first 20 values
correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
there are values for disulfid bridges (<em>FF_CYS2</em>), d-protonated histidine
(<em>FF_HISD</em>, default for <em>ost.conop.HIS</em> is <em>FF_HISE</em>) and <em>FF_XXX</em> for unknown
types. The full list of values is:</p>
<blockquote>
-<div><p><em>FF_ALA</em>, <em>FF_ARG</em>, <em>FF_ASN</em>, <em>FF_ASP</em>, <em>FF_GLN</em>, <em>FF_GLU</em>, <em>FF_LYS</em>,
+<div><em>FF_ALA</em>, <em>FF_ARG</em>, <em>FF_ASN</em>, <em>FF_ASP</em>, <em>FF_GLN</em>, <em>FF_GLU</em>, <em>FF_LYS</em>,
<em>FF_SER</em>, <em>FF_CYS</em>, <em>FF_MET</em>, <em>FF_TRP</em>, <em>FF_TYR</em>, <em>FF_THR</em>, <em>FF_VAL</em>,
<em>FF_ILE</em>, <em>FF_LEU</em>, <em>FF_GLY</em>, <em>FF_PRO</em> <em>FF_HISE</em>, <em>FF_PHE</em>, <em>FF_CYS2</em>,
-<em>FF_HISD</em>, <em>FF_XXX</em></p>
-</div></blockquote>
+<em>FF_HISD</em>, <em>FF_XXX</em></div></blockquote>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldConnectivity">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldConnectivity</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldConnectivity</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity" title="Permalink to this definition">¶</a></dt>
<dd><p>Contains lists of bonds, angles, dihedrals, impropers and LJ pairs (exclusions
are the combination of all bonds and 1,3 pairs of angles and are not stored
separately). Each type of connectivity has it’s own class (see below) storing
@@ -839,481 +932,601 @@ of the two residues. For disulfid bridges, <em>N1</em> = <em>N2</em> = <em>GetNu
False, False)</em>.</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.harmonic_bonds">
-<code class="sig-name descname">harmonic_bonds</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_bonds" title="Permalink to this definition">¶</a></dt>
+<code class="descname">harmonic_bonds</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_bonds" title="Permalink to this definition">¶</a></dt>
<dd><p>List of harmonic bonds.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldBondInfo" title="promod3.loop.ForcefieldBondInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldBondInfo</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldBondInfo" title="promod3.loop.ForcefieldBondInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldBondInfo</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.harmonic_angles">
-<code class="sig-name descname">harmonic_angles</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_angles" title="Permalink to this definition">¶</a></dt>
+<code class="descname">harmonic_angles</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_angles" title="Permalink to this definition">¶</a></dt>
<dd><p>List of harmonic angles.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="promod3.loop.ForcefieldHarmonicAngleInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldHarmonicAngleInfo</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="promod3.loop.ForcefieldHarmonicAngleInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldHarmonicAngleInfo</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.urey_bradley_angles">
-<code class="sig-name descname">urey_bradley_angles</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.urey_bradley_angles" title="Permalink to this definition">¶</a></dt>
+<code class="descname">urey_bradley_angles</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.urey_bradley_angles" title="Permalink to this definition">¶</a></dt>
<dd><p>List of Urey-Bradley angles.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="promod3.loop.ForcefieldUreyBradleyAngleInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldUreyBradleyAngleInfo</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="promod3.loop.ForcefieldUreyBradleyAngleInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldUreyBradleyAngleInfo</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.periodic_dihedrals">
-<code class="sig-name descname">periodic_dihedrals</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.periodic_dihedrals" title="Permalink to this definition">¶</a></dt>
+<code class="descname">periodic_dihedrals</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.periodic_dihedrals" title="Permalink to this definition">¶</a></dt>
<dd><p>List of periodic dihedrals.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="promod3.loop.ForcefieldPeriodicDihedralInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldPeriodicDihedralInfo</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="promod3.loop.ForcefieldPeriodicDihedralInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldPeriodicDihedralInfo</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.periodic_impropers">
-<code class="sig-name descname">periodic_impropers</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.periodic_impropers" title="Permalink to this definition">¶</a></dt>
+<code class="descname">periodic_impropers</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.periodic_impropers" title="Permalink to this definition">¶</a></dt>
<dd><p>List of periodic impropers.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="promod3.loop.ForcefieldPeriodicDihedralInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldPeriodicDihedralInfo</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="promod3.loop.ForcefieldPeriodicDihedralInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldPeriodicDihedralInfo</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.harmonic_impropers">
-<code class="sig-name descname">harmonic_impropers</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_impropers" title="Permalink to this definition">¶</a></dt>
+<code class="descname">harmonic_impropers</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.harmonic_impropers" title="Permalink to this definition">¶</a></dt>
<dd><p>List of harmonic impropers.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="promod3.loop.ForcefieldHarmonicImproperInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldHarmonicImproperInfo</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="promod3.loop.ForcefieldHarmonicImproperInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldHarmonicImproperInfo</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldConnectivity.lj_pairs">
-<code class="sig-name descname">lj_pairs</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.lj_pairs" title="Permalink to this definition">¶</a></dt>
+<code class="descname">lj_pairs</code><a class="headerlink" href="#promod3.loop.ForcefieldConnectivity.lj_pairs" title="Permalink to this definition">¶</a></dt>
<dd><p>List of LJ pairs.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldLJPairInfo" title="promod3.loop.ForcefieldLJPairInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLJPairInfo</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.loop.ForcefieldLJPairInfo" title="promod3.loop.ForcefieldLJPairInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLJPairInfo</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldBondInfo">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.index_one">
-<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.index_two">
-<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.bond_length">
-<code class="sig-name descname">bond_length</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.bond_length" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bond_length</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.bond_length" title="Permalink to this definition">¶</a></dt>
<dd><p>Bond length in nm</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.force_constant">
-<code class="sig-name descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Force constant in kJ/mol/nm^2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one">
-<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_two">
-<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_three">
-<code class="sig-name descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_three" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_three" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 3</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.angle">
-<code class="sig-name descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.angle" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.angle" title="Permalink to this definition">¶</a></dt>
<dd><p>Angle in radians</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.force_constant">
-<code class="sig-name descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Force constant in kJ/mol/radian^2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define Urey-Bradley angle
(see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">
-<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_two">
-<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_three">
-<code class="sig-name descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_three" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_three" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 3</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.angle">
-<code class="sig-name descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle" title="Permalink to this definition">¶</a></dt>
<dd><p>Angle in radians</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.angle_force_constant">
-<code class="sig-name descname">angle_force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle_force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angle_force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.angle_force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Angle force constant kJ/mol/radian^2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_length">
-<code class="sig-name descname">bond_length</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_length" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bond_length</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_length" title="Permalink to this definition">¶</a></dt>
<dd><p>Bond length in nm</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_force_constant">
-<code class="sig-name descname">bond_force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="descname">bond_force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.bond_force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Bond force constant kJ/mol/nm^2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define periodic dihedral or improper (see
<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">
-<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_two">
-<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_three">
-<code class="sig-name descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_three" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_three" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 3</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_four">
-<code class="sig-name descname">index_four</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_four" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_four</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_four" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 4</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.multiplicity">
-<code class="sig-name descname">multiplicity</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.multiplicity" title="Permalink to this definition">¶</a></dt>
+<code class="descname">multiplicity</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.multiplicity" title="Permalink to this definition">¶</a></dt>
<dd><p>Multiplicity</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.phase">
-<code class="sig-name descname">phase</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.phase" title="Permalink to this definition">¶</a></dt>
+<code class="descname">phase</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.phase" title="Permalink to this definition">¶</a></dt>
<dd><p>Phase in radians</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.force_constant">
-<code class="sig-name descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Force constant in kJ/mol/radian^2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one">
-<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_two">
-<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_three">
-<code class="sig-name descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_three" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_three</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_three" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 3</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_four">
-<code class="sig-name descname">index_four</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_four" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_four</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_four" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 4</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.angle">
-<code class="sig-name descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.angle" title="Permalink to this definition">¶</a></dt>
+<code class="descname">angle</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.angle" title="Permalink to this definition">¶</a></dt>
<dd><p>Angle in radians</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.force_constant">
-<code class="sig-name descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.force_constant" title="Permalink to this definition">¶</a></dt>
+<code class="descname">force_constant</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.force_constant" title="Permalink to this definition">¶</a></dt>
<dd><p>Force constant kJ/mol/radian^2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.ForcefieldLJPairInfo">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.index_one">
-<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 1</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.index_two">
-<code class="sig-name descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_two" title="Permalink to this definition">¶</a></dt>
+<code class="descname">index_two</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_two" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of particle 2</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.sigma">
-<code class="sig-name descname">sigma</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.sigma" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sigma</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.sigma" title="Permalink to this definition">¶</a></dt>
<dd><p>Sigma in nm</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.epsilon">
-<code class="sig-name descname">epsilon</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.epsilon" title="Permalink to this definition">¶</a></dt>
+<code class="descname">epsilon</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.epsilon" title="Permalink to this definition">¶</a></dt>
<dd><p>Epsilon in kJ/mol</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -1323,7 +1536,6 @@ False, False)</em>.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -1344,12 +1556,12 @@ False, False)</em>.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -1366,7 +1578,7 @@ False, False)</em>.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li>Previous: <a href="all_atom.html" title="previous chapter">Handling All Atom Positions</a></li>
<li>Next: <a href="load_loop_objects.html" title="next chapter">Loading Precomputed Objects</a></li>
</ul></li>
@@ -1375,33 +1587,27 @@ False, False)</em>.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
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-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/mm_system_creation.rst.txt"
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 0c036f7842f4c5ee804f04fd9136a81a083f15a6..2ce5f6faeef242db1fc6f37ff534d74c46380d12 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Structural Data — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Structural Data — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="structural-data">
@@ -45,11 +44,11 @@ optionally be stored. E.g. sequence profiles or secondary structure information.
Optional data includes:</p>
<blockquote>
<div><ul class="simple">
-<li><p>The phi/psi dihedral angles</p></li>
-<li><p>The secondary structure state as defined by dssp</p></li>
-<li><p>The solvent accessibility in square Angstrom</p></li>
-<li><p>The amino acid frequencies as given by an input sequence profile</p></li>
-<li><p>The residue depth - The residue depth is defined as the minimum distance of
+<li>The phi/psi dihedral angles</li>
+<li>The secondary structure state as defined by dssp</li>
+<li>The solvent accessibility in square Angstrom</li>
+<li>The amino acid frequencies as given by an input sequence profile</li>
+<li>The residue depth - The residue depth is defined as the minimum distance of
a residue towards any of the exposed residues.
Distances are calculated using CB positions (artificially constructed in case
of glycine) and exposed is defined as:
@@ -58,42 +57,42 @@ to the OUTER surface. To determine whether an atom is part of that outer
surface, the full structure is placed into a 3D grid and a flood fill
algorithm is used to determine the atoms of interest.
Internal cavities are excluded by using this approach. This is a simplified
-version of the residue depth as discussed in <a class="reference internal" href="../references.html#chakravarty1999" id="id1"><span>[chakravarty1999]</span></a> and gets
-directly calculated when structural information is added to the StructureDB.</p></li>
-<li><p>The amino acid frequency derived from structural alignments as described
-in <a class="reference internal" href="../references.html#zhou2005" id="id2"><span>[zhou2005]</span></a> - Since the calculation of such a profile already requires a
+version of the residue depth as discussed in <a class="reference internal" href="../references.html#chakravarty1999" id="id1">[chakravarty1999]</a> and gets
+directly calculated when structural information is added to the StructureDB.</li>
+<li>The amino acid frequency derived from structural alignments as described
+in <a class="reference internal" href="../references.html#zhou2005" id="id2">[zhou2005]</a> - Since the calculation of such a profile already requires a
StructureDB, we end up in a hen and egg problem here… When adding
structural information to the StructureDB, the according memory gets
just allocated and set to zero. The usage of this information
is therefore only meaningful if you calculate these profiles
-and manually set them (or load the provided default database).</p></li>
+and manually set them (or load the provided default database).</li>
</ul>
</div></blockquote>
<div class="section" id="defining-chains-and-fragments">
<h2>Defining Chains and Fragments<a class="headerlink" href="#defining-chains-and-fragments" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.CoordInfo">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">CoordInfo</code><a class="headerlink" href="#promod3.loop.CoordInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">CoordInfo</code><a class="headerlink" href="#promod3.loop.CoordInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>The CoordInfo gets automatically generated when new chains are added to
a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>. It contains internal information of how a
connected stretch of residues is stored in the database.</p>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.id">
-<code class="sig-name descname">id</code><a class="headerlink" href="#promod3.loop.CoordInfo.id" title="Permalink to this definition">¶</a></dt>
+<code class="descname">id</code><a class="headerlink" href="#promod3.loop.CoordInfo.id" title="Permalink to this definition">¶</a></dt>
<dd><p>An id string specified when adding the corresponding stretch to the
structure db</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.chain_name">
-<code class="sig-name descname">chain_name</code><a class="headerlink" href="#promod3.loop.CoordInfo.chain_name" title="Permalink to this definition">¶</a></dt>
+<code class="descname">chain_name</code><a class="headerlink" href="#promod3.loop.CoordInfo.chain_name" title="Permalink to this definition">¶</a></dt>
<dd><p>A chain name string specified when adding the corresponding stretch to the
structure db</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.offset">
-<code class="sig-name descname">offset</code><a class="headerlink" href="#promod3.loop.CoordInfo.offset" title="Permalink to this definition">¶</a></dt>
+<code class="descname">offset</code><a class="headerlink" href="#promod3.loop.CoordInfo.offset" title="Permalink to this definition">¶</a></dt>
<dd><p>All residues of the added stretch are stored in a linear memory layout.
The offset parameter tells us where it exactly starts in the global data
structure. (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
@@ -101,13 +100,13 @@ structure. (<a class="reference external" href="https://docs.python.org/3.7/libr
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.size">
-<code class="sig-name descname">size</code><a class="headerlink" href="#promod3.loop.CoordInfo.size" title="Permalink to this definition">¶</a></dt>
+<code class="descname">size</code><a class="headerlink" href="#promod3.loop.CoordInfo.size" title="Permalink to this definition">¶</a></dt>
<dd><p>The number of residues in that stretch (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.start_resnum">
-<code class="sig-name descname">start_resnum</code><a class="headerlink" href="#promod3.loop.CoordInfo.start_resnum" title="Permalink to this definition">¶</a></dt>
+<code class="descname">start_resnum</code><a class="headerlink" href="#promod3.loop.CoordInfo.start_resnum" title="Permalink to this definition">¶</a></dt>
<dd><p>Residue number of first residue in the added stretch. The residue number
is relative to the SEQRES provided in the input profile when adding the
stuff to the structure db. (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
@@ -115,7 +114,7 @@ stuff to the structure db. (<a class="reference external" href="https://docs.pyt
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.shift">
-<code class="sig-name descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
+<code class="descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
<dd><p>Translation from original coordinates that has been applied before storing
structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
</dd></dl>
@@ -124,34 +123,38 @@ structural information in db. (<a class="reference external" href="https://www.o
<dl class="class">
<dt id="promod3.loop.FragmentInfo">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">FragmentInfo</code><span class="sig-paren">(</span><em class="sig-param">chain_index</em>, <em class="sig-param">offset</em>, <em class="sig-param">length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragmentInfo" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FragmentInfo</code><span class="sig-paren">(</span><em>chain_index</em>, <em>offset</em>, <em>length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragmentInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>The FragmentInfo defines any fragment in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>. If you
implement your own accessor object, thats the information you want to store.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>chain_index</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.chain_index" title="promod3.loop.FragmentInfo.chain_index"><code class="xref py py-attr docutils literal notranslate"><span class="pre">chain_index</span></code></a></p></li>
-<li><p><strong>offset</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.offset" title="promod3.loop.FragmentInfo.offset"><code class="xref py py-attr docutils literal notranslate"><span class="pre">offset</span></code></a></p></li>
-<li><p><strong>length</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.length" title="promod3.loop.FragmentInfo.length"><code class="xref py py-attr docutils literal notranslate"><span class="pre">length</span></code></a></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>chain_index</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.chain_index" title="promod3.loop.FragmentInfo.chain_index"><code class="xref py py-attr docutils literal notranslate"><span class="pre">chain_index</span></code></a></li>
+<li><strong>offset</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.offset" title="promod3.loop.FragmentInfo.offset"><code class="xref py py-attr docutils literal notranslate"><span class="pre">offset</span></code></a></li>
+<li><strong>length</strong> – Fills <a class="reference internal" href="#promod3.loop.FragmentInfo.length" title="promod3.loop.FragmentInfo.length"><code class="xref py py-attr docutils literal notranslate"><span class="pre">length</span></code></a></li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.chain_index">
-<code class="sig-name descname">chain_index</code><a class="headerlink" href="#promod3.loop.FragmentInfo.chain_index" title="Permalink to this definition">¶</a></dt>
+<code class="descname">chain_index</code><a class="headerlink" href="#promod3.loop.FragmentInfo.chain_index" title="Permalink to this definition">¶</a></dt>
<dd><p>The index of the chain (defined by <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoordInfo</span></code></a>) in the
<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> this particle belongs to. (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.offset">
-<code class="sig-name descname">offset</code><a class="headerlink" href="#promod3.loop.FragmentInfo.offset" title="Permalink to this definition">¶</a></dt>
+<code class="descname">offset</code><a class="headerlink" href="#promod3.loop.FragmentInfo.offset" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of residue in <strong>chain</strong> the fragment starts. (0-based, <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.length">
-<code class="sig-name descname">length</code><a class="headerlink" href="#promod3.loop.FragmentInfo.length" title="Permalink to this definition">¶</a></dt>
+<code class="descname">length</code><a class="headerlink" href="#promod3.loop.FragmentInfo.length" title="Permalink to this definition">¶</a></dt>
<dd><p>Length of the fragment (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
@@ -253,14 +256,14 @@ and fill it with content.</p>
the size of the database used as source. If you want to do this for a larger
database, you might want to consider two things:</p>
<ol class="arabic simple">
-<li><p>Use a database of limited size to generate the actual profiles (something
-in between 5000 and 10000 nonredundant chains is enough)</p></li>
-<li><p>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
-running in parallel</p></li>
+<li>Use a database of limited size to generate the actual profiles (something
+in between 5000 and 10000 nonredundant chains is enough)</li>
+<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+running in parallel</li>
</ol>
<dl class="class">
<dt id="promod3.loop.StructureDBDataType">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">StructureDBDataType</code><a class="headerlink" href="#promod3.loop.StructureDBDataType" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">StructureDBDataType</code><a class="headerlink" href="#promod3.loop.StructureDBDataType" title="Permalink to this definition">¶</a></dt>
<dd><p>The StructureDBDataType enum has to be passed at initialization of a
StructureDB in order to define what data you want to store additionally
to backbone coordinates and sequence.
@@ -277,80 +280,86 @@ AAFrequencies, AAFrequenciesStruct</p>
<dl class="class">
<dt id="promod3.loop.StructureDB">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">StructureDB</code><span class="sig-paren">(</span><em class="sig-param">data_to_store</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">StructureDB</code><span class="sig-paren">(</span><em>data_to_store</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates an empty <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> that can be filled with content
through <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-func docutils literal notranslate"><span class="pre">AddCoordinates()</span></code></a>. The information extracted there is defined by
<em>data_to_store</em>. Have a look at the <a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDBDataType</span></code></a>
documentation and at the example script…</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>data_to_store</strong> (<a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDBDataType</span></code></a>) – Specifies what data to store in the database, several
-flags can be combined with a bitwise or operator.</p>
-</dd>
-</dl>
-<dl class="method">
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data_to_store</strong> (<a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDBDataType</span></code></a>) – Specifies what data to store in the database, several
+flags can be combined with a bitwise or operator.</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.loop.StructureDB.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.StructureDB.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.StructureDB.Save" title="promod3.loop.StructureDB.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.loop.StructureDB.SavePortable" title="promod3.loop.StructureDB.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load the database.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded data base</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load the database.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded data base</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.StructureDB.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where the database will be saved</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where the database will be saved</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.HasData">
-<code class="sig-name descname">HasData</code><span class="sig-paren">(</span><em class="sig-param">data_type</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.HasData" title="Permalink to this definition">¶</a></dt>
+<code class="descname">HasData</code><span class="sig-paren">(</span><em>data_type</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.HasData" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks, whether requested data type is available in the current database.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>data_type</strong> (<a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDBDataType</span></code></a>) – Data type to check</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Whether the requested datatype is available</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data_type</strong> (<a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDBDataType</span></code></a>) – Data type to check</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether the requested datatype is available</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.AddCoordinates">
-<code class="sig-name descname">AddCoordinates</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">chain_name</em>, <em class="sig-param">ent</em>, <em class="sig-param">seqres</em>, <em class="sig-param">prof=None</em>, <em class="sig-param">only_longest_stretch=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.AddCoordinates" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddCoordinates</code><span class="sig-paren">(</span><em>id</em>, <em>chain_name</em>, <em>ent</em>, <em>seqres</em>, <em>prof=None</em>, <em>only_longest_stretch=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.AddCoordinates" title="Permalink to this definition">¶</a></dt>
<dd><p>This method takes an entity and adds coordinates and the sequence
of one of its chains to the structural database. Additionally, all
data as specified at the initialization of the database is extracted
@@ -377,428 +386,481 @@ be sufficient for most structures, but stretches exceeding this maximum
are discarded. For storing the structural data given these restraints,
a translation is applied that gets stored as the <em>shift</em> attribute
in the according <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoordInfo</span></code></a> object.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – identifier of the added structure (e.g. pdb id)</p></li>
-<li><p><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of the chain in <em>ent</em> you want to add</p></li>
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a> /
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – identifier of the added structure (e.g. pdb id)</li>
+<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of the chain in <em>ent</em> you want to add</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a> /
<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
-as specified by <em>chain_name</em>.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
-<em>chain_name</em>. The profile sequence must match <em>seqres</em>.</p></li>
-<li><p><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
+as specified by <em>chain_name</em>.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
+<em>chain_name</em>. The profile sequence must match <em>seqres</em>.</li>
+<li><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
connected stretch of residues are all connected
-stretches of residues</p></li>
+stretches of residues</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>indices of added stretches in db</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <cite>int</cite></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the residues in chain with
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">indices of added stretches in db</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <cite>int</cite></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the residues in chain with
name <em>chain_name</em> do not match <em>seqres</em> given the
residue numbers, when AAFrequencies have to to be extracted and
the sequence in <em>prof</em> does not match the <em>seqres</em> or <em>prof</em> is
invalid.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.RemoveCoordinates">
-<code class="sig-name descname">RemoveCoordinates</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.RemoveCoordinates" title="Permalink to this definition">¶</a></dt>
+<code class="descname">RemoveCoordinates</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.RemoveCoordinates" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes coordinates at specified location and all its associated data. This
has an impact on the offset values of all <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoordInfo</span></code></a> objects
that are internally stored afterwards and on the actual coord indices
(all shifted by one). So make sure that you adapt your data access
accordingly!</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Specifies coordinates to be removed</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>coord_idx</em> is invalid</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Specifies coordinates to be removed</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>coord_idx</em> is invalid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetCoordIdx">
-<code class="sig-name descname">GetCoordIdx</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">chain_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetCoordIdx" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> indices (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])
+<code class="descname">GetCoordIdx</code><span class="sig-paren">(</span><em>id</em>, <em>chain_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetCoordIdx" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> indices (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])
of all coords (connected stretches) with matching
<em>id</em> / <em>chain_name</em>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>id</strong> – Identifier given when calling <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddCoordinates()</span></code></a></p></li>
-<li><p><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of chain given when calling <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddCoordinates()</span></code></a></p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>id</strong> – Identifier given when calling <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddCoordinates()</span></code></a></li>
+<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of chain given when calling <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddCoordinates()</span></code></a></li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetCoordInfo">
-<code class="sig-name descname">GetCoordInfo</code><span class="sig-paren">(</span><em class="sig-param">idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetCoordInfo" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Object describing the stretch of connected residues with
-index <em>idx</em>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoordInfo</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> index (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</p>
-</dd>
-</dl>
+<code class="descname">GetCoordInfo</code><span class="sig-paren">(</span><em>idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetCoordInfo" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Object describing the stretch of connected residues with
+index <em>idx</em>.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoordInfo</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> index (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetNumCoords">
-<code class="sig-name descname">GetNumCoords</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetNumCoords" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of connected stretches of residues that have been added to
-the database.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetNumCoords</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetNumCoords" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of connected stretches of residues that have been added to
+the database.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.PrintStatistics">
-<code class="sig-name descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
+<code class="descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
<dd><p>Prints out some information about the db.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetBackboneList">
-<code class="sig-name descname">GetBackboneList</code><span class="sig-paren">(</span><em class="sig-param">fragment</em>, <em class="sig-param">sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetBackboneList" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>fragment</em>, <em>sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetBackboneList" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetBackboneList</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">fragment</em>, <em class="sig-param">sequence=""</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>fragment</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="sig-name descname">GetBackboneList</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em>, <em class="sig-param">sequence=""</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>coord_idx</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="sig-name descname">GetBackboneList</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">coord_idx</em>, <em class="sig-param">sequence=""</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Backbone list with positions extracted from <em>fragment</em> or
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>coord_idx</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Backbone list with positions extracted from <em>fragment</em> or
full entry at <em>coord_idx</em></p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract positions.</p></li>
-<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract positions.</p></li>
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the returned backbone list. If not
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract positions.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract positions.</li>
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the returned backbone list. If not
set, the original sequence at specified location in the
-database is used.</p></li>
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
-superposed onto.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
-superposed onto.</p></li>
+database is used.</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
+superposed onto.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
+superposed onto.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the length of <em>sequence</em> does
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the length of <em>sequence</em> does
not match with the desired backbone list, if <em>sequence</em> contains
a character which does not belong to the 20 proteinogenic amino
acids or if <em>fragment</em> or <em>coord_idx</em> is invalid. Fragment can
be invalid when it does not fully fit into one of the connected
stretches of residues in the database.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSequence">
-<code class="sig-name descname">GetSequence</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequence" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetSequence</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequence" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetSequence</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The sequence of <em>fragment</em> or full entry at <em>coord_idx</em></p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence.</p></li>
-<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the sequence</p></li>
+<code class="descname">GetSequence</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The sequence of <em>fragment</em> or full entry at <em>coord_idx</em></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the sequence</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if fragment or coord_idx is
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if fragment or coord_idx is
invalid. Fragment can be invalid when it does not fully fit into
one of the connected stretches of residues in the database.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetDSSPStates">
-<code class="sig-name descname">GetDSSPStates</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDSSPStates" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetDSSPStates</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDSSPStates" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetDSSPStates</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The dssp states of <em>fragment</em> or full entry at <em>coord_idx</em></p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the states.</p></li>
-<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the dssp states</p></li>
+<code class="descname">GetDSSPStates</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The dssp states of <em>fragment</em> or full entry at <em>coord_idx</em></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the states.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the dssp states</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain dssp
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain dssp
data or if fragment/ coord_idx is invalid. Fragment can be invalid
when it does not fully fit into one of the connected stretches of
residues in the database.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetDihedralAngles">
-<code class="sig-name descname">GetDihedralAngles</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDihedralAngles" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetDihedralAngles</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDihedralAngles" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetDihedralAngles</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The phi and psi dihedral angles of every residue of <em>fragment</em>
+<code class="descname">GetDihedralAngles</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The phi and psi dihedral angles of every residue of <em>fragment</em>
or full entry at <em>coord_idx</em></p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of pairs (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a>)</p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the dihedrals.</p></li>
-<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the dihedral angles</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of pairs (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a>)</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the dihedrals.</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the dihedral angles</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
dihedral angle data or if fragment/ coord_idx is invalid.
Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetResidueDepths">
-<code class="sig-name descname">GetResidueDepths</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetResidueDepths" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetResidueDepths</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetResidueDepths" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetResidueDepths</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Residue depth for each residue of <em>fragment</em> or full entry
+<code class="descname">GetResidueDepths</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Residue depth for each residue of <em>fragment</em> or full entry
at <em>coord_idx</em></p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the residue
-depths</p></li>
-<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the residue depths</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the residue
+depths</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the residue depths</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
residue depth data or if fragment/ coord_idx is invalid.
Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSolventAccessibilitites">
-<code class="sig-name descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSolventAccessibilitites" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSolventAccessibilitites" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Solvent accessibility for each residue of <em>fragment</em> or full entry
+<code class="descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Solvent accessibility for each residue of <em>fragment</em> or full entry
at <em>coord_idx</em> in square A as calculated by
<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Accessibility()</span></code></a> when adding the structure to
the database.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the solvent
-accessibilities</p></li>
-<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the solvent
-accessibilities</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the solvent
+accessibilities</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the solvent
+accessibilities</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
solvent accessibility data or if fragment/ coord_idx is invalid.
Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSequenceProfile">
-<code class="sig-name descname">GetSequenceProfile</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequenceProfile" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetSequenceProfile</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequenceProfile" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetSequenceProfile</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The sequence profile for the residues defined by <em>fragment</em> or
+<code class="descname">GetSequenceProfile</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The sequence profile for the residues defined by <em>fragment</em> or
full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
model.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence
-profile</p></li>
-<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the sequence profile</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence
+profile</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the sequence profile</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
sequence profile data or if fragment/ coord_idx is invalid.
Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetStructureProfile">
-<code class="sig-name descname">GetStructureProfile</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetStructureProfile" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetStructureProfile</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetStructureProfile" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetStructureProfile</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The structure profile for the residues defined by <em>fragment</em> or
+<code class="descname">GetStructureProfile</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The structure profile for the residues defined by <em>fragment</em> or
full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
model.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the structure
-profile</p></li>
-<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the structure profile</p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the structure
+profile</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of entry from which to extract the structure profile</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if database does not contain
structure profile data or if fragment/ coord_idx is invalid.
Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GenerateStructureProfile">
-<code class="sig-name descname">GenerateStructureProfile</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">residue_depths</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GenerateStructureProfile" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GenerateStructureProfile</code><span class="sig-paren">(</span><em>bb_list</em>, <em>residue_depths</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GenerateStructureProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a structure profile for <em>bb_list</em> with given <em>residue_depths</em>
using the full internal data of this StructureDB.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Positions for which to calculate the structural profile</p></li>
-<li><p><strong>residue_depths</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The residue depth for each residue in <em>bb_list</em>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Positions for which to calculate the structural profile</li>
+<li><strong>residue_depths</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The residue depth for each residue in <em>bb_list</em>
as you would extract it from any StructureDB
-containing that data.</p></li>
+containing that data.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The structure profile for the input with the BLOSUM62
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The structure profile for the input with the BLOSUM62
probabilities as NULL model.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> and
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> and
<em>residue_depths</em> differ in size, when their size is 0
or when database does not contain residue depth data.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.SetStructureProfile">
-<code class="sig-name descname">SetStructureProfile</code><span class="sig-paren">(</span><em class="sig-param">coord_idx</em>, <em class="sig-param">prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SetStructureProfile" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetStructureProfile</code><span class="sig-paren">(</span><em>coord_idx</em>, <em>prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SetStructureProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes the <em>prof</em> and sets the corresponding StructureProfile
frequencies in entry with <em>coord_idx</em></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</p></li>
-<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
-(in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
+(in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>coord_idx</em> does not match
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>coord_idx</em> does not match
any entry in the db, when the size of the <em>prof</em> does not
exactly match the size of entry at <em>coord_idx</em> or when database
does not contain aa frequency struct data.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSubDB">
-<code class="sig-name descname">GetSubDB</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSubDB" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>A new database containing only the structural infos specified by
+<code class="descname">GetSubDB</code><span class="sig-paren">(</span><em>indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSubDB" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A new database containing only the structural infos specified by
your input. This might be useful if you’re testing stuff and want
-to make sure that you have no close homologue in the database.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Indices of chains to be added to the sub database (in [0,
-<a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if you provide an invalid index</p>
-</dd>
-</dl>
+to make sure that you have no close homologue in the database.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Indices of chains to be added to the sub database (in [0,
+<a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if you provide an invalid index</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -852,91 +914,101 @@ accessed through a hash table, making searching the database ultra fast.</p>
</div>
<dl class="class">
<dt id="promod3.loop.FragDB">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">FragDB</code><span class="sig-paren">(</span><em class="sig-param">dist_bin_size</em>, <em class="sig-param">angle_bin_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>dist_bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Size of the distance parameter binning in A</p></li>
-<li><p><strong>angle_bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Size of the angle parameter binning in degree</p></li>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FragDB</code><span class="sig-paren">(</span><em>dist_bin_size</em>, <em>angle_bin_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>dist_bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Size of the distance parameter binning in A</li>
+<li><strong>angle_bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Size of the angle parameter binning in degree</li>
</ul>
-</dd>
-</dl>
-<dl class="method">
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.loop.FragDB.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.FragDB.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.FragDB.Save" title="promod3.loop.FragDB.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.loop.FragDB.SavePortable" title="promod3.loop.FragDB.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load the database.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded database</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load the database.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded database</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.FragDB.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – path to the file where the database will be saved</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – path to the file where the database will be saved</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.GetAngularBinSize">
-<code class="sig-name descname">GetAngularBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetAngularBinSize" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetAngularBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetAngularBinSize" title="Permalink to this definition">¶</a></dt>
<dd><p>The size of the bins for the 4 angles describing the stem geometry and used
to organize the fragments in the database.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The bin size in degrees</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The bin size in degrees</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.GetDistBinSize">
-<code class="sig-name descname">GetDistBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetDistBinSize" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetDistBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetDistBinSize" title="Permalink to this definition">¶</a></dt>
<dd><p>The size of the bins for the distance describing the stem geometry and used
to organize the fragments in the database.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The bin size</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The bin size</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.AddFragments">
-<code class="sig-name descname">AddFragments</code><span class="sig-paren">(</span><em class="sig-param">fragment_length</em>, <em class="sig-param">rmsd_cutoff</em>, <em class="sig-param">structure_db</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.AddFragments" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddFragments</code><span class="sig-paren">(</span><em>fragment_length</em>, <em>rmsd_cutoff</em>, <em>structure_db</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.AddFragments" title="Permalink to this definition">¶</a></dt>
<dd><p>Iterates over all fragments of length <strong>fragment_length</strong> in
<strong>structure_db</strong> and adds them to the fragment database.
Fragments will be skipped if there is already a fragment in the database
@@ -944,122 +1016,135 @@ that has an RMSD smaller than <strong>rmsd_cutoff</strong>, where RMSD is calcul
upon superposing the stem residues.
As the fragments are added they are organized in bins described by their
length and the geometry of their N and C stem.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments that should be added to the databse</p></li>
-<li><p><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The minimal RMSD between two fragments in the fragment database</p></li>
-<li><p><strong>structure_db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Database delivering the structural info</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments that should be added to the databse</li>
+<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The minimal RMSD between two fragments in the fragment database</li>
+<li><strong>structure_db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Database delivering the structural info</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.PrintStatistics">
-<code class="sig-name descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
+<code class="descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
<dd><p>Prints statistics about the fragment database, notably:</p>
<ol class="arabic simple">
-<li><p>the number of different stem groups (number of bins used to group the
-fragments according to the geometry of their stem residues)</p></li>
-<li><p>The total number of fragments in the database</p></li>
-<li><p>The minimal and maximal number of fragments found in a stem group.</p></li>
+<li>the number of different stem groups (number of bins used to group the
+fragments according to the geometry of their stem residues)</li>
+<li>The total number of fragments in the database</li>
+<li>The minimal and maximal number of fragments found in a stem group.</li>
</ol>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.GetNumStemPairs">
-<code class="sig-name descname">GetNumStemPairs</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetNumStemPairs" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetNumStemPairs</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetNumStemPairs" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetNumStemPairs</code><span class="sig-paren">(</span><em class="sig-param">loop_length</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetNumStemPairs</code><span class="sig-paren">(</span><em>loop_length</em><span class="sig-paren">)</span></dt>
<dd><p>Returns the number of stem groups (number of bins used to group the
fragments according to the geometry of their stem residues) for the whole db
or for fragments of a given length.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The number of groups</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The number of groups</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.GetNumFragments">
-<code class="sig-name descname">GetNumFragments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetNumFragments" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetNumFragments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.GetNumFragments" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">GetNumFragments</code><span class="sig-paren">(</span><em class="sig-param">loop_length</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetNumFragments</code><span class="sig-paren">(</span><em>loop_length</em><span class="sig-paren">)</span></dt>
<dd><p>Returns the number of fragments in the database in total or for fragments of
a given length.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Number of fragments</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Number of fragments</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.HasFragLength">
-<code class="sig-name descname">HasFragLength</code><span class="sig-paren">(</span><em class="sig-param">loop_length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.HasFragLength" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>True if fragments of given length exist.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">HasFragLength</code><span class="sig-paren">(</span><em>loop_length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.HasFragLength" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The length of the fragments</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">True if fragments of given length exist.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.MaxFragLength">
-<code class="sig-name descname">MaxFragLength</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.MaxFragLength" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Maximal fragment length contained in db.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">MaxFragLength</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.MaxFragLength" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Maximal fragment length contained in db.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FragDB.SearchDB">
-<code class="sig-name descname">SearchDB</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">frag_size</em>, <em class="sig-param">extra_bins=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.SearchDB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SearchDB</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>frag_size</em>, <em>extra_bins=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.SearchDB" title="Permalink to this definition">¶</a></dt>
<dd><p>Search the database for fragments matching the geometry of the <strong>n_stem</strong>
and <strong>c_stem</strong> and of the same length as the <strong>frag_size</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</p></li>
-<li><p><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues of the fragment</p></li>
-<li><p><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
+<li><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues of the fragment</li>
+<li><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
<em>extra_bins</em> additional bins surrounding the bin given by
the <em>n_stem</em> and <em>c_stem</em> geometry. If odd, we extend to
-the closer bin, otherwise symmetrically.</p></li>
+the closer bin, otherwise symmetrically.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A list of <a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a> objects. These objects are related
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A list of <a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a> objects. These objects are related
to the structural database with which you called the AddFragments
function.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -1076,30 +1161,30 @@ wrapped in a full fletched pipeline implemented in
<a class="reference internal" href="../modelling/algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a> or search for fragments from scratch
using an arbitrary linear combination of scores:</p>
<ul class="simple">
-<li><p><strong>SeqID</strong>:
+<li><strong>SeqID</strong>:
Calculates the fraction of amino acids being identical when comparing
-a potential fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> and the target sequence</p></li>
-<li><p><strong>SeqSim</strong>:
+a potential fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> and the target sequence</li>
+<li><strong>SeqSim</strong>:
Calculates the avg. substitution matrix based sequence similarity of amino acids
when comparing a potential fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> and the target
-sequence</p></li>
-<li><p><strong>SSAgree</strong>:
-Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id3"><span>[Jones1999]</span></a>
-and the dssp <a class="reference internal" href="../references.html#kabsch1983" id="id4"><span>[kabsch1983]</span></a> assignment stored in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>.
-The Agreement term is based on a probabilistic approach also used in HHSearch <a class="reference internal" href="../references.html#soding2005" id="id5"><span>[soding2005]</span></a>.</p></li>
-<li><p><strong>TorsionProbability</strong>:
+sequence</li>
+<li><strong>SSAgree</strong>:
+Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id3">[Jones1999]</a>
+and the dssp <a class="reference internal" href="../references.html#kabsch1983" id="id4">[kabsch1983]</a> assignment stored in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>.
+The Agreement term is based on a probabilistic approach also used in HHSearch <a class="reference internal" href="../references.html#soding2005" id="id5">[soding2005]</a>.</li>
+<li><strong>TorsionProbability</strong>:
Calculates the avg. probability of observing the phi/psi dihedral angles of a potential
fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> given the target sequence. The probabilities are
-extracted from the <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> class.</p></li>
-<li><p><strong>SequenceProfile</strong>:
+extracted from the <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> class.</li>
+<li><strong>SequenceProfile</strong>:
Calculates the avg. profile score between the amino acid frequencies of a potential
fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> and a target profile assuming a gapfree alignment
-in between them. The scores are calculated as L1 distances between the profile columns.</p></li>
-<li><p><strong>StructureProfile</strong>:
+in between them. The scores are calculated as L1 distances between the profile columns.</li>
+<li><strong>StructureProfile</strong>:
Calculates the avg. profile score between the amino acid frequencies of a potential
fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> and a target profile assuming a gapfree alignment
in between them. The scores are calculated as L1 distances between the profile columns.
-In this case, the amino acid frequencies extracted from structural alignments are used.</p></li>
+In this case, the amino acid frequencies extracted from structural alignments are used.</li>
</ul>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
@@ -1150,195 +1235,237 @@ In this case, the amino acid frequencies extracted from structural alignments ar
</div>
<dl class="class">
<dt id="promod3.loop.Fragger">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">Fragger</code><span class="sig-paren">(</span><em class="sig-param">seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">Fragger</code><span class="sig-paren">(</span><em>seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger" title="Permalink to this definition">¶</a></dt>
<dd><p>A Fragger object to search a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a> for fragments with <strong>seq</strong>
as target sequence. You need to add some score components before you can
finally call the Fill function.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of fragments to be searched</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of fragments to be searched</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.loop.Fragger.Fill">
-<code class="sig-name descname">Fill</code><span class="sig-paren">(</span><em class="sig-param">db</em>, <em class="sig-param">rmsd_thresh</em>, <em class="sig-param">num_fragments</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.Fill" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Fill</code><span class="sig-paren">(</span><em>db</em>, <em>rmsd_thresh</em>, <em>num_fragments</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.Fill" title="Permalink to this definition">¶</a></dt>
<dd><p>Searches <strong>db</strong> for <strong>num_fragments</strong> fragments with maximal
score based on the defined score components.
There will be no pair of fragments with RMSD below <strong>rmsd_thresh</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Source of structural data</p></li>
-<li><p><strong>rmsd_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – To guarantee structural diversity</p></li>
-<li><p><strong>num_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to be extracted</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Source of structural data</li>
+<li><strong>rmsd_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – To guarantee structural diversity</li>
+<li><strong>num_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to be extracted</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddSeqIDParameters">
-<code class="sig-name descname">AddSeqIDParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSeqIDParameters" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddSeqIDParameters</code><span class="sig-paren">(</span><em>w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSeqIDParameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Add SeqID score component with linear weight <strong>w</strong></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddSeqSimParameters">
-<code class="sig-name descname">AddSeqSimParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">subst</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSeqSimParameters" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddSeqSimParameters</code><span class="sig-paren">(</span><em>w</em>, <em>subst</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSeqSimParameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Add SeqSim score component with linear weight <strong>w</strong></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
-<li><p><strong>subst</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SubstWeightMatrix</span></code>) – Substitution matrix to calculate sequence similarity</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</li>
+<li><strong>subst</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SubstWeightMatrix</span></code>) – Substitution matrix to calculate sequence similarity</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddSSAgreeParameters">
-<code class="sig-name descname">AddSSAgreeParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">psipred_prediction</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSSAgreeParameters" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddSSAgreeParameters</code><span class="sig-paren">(</span><em>w</em>, <em>psipred_prediction</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSSAgreeParameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Add SSAgree score component with linear weight <strong>w</strong></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – linear weight</p></li>
-<li><p><strong>psipred_prediction</strong> (<a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a>) – Psipred prediction for fraggers target_sequence</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – linear weight</li>
+<li><strong>psipred_prediction</strong> (<a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a>) – Psipred prediction for fraggers target_sequence</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddTorsionProbabilityParameters">
-<code class="sig-name descname">AddTorsionProbabilityParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">aa_before</em>, <em class="sig-param">aa_after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddTorsionProbabilityParameters" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddTorsionProbabilityParameters</code><span class="sig-paren">(</span><em>w</em>, <em>torsion_sampler</em>, <em>aa_before</em>, <em>aa_after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddTorsionProbabilityParameters" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">AddTorsionProbabilityParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">torsion_sampler_list</em>, <em class="sig-param">aa_before</em>, <em class="sig-param">aa_after</em><span class="sig-paren">)</span></dt>
+<code class="descname">AddTorsionProbabilityParameters</code><span class="sig-paren">(</span><em>w</em>, <em>torsion_sampler_list</em>, <em>aa_before</em>, <em>aa_after</em><span class="sig-paren">)</span></dt>
<dd><p>Add TorsionProbability component of linear weight <strong>w</strong></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Torsion sampler to be used for all residues.</p></li>
-<li><p><strong>torsion_sampler_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – One torsion sampler for each residue.</p></li>
-<li><p><strong>aa_before</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue before the sequence
-linked to this object.</p></li>
-<li><p><strong>aa_after</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue after the sequence
-linked to this object.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Torsion sampler to be used for all residues.</li>
+<li><strong>torsion_sampler_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – One torsion sampler for each residue.</li>
+<li><strong>aa_before</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue before the sequence
+linked to this object.</li>
+<li><strong>aa_after</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue after the sequence
+linked to this object.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddSequenceProfileParameters">
-<code class="sig-name descname">AddSequenceProfileParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSequenceProfileParameters" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddSequenceProfileParameters</code><span class="sig-paren">(</span><em>w</em>, <em>prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddSequenceProfileParameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Add SequenceProfile component of linear weight <strong>w</strong></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.AddStructureProfileParameters">
-<code class="sig-name descname">AddStructureProfileParameters</code><span class="sig-paren">(</span><em class="sig-param">w</em>, <em class="sig-param">prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddStructureProfileParameters" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddStructureProfileParameters</code><span class="sig-paren">(</span><em>w</em>, <em>prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.AddStructureProfileParameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Add StructureProfile component of linear weight <strong>w</strong></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.__len__">
-<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of fragments stored in fragger.</p>
-</dd>
-</dl>
+<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of fragments stored in fragger.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.__getitem__">
-<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.__getitem__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> – Item to extract</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Fragment at given position</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.__getitem__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> – Item to extract</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Fragment at given position</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.GetFragmentInfo">
-<code class="sig-name descname">GetFragmentInfo</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.GetFragmentInfo" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of fragment</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a> of fragment at position <strong>index</strong></p>
-</dd>
-</dl>
+<code class="descname">GetFragmentInfo</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.GetFragmentInfo" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of fragment</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a> of fragment at position <strong>index</strong></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.Fragger.GetScore">
-<code class="sig-name descname">GetScore</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.GetScore" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetScore</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.Fragger.GetScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the final score of fragment defined by <strong>index</strong></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of fragment</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Score of fragment at position <strong>index</strong></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of fragment</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Score of fragment at position <strong>index</strong></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">GetScore</code><span class="sig-paren">(</span><em class="sig-param">parameter_index</em>, <em class="sig-param">index</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetScore</code><span class="sig-paren">(</span><em>parameter_index</em>, <em>index</em><span class="sig-paren">)</span></dt>
<dd><p>Returns the single feature score defined by <strong>parameter_index</strong> of
fragment defined by <strong>index</strong> with parameter indexing based on the order
you added them to the <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>parameter_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of score (0-indexed in order of score
-components that were added)</p></li>
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of fragment</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>parameter_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of score (0-indexed in order of score
+components that were added)</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of fragment</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.loop.FraggerMap">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">FraggerMap</code><a class="headerlink" href="#promod3.loop.FraggerMap" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FraggerMap</code><a class="headerlink" href="#promod3.loop.FraggerMap" title="Permalink to this definition">¶</a></dt>
<dd><p>A simple storable map of Fragger objects. The idea is that one can use the map
to cache fragger lists that have already been generated.</p>
<p>You can use <a class="reference internal" href="#promod3.loop.FraggerMap.Contains" title="promod3.loop.FraggerMap.Contains"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Contains()</span></code></a> to check if an item with a given key
@@ -1347,98 +1474,108 @@ to cache fragger lists that have already been generated.</p>
<p>Serialization is meant to be temporary and is not guaranteed to be portable.</p>
<dl class="method">
<dt id="promod3.loop.FraggerMap.Load">
-<code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em>, <em class="sig-param">db</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Load" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em>, <em>db</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Load" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.FraggerMap.Save" title="promod3.loop.FraggerMap.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</p></li>
-<li><p><strong>db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Source of structural data used when filling the fragments.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</li>
+<li><strong>db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Source of structural data used when filling the fragments.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded map.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.FraggerMap" title="promod3.loop.FraggerMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerMap</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The loaded map.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.FraggerMap" title="promod3.loop.FraggerMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerMap</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FraggerMap.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Save" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves raw binary representation of this map. Only fragment infos and scores
are stored and not the parameters for scoring. The coordinates are to be
reread from a structure db.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FraggerMap.LoadBB">
-<code class="sig-name descname">LoadBB</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.LoadBB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">LoadBB</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.LoadBB" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.FraggerMap.SaveBB" title="promod3.loop.FraggerMap.SaveBB"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SaveBB()</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded map.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.FraggerMap" title="promod3.loop.FraggerMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerMap</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded map.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.FraggerMap" title="promod3.loop.FraggerMap"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerMap</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FraggerMap.SaveBB">
-<code class="sig-name descname">SaveBB</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.SaveBB" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SaveBB</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.SaveBB" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves raw binary representation of this map. Only fragments and scores
are stored and not the parameters for scoring. Here, we also store the
coordinates. This file will hence be much larger than the one saved with
<a class="reference internal" href="#promod3.loop.FraggerMap.Save" title="promod3.loop.FraggerMap.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FraggerMap.Contains">
-<code class="sig-name descname">Contains</code><span class="sig-paren">(</span><em class="sig-param">id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Contains" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, iff a fragger object for this id is already in the map.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">Contains</code><span class="sig-paren">(</span><em>id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.Contains" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff a fragger object for this id is already in the map.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.FraggerMap.__getitem__">
-<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.__getitem__" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.FraggerMap.__setitem__">
-<code class="sig-name descname">__setitem__</code><span class="sig-paren">(</span><em class="sig-param">id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.__setitem__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__setitem__</code><span class="sig-paren">(</span><em>id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerMap.__setitem__" title="Permalink to this definition">¶</a></dt>
<dd><p>Allow read/write access (with [<em>id</em>]) to fragger object with given ID.</p>
</dd></dl>
@@ -1449,157 +1586,186 @@ coordinates. This file will hence be much larger than the one saved with
<h2>The PsipredPrediction class<a class="headerlink" href="#the-psipredprediction-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.PsipredPrediction">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">PsipredPrediction</code><a class="headerlink" href="#promod3.loop.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
-<dd><p>A container for the secondary structure prediction by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id6"><span>[Jones1999]</span></a>.</p>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">PsipredPrediction</code><a class="headerlink" href="#promod3.loop.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
+<dd><p>A container for the secondary structure prediction by PSIPRED <a class="reference internal" href="../references.html#jones1999" id="id6">[Jones1999]</a>.</p>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.PsipredPrediction">
-<code class="sig-name descname">PsipredPrediction</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
+<code class="descname">PsipredPrediction</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.PsipredPrediction" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs empty container</p>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">PsipredPrediction</code><span class="sig-paren">(</span><em class="sig-param">prediction</em>, <em class="sig-param">confidence</em><span class="sig-paren">)</span></dt>
+<code class="descname">PsipredPrediction</code><span class="sig-paren">(</span><em>prediction</em>, <em>confidence</em><span class="sig-paren">)</span></dt>
<dd><p>Constructs container with given content</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>prediction</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Secondary structure prediction as element in [‘H’,’E’,’C’]</p></li>
-<li><p><strong>confidence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Confidence of prediction as element in [0,9]</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>prediction</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Secondary structure prediction as element in [‘H’,’E’,’C’]</li>
+<li><strong>confidence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Confidence of prediction as element in [0,9]</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if size of <strong>prediction</strong> and
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if size of <strong>prediction</strong> and
<strong>confidence</strong> are inconsistent or if they contain an invalid
element</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.FromHHM">
-<code class="sig-name descname">FromHHM</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.FromHHM" title="Permalink to this definition">¶</a></dt>
+<code class="descname">FromHHM</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.FromHHM" title="Permalink to this definition">¶</a></dt>
<dd><p>Static function to Load a <a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a> object from hhm file,
as they are provided by the hhsearch suite</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of file</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of file</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.FromHoriz">
-<code class="sig-name descname">FromHoriz</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.FromHoriz" title="Permalink to this definition">¶</a></dt>
+<code class="descname">FromHoriz</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.FromHoriz" title="Permalink to this definition">¶</a></dt>
<dd><p>Static function to Load a <a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a> object from horiz file,
as they are produced by the psipred executable</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of file</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of file</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.Add">
-<code class="sig-name descname">Add</code><span class="sig-paren">(</span><em class="sig-param">prediction</em>, <em class="sig-param">confidence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.Add" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Add</code><span class="sig-paren">(</span><em>prediction</em>, <em>confidence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.Add" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds and appends a single residue psipred prediction at the end</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>prediction</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Prediction, must be one in [‘H’,’E’,’C’]</p></li>
-<li><p><strong>confidence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Confidence of prediction, must be in [0,9]</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>prediction</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Prediction, must be one in [‘H’,’E’,’C’]</li>
+<li><strong>confidence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Confidence of prediction, must be in [0,9]</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if input contains invalid elements</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if input contains invalid elements</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.Extract">
-<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">from</em>, <em class="sig-param">to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.Extract" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Extract</code><span class="sig-paren">(</span><em>from</em>, <em>to</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.Extract" title="Permalink to this definition">¶</a></dt>
<dd><p>Extracts content and returns a sub-<a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a> with range <strong>from</strong>
to <strong>to</strong>, not including <strong>to</strong> itself</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx to start</p></li>
-<li><p><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx to end</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx to start</li>
+<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx to end</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a> with the specified range</p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>from</strong> or <strong>to</strong> are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a> with the specified range</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>from</strong> or <strong>to</strong> are invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.GetPrediction">
-<code class="sig-name descname">GetPrediction</code><span class="sig-paren">(</span><em class="sig-param">idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetPrediction" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index to get prediction from</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Psipred prediction at pos <strong>idx</strong></p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>idx</strong> is invalid</p>
-</dd>
-</dl>
+<code class="descname">GetPrediction</code><span class="sig-paren">(</span><em>idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetPrediction" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index to get prediction from</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Psipred prediction at pos <strong>idx</strong></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>idx</strong> is invalid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.GetConfidence">
-<code class="sig-name descname">GetConfidence</code><span class="sig-paren">(</span><em class="sig-param">idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetConfidence" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index to get confidence from</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Psipred confidence at pos <strong>idx</strong></p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>idx</strong> is invalid</p>
-</dd>
-</dl>
+<code class="descname">GetConfidence</code><span class="sig-paren">(</span><em>idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetConfidence" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index to get confidence from</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Psipred confidence at pos <strong>idx</strong></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>idx</strong> is invalid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.GetPredictions">
-<code class="sig-name descname">GetPredictions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetPredictions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetPredictions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetPredictions" title="Permalink to this definition">¶</a></dt>
<dd><p>Get all the predictions in the container</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> containing all the predictions in the container</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> containing all the predictions in the container</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.GetConfidences">
-<code class="sig-name descname">GetConfidences</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetConfidences" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetConfidences</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.GetConfidences" title="Permalink to this definition">¶</a></dt>
<dd><p>Get all the confidences in the container</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> containing all the confidences in the container</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> containing all the confidences in the container</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.PsipredPrediction.__len__">
-<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of elements in container</p>
-</dd>
-</dl>
+<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.PsipredPrediction.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of elements in container</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -1609,7 +1775,6 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -1630,12 +1795,12 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
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<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -1652,7 +1817,7 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li>Previous: <a href="torsion_sampler.html" title="previous chapter">Sampling Dihedral Angles</a></li>
<li>Next: <a href="all_atom.html" title="next chapter">Handling All Atom Positions</a></li>
</ul></li>
@@ -1661,33 +1826,27 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
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+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
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- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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<a href="../_sources/loop/structure_db.rst.txt"
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index cdb56db84434b425bc4dec86202d2c0c57c0a0a0..fa34d776bc15cf23340f75e569d3dbc290de5bc1 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Sampling Dihedral Angles — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Sampling Dihedral Angles — ProMod3 3.2.1 documentation</title>
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<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="sampling-dihedral-angles">
@@ -101,360 +100,430 @@ decisive.</p>
<h2>The Torsion Sampler Class<a class="headerlink" href="#the-torsion-sampler-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.TorsionSampler">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">TorsionSampler</code><span class="sig-paren">(</span><em class="sig-param">group_definitions</em>, <em class="sig-param">bins_per_dimension</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">TorsionSampler</code><span class="sig-paren">(</span><em>group_definitions</em>, <em>bins_per_dimension</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>Basic object used to sample the backbone torsion angles phi and psi.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>group_definitions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – List of group definitions defining amino acid triplets</p></li>
-<li><p><strong>bins_per_dimension</strong> – Number of bins to represent the 360 degrees of each
-torsion angle</p></li>
-<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for random number generator</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>group_definitions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – List of group definitions defining amino acid triplets</li>
+<li><strong>bins_per_dimension</strong> – Number of bins to represent the 360 degrees of each
+torsion angle</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for random number generator</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeException</span></code> when there is a
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal notranslate"><span class="pre">RuntimeException</span></code> when there is a
possible combination of the 20 standard amino
acids not matching any of the group definitions.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.ExtractStatistics">
-<code class="sig-name descname">ExtractStatistics</code><span class="sig-paren">(</span><em class="sig-param">view</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.ExtractStatistics" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ExtractStatistics</code><span class="sig-paren">(</span><em>view</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.ExtractStatistics" title="Permalink to this definition">¶</a></dt>
<dd><p>Extracts backbone torsion angles from the structure and adds them to the appropriate histograms in the sampler.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.UpdateDistributions">
-<code class="sig-name descname">UpdateDistributions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.UpdateDistributions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">UpdateDistributions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.UpdateDistributions" title="Permalink to this definition">¶</a></dt>
<dd><p>Recalculates the probability distributions from the histograms.</p>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.loop.TorsionSampler.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.TorsionSampler.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.TorsionSampler.Save" title="promod3.loop.TorsionSampler.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.loop.TorsionSampler.SavePortable" title="promod3.loop.TorsionSampler.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load the sampler.</p></li>
-<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for random number generator (not saved in file).</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load the sampler.</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for random number generator (not saved in file).</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A torsion sampler</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A torsion sampler</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.TorsionSampler.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where the sampler will be saved</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where the sampler will be saved</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetHistogramIndex">
-<code class="sig-name descname">GetHistogramIndex</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetHistogramIndex" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<code class="descname">GetHistogramIndex</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetHistogramIndex" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The index of the histogram corresponding to the triplet of residues specified.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The index of the histogram corresponding to the triplet of residues specified.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetHistogramIndices">
-<code class="sig-name descname">GetHistogramIndices</code><span class="sig-paren">(</span><em class="sig-param">sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetHistogramIndices" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of length n from which histogram indices
-should created.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>List of length n-2 containing histogram indices of
-all consecutive amino acid triplets in <strong>sequence</strong></p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>sequence</strong> contains non
-standard amino acid</p>
-</dd>
-</dl>
+<code class="descname">GetHistogramIndices</code><span class="sig-paren">(</span><em>sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetHistogramIndices" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of length n from which histogram indices
+should created.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">List of length n-2 containing histogram indices of
+all consecutive amino acid triplets in <strong>sequence</strong></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <strong>sequence</strong> contains non
+standard amino acid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.Draw">
-<code class="sig-name descname">Draw</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Draw" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Draw</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.Draw" title="Permalink to this definition">¶</a></dt>
<dd><p>Draws a pair of dihedral angles for the <em>central</em> residue from the distribution specific for such a triplet of residues.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A pair of phi/psi angles</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A pair of phi/psi angles</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">Draw</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span></dt>
+<code class="descname">Draw</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span></dt>
<dd><p>Draws a pair of dihedral angles from the distribution specified by the <em>index</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution from which a phi/psi pair will be drawn.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A pair of phi/psi angles</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution from which a phi/psi pair will be drawn.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A pair of phi/psi angles</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.DrawPhiGivenPsi">
-<code class="sig-name descname">DrawPhiGivenPsi</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.DrawPhiGivenPsi" title="Permalink to this definition">¶</a></dt>
+<code class="descname">DrawPhiGivenPsi</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.DrawPhiGivenPsi" title="Permalink to this definition">¶</a></dt>
<dd><p>Draws a <em>phi</em> angle for the <em>central</em> residue from the conditional distribution P( <em>phi</em> | <em>psi</em> ) specific for such a triplet of residues.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>psi</em> angle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>psi</em> angle</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>An angle</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">An angle</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">DrawPhiGivenPsi</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span></dt>
+<code class="descname">DrawPhiGivenPsi</code><span class="sig-paren">(</span><em>index</em>, <em>psi</em><span class="sig-paren">)</span></dt>
<dd><p>Draws a <em>phi</em> angle from the conditional distribution P( <em>phi</em> | <em>psi</em> ) specified by the <em>index</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution from which a <em>phi</em> angle will be drawn.</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>psi</em> angle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution from which a <em>phi</em> angle will be drawn.</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>psi</em> angle</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>An angle</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">An angle</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.DrawPsiGivenPhi">
-<code class="sig-name descname">DrawPsiGivenPhi</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em>, <em class="sig-param">phi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.DrawPsiGivenPhi" title="Permalink to this definition">¶</a></dt>
+<code class="descname">DrawPsiGivenPhi</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>phi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.DrawPsiGivenPhi" title="Permalink to this definition">¶</a></dt>
<dd><p>Draws a <em>phi</em> angle for the <em>central</em> residue from the conditional distribution P( <em>psi</em> | <em>phi</em> ) specific for such a triplet of residues.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>phi</em> angle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>phi</em> angle</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>An angle</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">An angle</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">DrawPsiGivenPhi</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em><span class="sig-paren">)</span></dt>
+<code class="descname">DrawPsiGivenPhi</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em><span class="sig-paren">)</span></dt>
<dd><p>Draws a <em>phi</em> angle from the conditional distribution P( <em>psi</em> | <em>phi</em> ) specified by the <em>index</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution from which a psi angle will be drawn.</p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>phi</em> angle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution from which a psi angle will be drawn.</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>phi</em> angle</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>An angle</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">An angle</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetProbability">
-<code class="sig-name descname">GetProbability</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetProbability" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetProbability</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>phi</em>, <em>psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetProbability" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the probability of a specific pair of phi/psi angles for the central residue from the corresponding distribution.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A probability</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">GetProbability</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetProbability</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>psi</em><span class="sig-paren">)</span></dt>
<dd><p>Returns the probability of a specific pair of phi/psi angles calulated from the distribution specified by <em>index</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution.</p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution.</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A probability</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi">
-<code class="sig-name descname">GetPhiProbabilityGivenPsi</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetPhiProbabilityGivenPsi</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>phi</em>, <em>psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns P( <em>phi</em> | <em>psi</em> ) for the central residue from the corresponding distribution.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A probability</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi">
-<code class="sig-name descname">GetPsiProbabilityGivenPhi</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">central</em>, <em class="sig-param">after</em>, <em class="sig-param">psi</em>, <em class="sig-param">phi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetPsiProbabilityGivenPhi</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>psi</em>, <em>phi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns P( <em>psi</em> | <em>phi</em> ) for the central residue from the corresponding distribution.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A probability</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">GetPhiProbabilityGivenPsi</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetPhiProbabilityGivenPsi</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>psi</em><span class="sig-paren">)</span></dt>
<dd><p>Returns P( <em>phi</em> | <em>psi</em> ) for the central residue from the corresponding distribution.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution.</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution.</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A probability</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">GetPsiProbabilityGivenPhi</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">psi</em>, <em class="sig-param">phi</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetPsiProbabilityGivenPhi</code><span class="sig-paren">(</span><em>index</em>, <em>psi</em>, <em>phi</em><span class="sig-paren">)</span></dt>
<dd><p>Returns P( <em>psi</em> | <em>phi</em> ) for the central residue from the corresponding distribution.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution.</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the distribution.</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A probability</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A probability</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetBinsPerDimension">
-<code class="sig-name descname">GetBinsPerDimension</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetBinsPerDimension" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetBinsPerDimension</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetBinsPerDimension" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the number of bins per dimension of the distributions.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetBinSize">
-<code class="sig-name descname">GetBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetBinSize" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetBinSize</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.GetBinSize" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the size of the bins (in radians) of the distributions.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -464,7 +533,6 @@ standard amino acid</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -485,12 +553,12 @@ standard amino acid</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -507,7 +575,7 @@ standard amino acid</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li>Previous: <a href="backbone.html" title="previous chapter">Representing Loops</a></li>
<li>Next: <a href="structure_db.html" title="next chapter">Structural Data</a></li>
</ul></li>
@@ -516,33 +584,27 @@ standard amino acid</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
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<script type="text/javascript">$('#searchbox').show(0);</script>
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-
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</div>
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</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/torsion_sampler.rst.txt"
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 52fbe89c8cf0175e4df0be3faf5572b2c74428ba..b50786148354be50f4cf7124d841b262debf706d 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Modelling Algorithms — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Modelling Algorithms — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="modelling-algorithms">
@@ -58,28 +57,30 @@ also present in solution B. As a final result, the algorithm therefore detects
common rigid subsets of positions.</p>
<dl class="method">
<dt id="promod3.modelling.RigidBlocks">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RigidBlocks</code><span class="sig-paren">(</span><em class="sig-param">bb_list_one</em>, <em class="sig-param">bb_list_two</em><span class="optional">[</span>, <em class="sig-param">window_length = 12</em>, <em class="sig-param">max_iterations=20</em>, <em class="sig-param">distance_thresh=3.0</em>, <em class="sig-param">cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RigidBlocks" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">RigidBlocks</code><span class="sig-paren">(</span><em>bb_list_one</em>, <em>bb_list_two</em><span class="optional">[</span>, <em>window_length = 12</em>, <em>max_iterations=20</em>, <em>distance_thresh=3.0</em>, <em>cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RigidBlocks" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs the RigidBlock algorithm on given input</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>bb_list_one</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – First piece structural information from which CA
-positions will be extracted</p></li>
-<li><p><strong>bb_list_two</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Second piece of structural information from which CA
-positions will be extracted</p></li>
-<li><p><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</p></li>
-<li><p><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
-iterative superposition</p></li>
-<li><p><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>bb_list_one</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – First piece structural information from which CA
+positions will be extracted</li>
+<li><strong>bb_list_two</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Second piece of structural information from which CA
+positions will be extracted</li>
+<li><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</li>
+<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
+iterative superposition</li>
+<li><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
considered in the same rigid block and to select
the common subset for the next iteration of the
-iterative superposition</p></li>
-<li><p><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
-of the solutions</p></li>
+iterative superposition</li>
+<li><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
+of the solutions</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> defining the
indices of the common subsets (rigid blocks) relative
to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
@@ -87,36 +88,40 @@ and the second element being a <a class="reference external" href="https://docs.
<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>bb_list_one</strong>
onto <strong>bb_list_two</strong></p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RigidBlocks</code><span class="sig-paren">(</span><em class="sig-param">aln</em><span class="optional">[</span>, <em class="sig-param">seq_one_idx=0</em>, <em class="sig-param">seq_two_idx=1</em>, <em class="sig-param">window_length = 12</em>, <em class="sig-param">max_iterations=20</em>, <em class="sig-param">distance_thresh=3.0</em>, <em class="sig-param">cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">RigidBlocks</code><span class="sig-paren">(</span><em>aln</em><span class="optional">[</span>, <em>seq_one_idx=0</em>, <em>seq_two_idx=1</em>, <em>window_length = 12</em>, <em>max_iterations=20</em>, <em>distance_thresh=3.0</em>, <em>cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>Performs the RigidBlock algorithm on given input</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>
-objects from which the positions are extracted</p></li>
-<li><p><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
-positions will be extracted</p></li>
-<li><p><strong>seq_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The idx of the second sequence from which the CA
-positions will be extracted</p></li>
-<li><p><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</p></li>
-<li><p><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
-iterative superposition</p></li>
-<li><p><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>
+objects from which the positions are extracted</li>
+<li><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
+positions will be extracted</li>
+<li><strong>seq_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The idx of the second sequence from which the CA
+positions will be extracted</li>
+<li><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</li>
+<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
+iterative superposition</li>
+<li><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
considered in the same rigid block and to select
the common subset for the next iteration of the
-iterative superposition</p></li>
-<li><p><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
-of the solutions</p></li>
+iterative superposition</li>
+<li><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
+of the solutions</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> defining the
column indices of the common subsets (rigid blocks)
relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
@@ -124,32 +129,36 @@ and the second element being a <a class="reference external" href="https://docs.
<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions from the first
sequence onto the second sequence.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RigidBlocks</code><span class="sig-paren">(</span><em class="sig-param">pos_one</em>, <em class="sig-param">pos_two</em><span class="optional">[</span>, <em class="sig-param">window_length = 12</em>, <em class="sig-param">max_iterations=20</em>, <em class="sig-param">distance_thresh=3.0</em>, <em class="sig-param">cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">RigidBlocks</code><span class="sig-paren">(</span><em>pos_one</em>, <em>pos_two</em><span class="optional">[</span>, <em>window_length = 12</em>, <em>max_iterations=20</em>, <em>distance_thresh=3.0</em>, <em>cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>Performs the RigidBlock algorithm on given input</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – First piece position information</p></li>
-<li><p><strong>pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Second piece of position information</p></li>
-<li><p><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</p></li>
-<li><p><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
-iterative superposition</p></li>
-<li><p><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – First piece position information</li>
+<li><strong>pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Second piece of position information</li>
+<li><strong>window_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of sliding window to generate initial subsets</li>
+<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal numbers of iterations for every single
+iterative superposition</li>
+<li><strong>distance_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two CA positions can have to be
considered in the same rigid block and to select
the common subset for the next iteration of the
-iterative superposition</p></li>
-<li><p><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
-of the solutions</p></li>
+iterative superposition</li>
+<li><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold of similarity to perform the final merging
+of the solutions</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> defining the
indices of the common subsets (rigid blocks) relative
to the input <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code> objects
@@ -157,8 +166,10 @@ and the second element being a <a class="reference external" href="https://docs.
<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>pos_one</strong>
onto <strong>pos_two</strong></p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -170,7 +181,7 @@ as well as a convenient function to combine the functionalities into an
example pipeline.</p>
<dl class="class">
<dt id="promod3.modelling.FraggerHandle">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FraggerHandle</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">profile=None</em>, <em class="sig-param">psipred_pred=None</em>, <em class="sig-param">fragment_length=9</em>, <em class="sig-param">fragments_per_position=100</em>, <em class="sig-param">rmsd_thresh=0.0</em>, <em class="sig-param">structure_db=None</em>, <em class="sig-param">torsion_sampler_coil=None</em>, <em class="sig-param">torsion_sampler_helix=None</em>, <em class="sig-param">torsion_sampler_extended=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">FraggerHandle</code><span class="sig-paren">(</span><em>sequence</em>, <em>profile=None</em>, <em>psipred_pred=None</em>, <em>fragment_length=9</em>, <em>fragments_per_position=100</em>, <em>rmsd_thresh=0.0</em>, <em>structure_db=None</em>, <em>torsion_sampler_coil=None</em>, <em>torsion_sampler_helix=None</em>, <em>torsion_sampler_extended=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle" title="Permalink to this definition">¶</a></dt>
<dd><p>Handler for <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> objects linked to a
specific chain.</p>
<p>Tries to get the most accurate fragments given your input.
@@ -180,30 +191,26 @@ You can massively increase the accuracy of the found fragments by
providing a secondary structure prediction and / or sequence profile.</p>
<p>Following features influence the fragment search given your input:</p>
<ul class="simple">
-<li><p><strong>sequence</strong>:</p>
-<ul>
-<li><p>Sequence Similarity with BLOSUM62</p></li>
+<li><strong>sequence</strong>:<ul>
+<li>Sequence Similarity with BLOSUM62</li>
</ul>
</li>
-<li><p><strong>sequence</strong>, <strong>psipred_pred</strong>:</p>
-<ul>
-<li><p>Sequence Similarity with BLOSUM62</p></li>
-<li><p>Secondary Structure Agreement</p></li>
-<li><p>Secondary Structure Dependent Torsion Probabilities</p></li>
+<li><strong>sequence</strong>, <strong>psipred_pred</strong>:<ul>
+<li>Sequence Similarity with BLOSUM62</li>
+<li>Secondary Structure Agreement</li>
+<li>Secondary Structure Dependent Torsion Probabilities</li>
</ul>
</li>
-<li><p><strong>sequence</strong>, <strong>profile</strong>:</p>
-<ul>
-<li><p>Sequence Profile Score</p></li>
-<li><p>Structure Profile Score</p></li>
+<li><strong>sequence</strong>, <strong>profile</strong>:<ul>
+<li>Sequence Profile Score</li>
+<li>Structure Profile Score</li>
</ul>
</li>
-<li><p><strong>sequence</strong>, <strong>psipred_pred</strong>, <strong>profile</strong>:</p>
-<ul>
-<li><p>Secondary Structure Agreement</p></li>
-<li><p>Secondary Structure Dependent Torsion Probabilities</p></li>
-<li><p>Sequence Profile Score</p></li>
-<li><p>Structure Profile Score</p></li>
+<li><strong>sequence</strong>, <strong>psipred_pred</strong>, <strong>profile</strong>:<ul>
+<li>Secondary Structure Agreement</li>
+<li>Secondary Structure Dependent Torsion Probabilities</li>
+<li>Sequence Profile Score</li>
+<li>Structure Profile Score</li>
</ul>
</li>
</ul>
@@ -214,65 +221,74 @@ disk. When loading the FraggerHandle again, you need to provide all parameters
again. These parameters must be exactly the same than the ones you used when
initially constructing the FraggerHandle, especially the structure database.
Weird things are happening otherwise.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</p></li>
-<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</p></li>
-<li><p><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</p></li>
-<li><p><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length (num. residues) of fragments to be extracted.</p></li>
-<li><p><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
-position.</p></li>
-<li><p><strong>rmsd_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – To guarantee structural diversity, no pair of fragments
-at a given position will have RMSD below <cite>rmsd_thresh</cite>.</p></li>
-<li><p><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.StructureDB</span></code></a>) – Source of structural data</p></li>
-<li><p><strong>torsion_sampler_coil</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for coil residues.</p></li>
-<li><p><strong>torsion_sampler_helix</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for helical residues.</p></li>
-<li><p><strong>torsion_sampler_extended</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for extended residues.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
+<li><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</li>
+<li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length (num. residues) of fragments to be extracted.</li>
+<li><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
+position.</li>
+<li><strong>rmsd_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – To guarantee structural diversity, no pair of fragments
+at a given position will have RMSD below <cite>rmsd_thresh</cite>.</li>
+<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.StructureDB</span></code></a>) – Source of structural data</li>
+<li><strong>torsion_sampler_coil</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for coil residues.</li>
+<li><strong>torsion_sampler_helix</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for helical residues.</li>
+<li><strong>torsion_sampler_extended</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Torsion sampler for extended residues.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.FraggerHandle.Get">
-<code class="sig-name descname">Get</code><span class="sig-paren">(</span><em class="sig-param">frag_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.Get" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Get</code><span class="sig-paren">(</span><em>frag_pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.Get" title="Permalink to this definition">¶</a></dt>
<dd><p>Get fragger for sequence at index frag_pos..frag_pos+frag_length-1.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>frag_pos</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start-index (note that sequence-indexing starts at 0)</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A <code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code> object.</p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">ValueError</span></code> if index out-of-bounds.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frag_pos</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start-index (note that sequence-indexing starts at 0)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A <code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code> object.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">ValueError</span></code> if index out-of-bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.FraggerHandle.GetList">
-<code class="sig-name descname">GetList</code><span class="sig-paren">(</span><em class="sig-param">pos_start=0</em>, <em class="sig-param">pos_end=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.GetList" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetList</code><span class="sig-paren">(</span><em>pos_start=0</em>, <em>pos_end=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.GetList" title="Permalink to this definition">¶</a></dt>
<dd><p>Get List of fraggers covering sequence indices pos_start..pos_end.</p>
<p>This will return an empty list if range is smaller than fragment_length.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>pos_start</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start-index (note that sequence-indexing starts at 0)</p></li>
-<li><p><strong>pos_end</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – End-index or -1 if it should go to the sequence-end.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>pos_start</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start-index (note that sequence-indexing starts at 0)</li>
+<li><strong>pos_end</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – End-index or -1 if it should go to the sequence-end.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code> objects.</p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">ValueError</span></code> if indices out-of-bounds.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code> objects.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">ValueError</span></code> if indices out-of-bounds.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.FraggerHandle.LoadCached">
-<code class="sig-name descname">LoadCached</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.LoadCached" title="Permalink to this definition">¶</a></dt>
+<code class="descname">LoadCached</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.LoadCached" title="Permalink to this definition">¶</a></dt>
<dd><p>Load fragger objects stored with <a class="reference internal" href="#promod3.modelling.FraggerHandle.SaveCached" title="promod3.modelling.FraggerHandle.SaveCached"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SaveCached()</span></code></a>.
Note that here we require that the same structure db is set as was
used when <cite>filename</cite> was saved.</p>
@@ -280,7 +296,7 @@ used when <cite>filename</cite> was saved.</p>
<dl class="method">
<dt id="promod3.modelling.FraggerHandle.SaveCached">
-<code class="sig-name descname">SaveCached</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.SaveCached" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SaveCached</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FraggerHandle.SaveCached" title="Permalink to this definition">¶</a></dt>
<dd><p>Save cached fraggers.</p>
</dd></dl>
@@ -288,46 +304,50 @@ used when <cite>filename</cite> was saved.</p>
<dl class="function">
<dt id="promod3.modelling.GenerateDeNovoTrajectories">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">GenerateDeNovoTrajectories</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">num_trajectories=200</em>, <em class="sig-param">avg_sampling_per_position=600</em>, <em class="sig-param">profile=None</em>, <em class="sig-param">psipred_prediction=None</em>, <em class="sig-param">fragment_handler=None</em>, <em class="sig-param">scorer=None</em>, <em class="sig-param">scorer_env=None</em>, <em class="sig-param">scoring_weights=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GenerateDeNovoTrajectories" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">GenerateDeNovoTrajectories</code><span class="sig-paren">(</span><em>sequence</em>, <em>num_trajectories=200</em>, <em>avg_sampling_per_position=600</em>, <em>profile=None</em>, <em>psipred_prediction=None</em>, <em>fragment_handler=None</em>, <em>scorer=None</em>, <em>scorer_env=None</em>, <em>scoring_weights=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GenerateDeNovoTrajectories" title="Permalink to this definition">¶</a></dt>
<dd><p>Example de novo modelling pipeline based on Fragment sampling and
backbone scoring. Take this as a starting point for more advanced
de novo procedures.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence you want to sample</p></li>
-<li><p><strong>num_trajectories</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The number of sampling trajectories you
-want to generate</p></li>
-<li><p><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence you want to sample</li>
+<li><strong>num_trajectories</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The number of sampling trajectories you
+want to generate</li>
+<li><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
the total number is:
-len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></p></li>
-<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
-fragment search performance.</p></li>
-<li><p><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
-increases the fragment search performance</p></li>
-<li><p><strong>fragment_handler</strong> (<a class="reference internal" href="#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>) – You can provide already initialized fragments.
+len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></li>
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
+fragment search performance.</li>
+<li><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
+increases the fragment search performance</li>
+<li><strong>fragment_handler</strong> (<a class="reference internal" href="#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>) – You can provide already initialized fragments.
If you pass this parameter, <strong>profile</strong> and
<strong>psipred_prediction</strong> get neglected and do
not influence the fragment search, the
ones you initialized <strong>fragment_handler</strong> with
-get used instead.</p></li>
-<li><p><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.scoring.BackboneOverallScorer</span></code></a>) – Scorer doing the backbone scoring. If not provided, a
+get used instead.</li>
+<li><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.scoring.BackboneOverallScorer</span></code></a>) – Scorer doing the backbone scoring. If not provided, a
default one gets loaded with default objects with
following keys: clash, reduced, cb_packing, hbond, cbeta,
-torsion and pairwise</p></li>
-<li><p><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.scoring.BackboneScoreEnv</span></code></a>) – The scoring env that relates to <strong>scorer</strong>
-This environment will be changed!</p></li>
-<li><p><strong>scoring_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a>) – Linear weights for different scores. If not provided,
+torsion and pairwise</li>
+<li><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.scoring.BackboneScoreEnv</span></code></a>) – The scoring env that relates to <strong>scorer</strong>
+This environment will be changed!</li>
+<li><strong>scoring_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a>) – Linear weights for different scores. If not provided,
the output of ScoringWeights.GetWeights() is used.
Please note, that the weights must be consistent
-with the keys of the scores in <strong>scorer</strong></p></li>
+with the keys of the scores in <strong>scorer</strong></li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A <code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.LoopCandidates</span></code> object containing
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A <code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.LoopCandidates</span></code> object containing
<strong>num_trajectories</strong> elements for further processing</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -336,7 +356,7 @@ with the keys of the scores in <strong>scorer</strong></p></li>
<p>Distinct spatial arrangements of atoms or functional groups are key for protein
function. For their detection, ProMod3 implements the MotifFinder algorithm
which is based on geometric hashing as described by Nussinov and Wolfson
-<a class="reference internal" href="../references.html#nussinov1991" id="id1"><span>[nussinov1991]</span></a>. The algorithm consists of a learning stage, a detection stage
+<a class="reference internal" href="../references.html#nussinov1991" id="id1">[nussinov1991]</a>. The algorithm consists of a learning stage, a detection stage
and a refinement stage.</p>
<p>Learning Stage: A motif (query) is represented by a set of coordinates. Triplets
(p1, p2, p3) of coordinates are selected that define triangles. For each
@@ -445,78 +465,91 @@ iteration.</p>
</div>
<dl class="class">
<dt id="promod3.modelling.MotifQuery">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MotifQuery</code><span class="sig-paren">(</span><em class="sig-param">positions</em>, <em class="sig-param">identifier</em>, <em class="sig-param">min_triangle_edge_length</em>, <em class="sig-param">max_triangle_edge_length</em>, <em class="sig-param">bin_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>positions</em>, <em>identifier</em>, <em>min_triangle_edge_length</em>, <em>max_triangle_edge_length</em>, <em>bin_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MotifQuery</code><span class="sig-paren">(</span><em class="sig-param">positions</em>, <em class="sig-param">identifier</em>, <em class="sig-param">min_triangle_edge_length</em>, <em class="sig-param">max_triangle_edge_length</em>, <em class="sig-param">bin_size</em>, <em class="sig-param">flags</em><span class="sig-paren">)</span></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>positions</em>, <em>identifier</em>, <em>min_triangle_edge_length</em>, <em>max_triangle_edge_length</em>, <em>bin_size</em>, <em>flags</em><span class="sig-paren">)</span></dt>
<dt>
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MotifQuery</code><span class="sig-paren">(</span><em class="sig-param">query_list</em><span class="sig-paren">)</span></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>query_list</em><span class="sig-paren">)</span></dt>
<dd><p>A single query or a container of queries.
The constructor performs the learning stage of a single query or combines
several queries, so they can be searched at once.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>positions</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Coordinates of the query</p></li>
-<li><p><strong>identifier</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Descriptor of the query</p></li>
-<li><p><strong>min_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – To avoid the full O(n^3) hell, triangles
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>positions</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Coordinates of the query</li>
+<li><strong>identifier</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Descriptor of the query</li>
+<li><strong>min_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – To avoid the full O(n^3) hell, triangles
with any edge length below <em>min_triangle_edge_length</em>
-are skipped</p></li>
-<li><p><strong>max_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Same as <em>min_triangle_edge_length</em> but
-upper bound</p></li>
-<li><p><strong>bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Bin size in A, relevant to generate hash map keys</p></li>
-<li><p><strong>flags</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Flag in range [0,63] for every coordinate in <em>positions</em>.
+are skipped</li>
+<li><strong>max_triangle_edge_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Same as <em>min_triangle_edge_length</em> but
+upper bound</li>
+<li><strong>bin_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Bin size in A, relevant to generate hash map keys</li>
+<li><strong>flags</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Flag in range [0,63] for every coordinate in <em>positions</em>.
They’re also added to the hash map keys (default: 0).
This means that additionally to having a matching
relative position, the coordinates must also have a
matching flag in the detection/refinement stage.
If not provided (in the query and in the search),
-only coordinates matter.</p></li>
-<li><p><strong>query_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal notranslate"><span class="pre">MotifQuery</span></code></a>) – E pluribus unum</p></li>
+only coordinates matter.</li>
+<li><strong>query_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal notranslate"><span class="pre">MotifQuery</span></code></a>) – E pluribus unum</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.MotifQuery.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Save" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves the query down to disk</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – filename</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – filename</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.modelling.MotifQuery.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Load" title="Permalink to this definition">¶</a></dt>
<dd><p>Load query from disk</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – filename</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – filename</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.MotifQuery.GetPositions">
-<code class="sig-name descname">GetPositions</code><span class="sig-paren">(</span><em class="sig-param">query_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetPositions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetPositions</code><span class="sig-paren">(</span><em>query_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetPositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns coordinates of specified query</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>query_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Query from which you want the positions</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>query_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Query from which you want the positions</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.MotifQuery.GetIdentifiers">
-<code class="sig-name descname">GetIdentifiers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetIdentifiers" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetIdentifiers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetIdentifiers" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a list of all query identifiers.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.MotifQuery.GetN">
-<code class="sig-name descname">GetN</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetN" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetN</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetN" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the number of queries</p>
</dd></dl>
@@ -524,23 +557,23 @@ only coordinates matter.</p></li>
<dl class="class">
<dt id="promod3.modelling.MotifMatch">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MotifMatch</code><a class="headerlink" href="#promod3.modelling.MotifMatch" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifMatch</code><a class="headerlink" href="#promod3.modelling.MotifMatch" title="Permalink to this definition">¶</a></dt>
<dd><p>Object that holds information about a match found in <a class="reference internal" href="#promod3.modelling.FindMotifs" title="promod3.modelling.FindMotifs"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FindMotifs()</span></code></a></p>
<dl class="attribute">
<dt id="promod3.modelling.MotifMatch.query_idx">
-<code class="sig-name descname">query_idx</code><a class="headerlink" href="#promod3.modelling.MotifMatch.query_idx" title="Permalink to this definition">¶</a></dt>
+<code class="descname">query_idx</code><a class="headerlink" href="#promod3.modelling.MotifMatch.query_idx" title="Permalink to this definition">¶</a></dt>
<dd><p>Index of matching query</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.MotifMatch.mat">
-<code class="sig-name descname">mat</code><a class="headerlink" href="#promod3.modelling.MotifMatch.mat" title="Permalink to this definition">¶</a></dt>
+<code class="descname">mat</code><a class="headerlink" href="#promod3.modelling.MotifMatch.mat" title="Permalink to this definition">¶</a></dt>
<dd><p>Transformation matrix to superpose matching query onto target</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.MotifMatch.alignment">
-<code class="sig-name descname">alignment</code><a class="headerlink" href="#promod3.modelling.MotifMatch.alignment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">alignment</code><a class="headerlink" href="#promod3.modelling.MotifMatch.alignment" title="Permalink to this definition">¶</a></dt>
<dd><p>List of tuples which define matching pairs of query/target coordinates</p>
</dd></dl>
@@ -548,30 +581,34 @@ only coordinates matter.</p></li>
<dl class="method">
<dt id="promod3.modelling.FindMotifs">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FindMotifs</code><span class="sig-paren">(</span><em class="sig-param">query</em>, <em class="sig-param">target_positions</em>, <em class="sig-param">hash_tresh=0.4</em>, <em class="sig-param">distance_thresh=1.0</em>, <em class="sig-param">refine_thresh=0.7</em>, <em class="sig-param">flags=list()</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FindMotifs" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">FindMotifs</code><span class="sig-paren">(</span><em>query</em>, <em>target_positions</em>, <em>hash_tresh=0.4</em>, <em>distance_thresh=1.0</em>, <em>refine_thresh=0.7</em>, <em>flags=list()</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FindMotifs" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs the detection and refinement stages of the geometric hashing
algorithm.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>query</strong> – Query to be searched</p></li>
-<li><p><strong>target_positions</strong> – Coordinates of the target</p></li>
-<li><p><strong>hash_thresh</strong> – Parameter relevant for detection stage</p></li>
-<li><p><strong>distance_thresh</strong> – Parameter relevant for refinement stage</p></li>
-<li><p><strong>refine_thresh</strong> – Parameter relevant for refinement stage</p></li>
-<li><p><strong>flags</strong> – Equivalent to <em>flags</em> in <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal notranslate"><span class="pre">MotifQuery</span></code></a>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>query</strong> – Query to be searched</li>
+<li><strong>target_positions</strong> – Coordinates of the target</li>
+<li><strong>hash_thresh</strong> – Parameter relevant for detection stage</li>
+<li><strong>distance_thresh</strong> – Parameter relevant for refinement stage</li>
+<li><strong>refine_thresh</strong> – Parameter relevant for refinement stage</li>
+<li><strong>flags</strong> – Equivalent to <em>flags</em> in <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal notranslate"><span class="pre">MotifQuery</span></code></a>
constructor. If you didn’t provide anything there,
this can be ignored. Only the actual coordinates
-matter in this case.</p></li>
+matter in this case.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>All found matches</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.MotifMatch" title="promod3.modelling.MotifMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">MotifMatch</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">All found matches</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.MotifMatch" title="promod3.modelling.MotifMatch"><code class="xref py py-class docutils literal notranslate"><span class="pre">MotifMatch</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -579,7 +616,6 @@ matter in this case.</p></li>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -600,12 +636,12 @@ matter in this case.</p></li>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -622,42 +658,36 @@ matter in this case.</p></li>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="sidechain_reconstruction.html" title="previous chapter">Sidechain Reconstruction</a></li>
- <li>Next: <a href="../sidechain/index.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+ <li>Next: <a href="../sidechain/index.html" title="next chapter"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
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-
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-
</div>
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</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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<a href="../_sources/modelling/algorithms.rst.txt"
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index bb636cf987354b08e0b3e1e1aefcceb68d1a73cb..33480a71923b4579ff5e5d80d23a55595592cbc6 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Handling Gaps — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Handling Gaps — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="handling-gaps">
@@ -41,210 +40,236 @@ classes / functions are used within the modelling pipeline.</p>
<h2>Gap classes<a class="headerlink" href="#gap-classes" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.modelling.StructuralGap">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">StructuralGap</code><span class="sig-paren">(</span><em class="sig-param">before</em>, <em class="sig-param">after</em>, <em class="sig-param">seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">StructuralGap</code><span class="sig-paren">(</span><em>before</em>, <em>after</em>, <em>seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap" title="Permalink to this definition">¶</a></dt>
<dd><p>Describes a structural gap, i.e. a loop to be modeled. The gap may either be
terminal or between two defined regions. The gap stores information of the
last residue before and the first residue after the gap as well as the
sequence of gap. Gaps at the N- and C-terminals can be defined by passing
invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a></p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></p></li>
-<li><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seq</span></code></a></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a></li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></li>
+<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seq</span></code></a></li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if both residues are invalid or when both
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first">A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if both residues are invalid or when both
are valid and:</p>
-<ul class="simple">
-<li><p>residues are from different chains (if both valid)</p></li>
-<li><p><cite>before</cite> is located after <cite>after</cite></p></li>
-<li><p><cite>seq</cite> has a length which is inconsistent with the gap</p></li>
+<ul class="last simple">
+<li>residues are from different chains (if both valid)</li>
+<li><cite>before</cite> is located after <cite>after</cite></li>
+<li><cite>seq</cite> has a length which is inconsistent with the gap</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.GetChainIndex">
-<code class="sig-name descname">GetChainIndex</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChainIndex" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Index of chain, the gap is belonging to</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetChainIndex</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChainIndex" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Index of chain, the gap is belonging to</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.GetChainName">
-<code class="sig-name descname">GetChainName</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChainName" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Name of chain, the gap is belonging to</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetChainName</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChainName" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Name of chain, the gap is belonging to</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.GetChain">
-<code class="sig-name descname">GetChain</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChain" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Chain, the gap is belonging to</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetChain</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetChain" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Chain, the gap is belonging to</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.IsNTerminal">
-<code class="sig-name descname">IsNTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsNTerminal" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, iff gap is N-terminal (i.e. <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a> is invalid
-and <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a> is valid)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">IsNTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsNTerminal" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff gap is N-terminal (i.e. <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a> is invalid
+and <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a> is valid)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.IsCTerminal">
-<code class="sig-name descname">IsCTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsCTerminal" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, iff gap is C-terminal (i.e. <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a> is valid
-and <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a> is invalid)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">IsCTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsCTerminal" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff gap is C-terminal (i.e. <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a> is valid
+and <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a> is invalid)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.IsTerminal">
-<code class="sig-name descname">IsTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsTerminal" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, iff gap is N- or C-terminal</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">IsTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.IsTerminal" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff gap is N- or C-terminal</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.ShiftCTerminal">
-<code class="sig-name descname">ShiftCTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ShiftCTerminal" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ShiftCTerminal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ShiftCTerminal" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to shift gap by one position towards C-terminal. Only possible if new
gap is not terminal and it doesn’t try to shift the gap past another gap.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, iff shift succeeded (gap is only updated in that case)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff shift succeeded (gap is only updated in that case)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.ExtendAtNTerm">
-<code class="sig-name descname">ExtendAtNTerm</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ExtendAtNTerm" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ExtendAtNTerm</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ExtendAtNTerm" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to extend gap at N-terminal end of gap.
Only possible if the gap is not at N-terminal and it doesn’t try to
extend the gap past another gap.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, iff extend succeeded (gap is only updated in that case)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff extend succeeded (gap is only updated in that case)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.ExtendAtCTerm">
-<code class="sig-name descname">ExtendAtCTerm</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ExtendAtCTerm" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ExtendAtCTerm</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.ExtendAtCTerm" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to extend gap at C-terminal end of gap.
Only possible if the gap is not at C-terminal and it doesn’t try to
extend the gap past another gap.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, iff extend succeeded (gap is only updated in that case)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, iff extend succeeded (gap is only updated in that case)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.GetLength">
-<code class="sig-name descname">GetLength</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetLength" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Length of the gap.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetLength</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.GetLength" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Length of the gap.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.StructuralGap.Copy">
-<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.Copy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Copy of the gap.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.StructuralGap.Copy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Copy of the gap.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.length">
-<code class="sig-name descname">length</code><a class="headerlink" href="#promod3.modelling.StructuralGap.length" title="Permalink to this definition">¶</a></dt>
+<code class="descname">length</code><a class="headerlink" href="#promod3.modelling.StructuralGap.length" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for <a class="reference internal" href="#promod3.modelling.StructuralGap.GetLength" title="promod3.modelling.StructuralGap.GetLength"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetLength()</span></code></a> (read-only, <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.seq">
-<code class="sig-name descname">seq</code><a class="headerlink" href="#promod3.modelling.StructuralGap.seq" title="Permalink to this definition">¶</a></dt>
+<code class="descname">seq</code><a class="headerlink" href="#promod3.modelling.StructuralGap.seq" title="Permalink to this definition">¶</a></dt>
<dd><p>Sequence string for the gap (read-only, <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.before">
-<code class="sig-name descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
+<code class="descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.after">
-<code class="sig-name descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
+<code class="descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.full_seq">
-<code class="sig-name descname">full_seq</code><a class="headerlink" href="#promod3.modelling.StructuralGap.full_seq" title="Permalink to this definition">¶</a></dt>
+<code class="descname">full_seq</code><a class="headerlink" href="#promod3.modelling.StructuralGap.full_seq" title="Permalink to this definition">¶</a></dt>
<dd><p>Full sequence, including stem residues (read-only)</p>
</dd></dl>
@@ -252,7 +277,7 @@ extend the gap past another gap.</p>
<dl class="class">
<dt id="promod3.modelling.StructuralGapList">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">StructuralGapList</code><a class="headerlink" href="#promod3.modelling.StructuralGapList" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">StructuralGapList</code><a class="headerlink" href="#promod3.modelling.StructuralGapList" title="Permalink to this definition">¶</a></dt>
<dd><p>Represents a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>.</p>
</dd></dl>
@@ -264,7 +289,7 @@ Extend() function to propose new gaps for loop modelling. The function returns
False if no new extension possible.</p>
<dl class="class">
<dt id="promod3.modelling.GapExtender">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">GapExtender</code><span class="sig-paren">(</span><em class="sig-param">gap</em>, <em class="sig-param">seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GapExtender" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">GapExtender</code><span class="sig-paren">(</span><em>gap</em>, <em>seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GapExtender" title="Permalink to this definition">¶</a></dt>
<dd><p>The extender cycles through the following steps:</p>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span> -
--
@@ -278,150 +303,174 @@ False if no new extension possible.</p>
----
</pre></div>
</div>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>An exception if a terminal gap is used to construct this.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">An exception if a terminal gap is used to construct this.</p>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.GapExtender.Extend">
-<code class="sig-name descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GapExtender.Extend" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GapExtender.Extend" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to extend <em>gap</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>False, if the <em>gap</em> cannot be extended any further. This happens
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">False, if the <em>gap</em> cannot be extended any further. This happens
if it reaches a terminal or another insertion gap.
Otherwise, the <em>gap</em> passed to the constructor is changed.
The gaps are extended with ascending length and will always have
-valid termini.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+valid termini.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.FullGapExtender">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FullGapExtender</code><span class="sig-paren">(</span><em class="sig-param">gap</em>, <em class="sig-param">seqres</em>, <em class="sig-param">max_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FullGapExtender" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">FullGapExtender</code><span class="sig-paren">(</span><em>gap</em>, <em>seqres</em>, <em>max_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FullGapExtender" title="Permalink to this definition">¶</a></dt>
<dd><p>Cycles as GapExtender, but continues even if another gap was encountered.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
-<li><p><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
-<li><p>If -1, all possible non-terminal gaps are returned.</p></li>
-<li><p>If >= 0, this restricts the max. gap-length
-(w/o termini) producable by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
+<li>If -1, all possible non-terminal gaps are returned.</li>
+<li>If >= 0, this restricts the max. gap-length
+(w/o termini) producable by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
</ul>
-</p></li>
+</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>An exception if a terminal gap is used to construct this.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">An exception if a terminal gap is used to construct this.</p>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.FullGapExtender.Extend">
-<code class="sig-name descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FullGapExtender.Extend" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FullGapExtender.Extend" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to extend <em>gap</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>False, if the <em>gap</em> cannot be extended without exceeding <em>max_length</em>.
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">False, if the <em>gap</em> cannot be extended without exceeding <em>max_length</em>.
Otherwise, the <em>gap</em> passed to the constructor is changed.
The gaps are extended with ascending length and will always have
-valid termini.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+valid termini.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.ScoringGapExtender">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ScoringGapExtender</code><span class="sig-paren">(</span><em class="sig-param">gap</em>, <em class="sig-param">extension_penalty</em>, <em class="sig-param">penalties</em>, <em class="sig-param">seqres</em>, <em class="sig-param">max_length=-2</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringGapExtender" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ScoringGapExtender</code><span class="sig-paren">(</span><em>gap</em>, <em>extension_penalty</em>, <em>penalties</em>, <em>seqres</em>, <em>max_length=-2</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringGapExtender" title="Permalink to this definition">¶</a></dt>
<dd><p>The extender scores possible gap extensions and returns them in order of
their score when <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a> is called.
The score is penalized according to length and according to certain (well
conserved) regions in the structure as defined by <em>penalties</em>.
score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalties</cite> [i] )
(i = resnum - 1 of residues in extension)</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
-<li><p><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for length of gap.</p></li>
-<li><p><strong>penalties</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for each residue added to gap.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
-<li><p><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
-<li><p>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a>
-(i.e. it stops at gaps and termini).</p></li>
-<li><p>If -1, all possible non-terminal gaps are returned.</p></li>
-<li><p>If >= 0, this restricts the max. gap-length (w/o termini)
-producable by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
+<li><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for length of gap.</li>
+<li><strong>penalties</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for each residue added to gap.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
+<li>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a>
+(i.e. it stops at gaps and termini).</li>
+<li>If -1, all possible non-terminal gaps are returned.</li>
+<li>If >= 0, this restricts the max. gap-length (w/o termini)
+producable by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</li>
</ul>
-</p></li>
+</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>An exception if a terminal gap is used to construct this.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">An exception if a terminal gap is used to construct this.</p>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.ScoringGapExtender.Extend">
-<code class="sig-name descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringGapExtender.Extend" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringGapExtender.Extend" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to extend <em>gap</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>False, if the gap cannot be extended any further.
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">False, if the gap cannot be extended any further.
Otherwise, <em>gap</em> is changed and returned in ascending score.
-The updated <em>gap</em> will always have valid termini.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+The updated <em>gap</em> will always have valid termini.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.ShiftExtension">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ShiftExtension</code><span class="sig-paren">(</span><em class="sig-param">n_num</em>, <em class="sig-param">c_num</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ShiftExtension" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ShiftExtension</code><span class="sig-paren">(</span><em>n_num</em>, <em>c_num</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ShiftExtension" title="Permalink to this definition">¶</a></dt>
<dd><p>Implements the underlying extension scheme of the <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
It is not associated to any structural data, it just spits out the
residue numbers according to the extension scheme described above.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_num</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – N residue number to start with</p></li>
-<li><p><strong>c_num</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – C residue number to start with</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_num</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – N residue number to start with</li>
+<li><strong>c_num</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – C residue number to start with</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.ShiftExtension.Extend">
-<code class="sig-name descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ShiftExtension.Extend" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The next residue numbers for n_stem and c_stem</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">Extend</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ShiftExtension.Extend" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The next residue numbers for n_stem and c_stem</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -431,98 +480,114 @@ residue numbers according to the extension scheme described above.</p>
<h2>Gap Handling Functions<a class="headerlink" href="#gap-handling-functions" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.CountEnclosedGaps">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CountEnclosedGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CountEnclosedGaps" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">CountEnclosedGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CountEnclosedGaps" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.CountEnclosedInsertions">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CountEnclosedInsertions</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CountEnclosedInsertions" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">CountEnclosedInsertions</code><span class="sig-paren">(</span><em>mhandle</em>, <em>gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CountEnclosedInsertions" title="Permalink to this definition">¶</a></dt>
<dd><p>Counts all gaps from <cite>mhandle</cite> which are fully enclosed by given <cite>gap</cite>.
This is either all gaps or only insertions.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – Gap defining range in which gaps are to be removed.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – Gap defining range in which gaps are to be removed.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Number of gaps.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Number of gaps.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.ClearGaps">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ClearGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ClearGaps" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">ClearGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ClearGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes all gaps from <cite>mhandle</cite> which are fully enclosed by given <cite>gap</cite>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – Gap defining range in which gaps are to be removed.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – Gap defining range in which gaps are to be removed.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Index of next gap in mhandle.gaps after removal.
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Index of next gap in mhandle.gaps after removal.
Returns -1 if last gap was removed or no gaps in <em>mhandle</em>.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if any gap in mhandle.gaps is only partially
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if any gap in mhandle.gaps is only partially
enclosed by given gap.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.InsertLoopClearGaps">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">InsertLoopClearGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">bb_list</em>, <em class="sig-param">gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.InsertLoopClearGaps" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">InsertLoopClearGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>bb_list</em>, <em>gap</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.InsertLoopClearGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Insert loop into model, update scoring environments and remove all gaps from
<em>mhandle</em> which are fully enclosed by given <em>gap</em> (see <a class="reference internal" href="pipeline.html#promod3.modelling.InsertLoop" title="promod3.modelling.InsertLoop"><code class="xref py py-meth docutils literal notranslate"><span class="pre">InsertLoop()</span></code></a> and
<a class="reference internal" href="#promod3.modelling.ClearGaps" title="promod3.modelling.ClearGaps"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ClearGaps()</span></code></a>).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to insert (backbone only).</p></li>
-<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – Gap defining range of loop to insert (must be consistent!).</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to insert (backbone only).</li>
+<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – Gap defining range of loop to insert (must be consistent!).</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Index of next gap in mhandle.gaps after removal.
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Index of next gap in mhandle.gaps after removal.
Returns -1 if last gap was removed or no gaps in <em>mhandle</em>.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if <em>bb_list</em> and <em>gap</em> are inconsistent or
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if <em>bb_list</em> and <em>gap</em> are inconsistent or
if any gap in mhandle.gaps is only partially enclosed by <em>gap</em>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.MergeGaps">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MergeGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeGaps" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">MergeGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Merges two gaps <cite>mhandle.gaps[index]</cite> and <cite>mhandle.gaps[index+1]</cite>.
The residues in between the gaps are removed from <cite>mhandle.model</cite> and added
to the new <cite>mhandle.gaps[index]</cite>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of gap to merge with next one.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of gap to merge with next one.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if indices out of range or if trying to merge
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> if indices out of range or if trying to merge
gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -530,7 +595,6 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -551,12 +615,12 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -573,7 +637,7 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="model_checking.html" title="previous chapter">Model Checking</a></li>
<li>Next: <a href="loop_candidates.html" title="next chapter">Handling Loop Candidates</a></li>
</ul></li>
@@ -582,33 +646,27 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
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-
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</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/gap_handling.rst.txt"
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index de2b0d1641736d17426af9034b2dddd4c67b6072..72df0c020ef76b044551de040d7a72cfdd0944e8 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>modelling - Protein Modelling — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>modelling - Protein Modelling — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="module-promod3.modelling">
@@ -115,7 +114,6 @@ a model fully automatically as follows:</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -136,12 +134,12 @@ a model fully automatically as follows:</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -165,33 +163,27 @@ a model fully automatically as follows:</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/index.rst.txt"
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index 89ab41a29956cbc4a906d61a083d476712b298cf..a04ae292b2ed52770a63c7d47eed174fbcce7f13 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Handling Loop Candidates — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Handling Loop Candidates — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="handling-loop-candidates">
@@ -100,117 +99,130 @@ algorithms on all loop candidates. Example:</p>
<h2>The LoopCandidates class<a class="headerlink" href="#the-loopcandidates-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.modelling.LoopCandidates">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">LoopCandidates</code><span class="sig-paren">(</span><em class="sig-param">seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">LoopCandidates</code><span class="sig-paren">(</span><em>seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates" title="Permalink to this definition">¶</a></dt>
<dd><p>Initializes an empty container of loop candidates.</p>
<p>Candidates can be accessed and iterated as if it was a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence being enforced for all candidates</p>
-</dd>
-</dl>
-<dl class="method">
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence being enforced for all candidates</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.modelling.LoopCandidates.FillFromDatabase">
-<em class="property">static </em><code class="sig-name descname">FillFromDatabase</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">seq</em>, <em class="sig-param">frag_db</em>, <em class="sig-param">structural_db</em>, <em class="sig-param">extended_search=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">FillFromDatabase</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>seq</em>, <em>frag_db</em>, <em>structural_db</em>, <em>extended_search=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="Permalink to this definition">¶</a></dt>
<dd><p>Searches for loop candidates matching the length (number of residues in
<em>seq</em>) and geometry (of <em>n_stem</em> and <em>c_stem</em>) of the loop to be modelled in
a fragment database.</p>
<p>This call also adds fragment infos (<a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal notranslate"><span class="pre">HasFragmentInfos()</span></code></a> will be True).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</p></li>
-<li><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
-<em>n_stem</em> and <em>c_stem</em></p></li>
-<li><p><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – The fragment database</p></li>
-<li><p><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – The according structural database</p></li>
-<li><p><strong>extended_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether search should be extended to fragments
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
+<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
+<em>n_stem</em> and <em>c_stem</em></li>
+<li><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – The fragment database</li>
+<li><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – The according structural database</li>
+<li><strong>extended_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether search should be extended to fragments
matching the geometry of the <em>n_stem</em> and <em>c_stem</em>
-a bit less precisely.</p></li>
+a bit less precisely.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A list of loop candidates</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if stems do no contain N, CA and C
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A list of loop candidates</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if stems do no contain N, CA and C
atoms.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler">
-<em class="property">static </em><code class="sig-name descname">FillFromMonteCarloSampler</code><span class="sig-paren">(</span><em class="sig-param">seq</em>, <em class="sig-param">num_loops</em>, <em class="sig-param">steps</em>, <em class="sig-param">sampler</em>, <em class="sig-param">closer</em>, <em class="sig-param">scorer</em>, <em class="sig-param">cooler</em>, <em class="sig-param">random_seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">FillFromMonteCarloSampler</code><span class="sig-paren">(</span><em>seq</em>, <em>num_loops</em>, <em>steps</em>, <em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>random_seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="Permalink to this definition">¶</a></dt>
<dt>
-<em class="property">static </em><code class="sig-name descname">FillFromMonteCarloSampler</code><span class="sig-paren">(</span><em class="sig-param">initial_bb</em>, <em class="sig-param">seq</em>, <em class="sig-param">num_loops</em>, <em class="sig-param">steps</em>, <em class="sig-param">sampler</em>, <em class="sig-param">closer</em>, <em class="sig-param">scorer</em>, <em class="sig-param">cooler</em>, <em class="sig-param">random_seed=0</em><span class="sig-paren">)</span></dt>
+<em class="property">static </em><code class="descname">FillFromMonteCarloSampler</code><span class="sig-paren">(</span><em>initial_bb</em>, <em>seq</em>, <em>num_loops</em>, <em>steps</em>, <em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>random_seed=0</em><span class="sig-paren">)</span></dt>
<dd><p>Uses Monte Carlo simulated annealing to sample the loop to be modelled.
If <em>initial_bb</em> is given, every Monte Carlo run starts from that configuration.</p>
<div class="admonition warning">
-<p class="admonition-title">Warning</p>
-<p>The <a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>
+<p class="first admonition-title">Warning</p>
+<p class="last">The <a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>
attached to <em>scorer</em> will be altered in the specified stretch.
You might consider the Stash / Pop mechanism of the
<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> to restore to the
original state once the sampling is done.</p>
</div>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>initial_bb</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Initial configuration used for the sampling</p></li>
-<li><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence of residues to be sampled</p></li>
-<li><p><strong>num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of loop candidates to return</p></li>
-<li><p><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
-generated</p></li>
-<li><p><strong>sampler</strong> (<a class="reference internal" href="monte_carlo.html#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) – Used to generate a new configuration at each MC step</p></li>
-<li><p><strong>closer</strong> (<a class="reference internal" href="monte_carlo.html#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Used to close the loop after each MC step</p></li>
-<li><p><strong>scorer</strong> (<a class="reference internal" href="monte_carlo.html#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Used to score the generated configurations at each MC step</p></li>
-<li><p><strong>cooler</strong> (<a class="reference internal" href="monte_carlo.html#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Controls the temperature profile of the simulated annealing</p></li>
-<li><p><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed to feed the random number generator for
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>initial_bb</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Initial configuration used for the sampling</li>
+<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence of residues to be sampled</li>
+<li><strong>num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of loop candidates to return</li>
+<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
+generated</li>
+<li><strong>sampler</strong> (<a class="reference internal" href="monte_carlo.html#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) – Used to generate a new configuration at each MC step</li>
+<li><strong>closer</strong> (<a class="reference internal" href="monte_carlo.html#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Used to close the loop after each MC step</li>
+<li><strong>scorer</strong> (<a class="reference internal" href="monte_carlo.html#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Used to score the generated configurations at each MC step</li>
+<li><strong>cooler</strong> (<a class="reference internal" href="monte_carlo.html#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Controls the temperature profile of the simulated annealing</li>
+<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed to feed the random number generator for
accepting/rejecting proposed monte carlo steps.
For every monte carlo run, the random number generator
-gets refreshed and this seed gets increased by 1.</p></li>
+gets refreshed and this seed gets increased by 1.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The resulting candidates</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code>, if <em>initial_bb</em> is not given and
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The resulting candidates</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code>, if <em>initial_bb</em> is not given and
the Monte Carlo sampler failed to initialize (i.e. stems are too
far apart) or if <em>initial_bb</em> is given and it is inconsistent with
<em>seq</em>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.GetSequence">
-<code class="sig-name descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetSequence" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The Sequence</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetSequence</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetSequence" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Sequence</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.ApplyCCD">
-<code class="sig-name descname">ApplyCCD</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">max_iterations=1000</em>, <em class="sig-param">rmsd_cutoff=0.1</em>, <em class="sig-param">keep_non_converged=false</em>, <em class="sig-param">random_seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.ApplyCCD" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplyCCD</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>max_iterations=1000</em>, <em>rmsd_cutoff=0.1</em>, <em>keep_non_converged=false</em>, <em>random_seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.ApplyCCD" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">ApplyCCD</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">max_iterations=1000</em>, <em class="sig-param">rmsd_cutoff=0.1</em>, <em class="sig-param">keep_non_converged=false</em>, <em class="sig-param">random_seed=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">ApplyCCD</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>torsion_sampler</em>, <em>max_iterations=1000</em>, <em>rmsd_cutoff=0.1</em>, <em>keep_non_converged=false</em>, <em>random_seed=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="sig-name descname">ApplyCCD</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">torsion_samplers</em>, <em class="sig-param">max_iterations=1000</em>, <em class="sig-param">rmsd_cutoff=0.1</em>, <em class="sig-param">keep_non_converged=false</em>, <em class="sig-param">random_seed=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">ApplyCCD</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>torsion_samplers</em>, <em>max_iterations=1000</em>, <em>rmsd_cutoff=0.1</em>, <em>keep_non_converged=false</em>, <em>random_seed=0</em><span class="sig-paren">)</span></dt>
<dd><p>Closes all loop candidates in this container using the CCD algorithm (i.e.
modifies the candidates so that its stem residues match those of <em>n_stem</em>
and <em>c_stem</em>). CCD (cyclic coordinate descent, see <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD" title="promod3.modelling.CCD"><code class="xref py py-class docutils literal notranslate"><span class="pre">CCD</span></code></a>) is an
@@ -218,39 +230,43 @@ iterative minimization algorithm.</p>
<p>If <em>torsion_sampler</em> is given, it is used at each step of the closing to
calculate the probability of the proposed move, which is then accepted or
not depending on a metropolis criterium.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
-should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
-should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A torsion sampler (used for all residues) or a list
-of samplers (one per residue).</p></li>
-<li><p><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximum number of iterations</p></li>
-<li><p><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff in stem residue RMSD used to determine
-convergence</p></li>
-<li><p><strong>keep_non_converged</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to keep loop candidates for which the
-closing did not converge</p></li>
-<li><p><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – seed for random number generator used to
-accept/reject moves in CCD algorithm</p></li>
+of samplers (one per residue).</li>
+<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximum number of iterations</li>
+<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff in stem residue RMSD used to determine
+convergence</li>
+<li><strong>keep_non_converged</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to keep loop candidates for which the
+closing did not converge</li>
+<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – seed for random number generator used to
+accept/reject moves in CCD algorithm</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>An index for each kept candidate corresponding to the candidate
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">An index for each kept candidate corresponding to the candidate
index before this function was called. This is useful to keep track
of scores and other data extracted before.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.ApplyKIC">
-<code class="sig-name descname">ApplyKIC</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">pivot_one</em>, <em class="sig-param">pivot_two</em>, <em class="sig-param">pivot_three</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.ApplyKIC" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplyKIC</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>pivot_one</em>, <em>pivot_two</em>, <em>pivot_three</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.ApplyKIC" title="Permalink to this definition">¶</a></dt>
<dd><p>Closes all loop candidates in this container (i.e. modifies the candidates
so that its stem residues match those of <em>n_stem</em> and <em>c_stem</em>, which are
the stem residues of the loop being modelled), using the KIC algorithm. This
@@ -258,77 +274,85 @@ algorithm finds analytical solutions for closing the loop by modifying the
torsion angles of just three pivot residues. Due to the underlying
mathematical formalism in KIC, up to 16 solutions can be found for every
candidate. This leads to an increase in number of loops.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
-should match</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
-should match</p></li>
-<li><p><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First pivot residue</p></li>
-<li><p><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Second pivot residue</p></li>
-<li><p><strong>pivot_three</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Third pivot residue</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+should match</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+should match</li>
+<li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First pivot residue</li>
+<li><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Second pivot residue</li>
+<li><strong>pivot_three</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Third pivot residue</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>An index for each added candidate corresponding to the original
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">An index for each added candidate corresponding to the original
candidate index before this function was called (each candidate can
lead to multiple or no candidates after KIC is applied). This is
useful to keep track of scores and other data extracted before.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.CalculateBackboneScores">
-<code class="sig-name descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">scorer</em>, <em class="sig-param">scorer_env</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateBackboneScores" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>scorer</em>, <em>scorer_env</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateBackboneScores" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">scorer</em>, <em class="sig-param">scorer_env</em>, <em class="sig-param">keys</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>scorer</em>, <em>scorer_env</em>, <em>keys</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="sig-name descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">mhandle</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="sig-name descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">mhandle</em>, <em class="sig-param">keys</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>keys</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
<dt id="promod3.modelling.LoopCandidates.CalculateAllAtomScores">
-<code class="sig-name descname">CalculateAllAtomScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">mhandle</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateAllAtomScores" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateAllAtomScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateAllAtomScores" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">CalculateAllAtomScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">mhandle</em>, <em class="sig-param">keys</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">CalculateAllAtomScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>keys</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
<dd><p>Calculate backbone / all-atom scores for each loop candidate.
Note that (unless otherwise noted) a lower “score” is better!</p>
<p>The computed scores are in the same same order as the candidates in here.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the given
-key names (or the ones from <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a>)</p></li>
-<li><p><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a>) – Backbone scoring object with set environment for the
-particular loop modelling problem.</p></li>
-<li><p><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – The scoring environment attached to <em>scorer</em></p></li>
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle set up scoring (see
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the given
+key names (or the ones from <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a>)</li>
+<li><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a>) – Backbone scoring object with set environment for the
+particular loop modelling problem.</li>
+<li><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – The scoring environment attached to <em>scorer</em></li>
+<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle set up scoring (see
<a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultBackboneScoring()</span></code></a>
-<a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>).</p></li>
-<li><p><strong>keys</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Keys of the desired scorers. If not given, we use the set of
+<a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>).</li>
+<li><strong>keys</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Keys of the desired scorers. If not given, we use the set of
keys given by <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetBackboneScoringKeys" title="promod3.modelling.ScoringWeights.GetBackboneScoringKeys"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ScoringWeights.GetBackboneScoringKeys()</span></code></a> /
-<a class="reference internal" href="#promod3.modelling.ScoringWeights.GetAllAtomScoringKeys" title="promod3.modelling.ScoringWeights.GetAllAtomScoringKeys"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ScoringWeights.GetAllAtomScoringKeys()</span></code></a>.</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES.</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loops belong to.</p></li>
+<a class="reference internal" href="#promod3.modelling.ScoringWeights.GetAllAtomScoringKeys" title="promod3.modelling.ScoringWeights.GetAllAtomScoringKeys"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ScoringWeights.GetAllAtomScoringKeys()</span></code></a>.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loops belong to.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="pipeline.html#promod3.modelling.IsAllAtomScoringSetUp" title="promod3.modelling.IsAllAtomScoringSetUp"><code class="xref py py-func docutils literal notranslate"><span class="pre">IsAllAtomScoringSetUp()</span></code></a>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="pipeline.html#promod3.modelling.IsAllAtomScoringSetUp" title="promod3.modelling.IsAllAtomScoringSetUp"><code class="xref py py-func docutils literal notranslate"><span class="pre">IsAllAtomScoringSetUp()</span></code></a>
is False, if <em>keys</em> has a key for which no scorer exists or if
anything is raised when calculating the scores.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.CalculateSequenceProfileScores">
-<code class="sig-name descname">CalculateSequenceProfileScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">structure_db</em>, <em class="sig-param">prof</em>, <em class="sig-param">offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateSequenceProfileScores" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateSequenceProfileScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateSequenceProfileScores" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.LoopCandidates.CalculateStructureProfileScores">
-<code class="sig-name descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">structure_db</em>, <em class="sig-param">prof</em>, <em class="sig-param">offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a score comparing the given profile <em>prof</em> starting at <em>offset</em>
with the sequence / structure profile of each candidate as extracted from
<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
@@ -339,28 +363,32 @@ combining this to other scores, where it is commonly the other way around.</p>
given <em>structure_db</em> (e.g. <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a> must have been called
with this DB).</p>
<p>The computed scores are in the same same order as the candidates in here.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
-key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></p></li>
-<li><p><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a></p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</p></li>
-<li><p><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
+key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></li>
+<li><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a></li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
+<li><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal notranslate"><span class="pre">HasFragmentInfos()</span></code></a> is
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal notranslate"><span class="pre">HasFragmentInfos()</span></code></a> is
False, if <em>structure_db</em> is incompatible with the stored fragment
infos or if <em>prof</em> has less than <em>offset+len</em> elements (len =
length of loops stored in here).</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.CalculateStemRMSDs">
-<code class="sig-name descname">CalculateStemRMSDs</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStemRMSDs" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateStemRMSDs</code><span class="sig-paren">(</span><em>score_container</em>, <em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStemRMSDs" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates RMSD between the given stems and the first and last residue of
the loop candidates. This first superposes the first loop residue with
<em>n_stem</em> and then computes the RMSD between the last residue’s N, CA, C
@@ -368,208 +396,235 @@ positions and the corresponding atoms in <em>c_stem</em>.</p>
<p>Note that this score is only useful before calling <a class="reference internal" href="#promod3.modelling.LoopCandidates.ApplyCCD" title="promod3.modelling.LoopCandidates.ApplyCCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ApplyCCD()</span></code></a> or
<a class="reference internal" href="#promod3.modelling.LoopCandidates.ApplyKIC" title="promod3.modelling.LoopCandidates.ApplyKIC"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ApplyKIC()</span></code></a>.</p>
<p>The computed scores are in the same same order as the candidates in here.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
-key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></p></li>
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
+key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if stems do no contain N, CA and C
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if stems do no contain N, CA and C
atoms.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">CalculateSequenceProfileScores</code><span class="sig-paren">(</span><em class="sig-param">structure_db</em>, <em class="sig-param">prof</em>, <em class="sig-param">offset=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">CalculateSequenceProfileScores</code><span class="sig-paren">(</span><em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="sig-name descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em class="sig-param">structure_db</em>, <em class="sig-param">prof</em>, <em class="sig-param">offset=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="sig-name descname">CalculateStemRMSDs</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em><span class="sig-paren">)</span></dt>
+<code class="descname">CalculateStemRMSDs</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span></dt>
<dd><p>Same as the <em>score_container</em> variant above, but here we directly return the
score vector instead of storing it in a container.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Score for each candidate (same order as candidates in here).</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Score for each candidate (same order as candidates in here).</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.Add">
-<code class="sig-name descname">Add</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Add" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The loop candidate to be added.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if sequence of <em>bb_list</em> is not
-consistent with internal sequence</p>
-</dd>
-</dl>
+<code class="descname">Add</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Add" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The loop candidate to be added.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if sequence of <em>bb_list</em> is not
+consistent with internal sequence</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.AddFragmentInfo">
-<code class="sig-name descname">AddFragmentInfo</code><span class="sig-paren">(</span><em class="sig-param">fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.AddFragmentInfo" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddFragmentInfo</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.AddFragmentInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds a fragment info for the last candidate added with <a class="reference internal" href="#promod3.modelling.LoopCandidates.Add" title="promod3.modelling.LoopCandidates.Add"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Add()</span></code></a>. Note
that these infos are added automatically with <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a> and
updated whenever the candidates are copied, removed, clustered etc.. So you
will probably never need this function.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>fragment</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – The fragment info to add.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a>) – The fragment info to add.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.Remove">
-<code class="sig-name descname">Remove</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Remove" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Remove</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Remove" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove a loop candidate from the list of candidates.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the candidate that will be removed</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> is out of bounds.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the candidate that will be removed</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> is out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.HasFragmentInfos">
-<code class="sig-name descname">HasFragmentInfos</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if each loop candidate has a connected fragment info.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">HasFragmentInfos</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if each loop candidate has a connected fragment info.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.GetFragmentInfo">
-<code class="sig-name descname">GetFragmentInfo</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetFragmentInfo" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Fragment info connected to loop candidate at given <em>index</em>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the candidate.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal notranslate"><span class="pre">HasFragmentInfos()</span></code></a> is
-False or if <em>index</em> is out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">GetFragmentInfo</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetFragmentInfo" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Fragment info connected to loop candidate at given <em>index</em>.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragmentInfo</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the candidate.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <a class="reference internal" href="#promod3.modelling.LoopCandidates.HasFragmentInfos" title="promod3.modelling.LoopCandidates.HasFragmentInfos"><code class="xref py py-meth docutils literal notranslate"><span class="pre">HasFragmentInfos()</span></code></a> is
+False or if <em>index</em> is out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.Extract">
-<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Extract" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Container with candidates with given <em>indices</em>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Candidate indices to extract.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any index is out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">Extract</code><span class="sig-paren">(</span><em>indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.Extract" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Container with candidates with given <em>indices</em>.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Candidate indices to extract.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any index is out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.GetClusters">
-<code class="sig-name descname">GetClusters</code><span class="sig-paren">(</span><em class="sig-param">max_dist</em>, <em class="sig-param">superposed_rmsd = False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetClusters" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetClusters</code><span class="sig-paren">(</span><em>max_dist</em>, <em>superposed_rmsd = False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetClusters" title="Permalink to this definition">¶</a></dt>
<dd><p>Clusters the loop candidates according to their pairwise CA RMSD using an
agglomerative hierarchical clustering algorithm. Every candidate gets
assigned a unique cluster. At every clustering step, the two clusters with
shortest distance get merged, with the distance definition being the average
CA RMSD between any of the members of the two clusters.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two clusters can have to be merged</p></li>
-<li><p><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two clusters can have to be merged</li>
+<li><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
RMSD superposition or simply consider the current
-positions</p></li>
+positions</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Lists of loop candidate indices into this container</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Lists of loop candidate indices into this container</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.GetClusteredCandidates">
-<code class="sig-name descname">GetClusteredCandidates</code><span class="sig-paren">(</span><em class="sig-param">max_dist</em>, <em class="sig-param">neglect_size_one=True</em>, <em class="sig-param">superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetClusteredCandidates" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>List of loop candidates clustered as in <a class="reference internal" href="#promod3.modelling.LoopCandidates.GetClusters" title="promod3.modelling.LoopCandidates.GetClusters"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetClusters()</span></code></a>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two clusters can have to be merged</p></li>
-<li><p><strong>neglect_size_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether clusters should be added to the returned
-list if they only contain one loop candidate</p></li>
-<li><p><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
+<code class="descname">GetClusteredCandidates</code><span class="sig-paren">(</span><em>max_dist</em>, <em>neglect_size_one=True</em>, <em>superposed_rmsd=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetClusteredCandidates" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">List of loop candidates clustered as in <a class="reference internal" href="#promod3.modelling.LoopCandidates.GetClusters" title="promod3.modelling.LoopCandidates.GetClusters"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetClusters()</span></code></a>.</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance two clusters can have to be merged</li>
+<li><strong>neglect_size_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether clusters should be added to the returned
+list if they only contain one loop candidate</li>
+<li><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
RMSD superposition or simply consider the current
-positions</p></li>
+positions</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.GetLargestCluster">
-<code class="sig-name descname">GetLargestCluster</code><span class="sig-paren">(</span><em class="sig-param">max_dist</em>, <em class="sig-param">superposed_rmsd = False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetLargestCluster" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetLargestCluster</code><span class="sig-paren">(</span><em>max_dist</em>, <em>superposed_rmsd = False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.GetLargestCluster" title="Permalink to this definition">¶</a></dt>
<dd><p>Instead of performing a full clustering, the algorithm simply searches for
the candidate with the most other candidates having a CA RMSD below
<strong>max_dist</strong>. This candidate then serves as centroid for the return
cluster.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal CA RMSD to cluster centroid</p></li>
-<li><p><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal CA RMSD to cluster centroid</li>
+<li><strong>superposed_rmsd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to calculate the RMSD based on a minimal
RMSD superposition or simply consider the current
-positions</p></li>
+positions</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Largest possible cluster with all members having a
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Largest possible cluster with all members having a
CA RMSD below <strong>max_dist</strong> to cluster centroid.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -581,161 +636,175 @@ CA RMSD below <strong>max_dist</strong> to cluster centroid.</p>
on loop candidates.</p>
<dl class="class">
<dt id="promod3.modelling.ScoreContainer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ScoreContainer</code><a class="headerlink" href="#promod3.modelling.ScoreContainer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ScoreContainer</code><a class="headerlink" href="#promod3.modelling.ScoreContainer" title="Permalink to this definition">¶</a></dt>
<dd><p>Container to keep vectors of scores (one for each loop candidate) for each
scorer (one vector for each single scorer). Each score vector is guaranteed
to have the same number of values.</p>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.IsEmpty">
-<code class="sig-name descname">IsEmpty</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.IsEmpty" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if no loop candidates have been scored with any scorer yet.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">IsEmpty</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.IsEmpty" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if no loop candidates have been scored with any scorer yet.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Contains">
-<code class="sig-name descname">Contains</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Contains" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if a score vector for this key was already added.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
-</dd>
-</dl>
+<code class="descname">Contains</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Contains" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if a score vector for this key was already added.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Get">
-<code class="sig-name descname">Get</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Get" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Score vector for the given <em>key</em>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCandidates()</span></code></a> <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired score vector.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there are no scores for that
-<em>key</em>.</p>
-</dd>
-</dl>
+<code class="descname">Get</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Get" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Score vector for the given <em>key</em>.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCandidates()</span></code></a> <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired score vector.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there are no scores for that
+<em>key</em>.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Set">
-<code class="sig-name descname">Set</code><span class="sig-paren">(</span><em class="sig-param">key</em>, <em class="sig-param">scores</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Set" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Set scores for that <em>key</em>.</p></li>
-<li><p><strong>scores</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Score vector to set.</p></li>
+<code class="descname">Set</code><span class="sig-paren">(</span><em>key</em>, <em>scores</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Set" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Set scores for that <em>key</em>.</li>
+<li><strong>scores</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Score vector to set.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if this container contains other
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if this container contains other
score vectors with a different number of entries.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.GetNumCandidates">
-<code class="sig-name descname">GetNumCandidates</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of loop candidates that are scored here. This is the length
-of each score vector in this container.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetNumCandidates</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of loop candidates that are scored here. This is the length
+of each score vector in this container.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.LinearCombine">
-<code class="sig-name descname">LinearCombine</code><span class="sig-paren">(</span><em class="sig-param">linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.LinearCombine" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Weighted, linear combination of scores.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCandidates()</span></code></a> <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
-values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)) – Weights for each scorer.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a key for
-which no scores were added.</p>
-</dd>
-</dl>
+<code class="descname">LinearCombine</code><span class="sig-paren">(</span><em>linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.LinearCombine" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Weighted, linear combination of scores.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCandidates()</span></code></a> <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
+values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)) – Weights for each scorer.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a key for
+which no scores were added.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Copy">
-<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Copy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Full copy of this container.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Copy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Full copy of this container.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Extract">
-<code class="sig-name descname">Extract</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Extract" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Container with scores for a subset of loop candidates.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – List of loop candidate indices to pick
-(in [0, <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCandidates()</span></code></a>-1])</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any index is out of bounds.</p>
-</dd>
-</dl>
+<code class="descname">Extract</code><span class="sig-paren">(</span><em>indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Extract" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Container with scores for a subset of loop candidates.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – List of loop candidate indices to pick
+(in [0, <a class="reference internal" href="#promod3.modelling.ScoreContainer.GetNumCandidates" title="promod3.modelling.ScoreContainer.GetNumCandidates"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCandidates()</span></code></a>-1])</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any index is out of bounds.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ScoreContainer.Extend">
-<code class="sig-name descname">Extend</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Extend" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Extend</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoreContainer.Extend" title="Permalink to this definition">¶</a></dt>
<dd><p>Extend each score vector with the score vector of <em>other</em> (must have
matching keys).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Score container to be added to this one.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Score container to be added to this one.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.ScoringWeights">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ScoringWeights</code><a class="headerlink" href="#promod3.modelling.ScoringWeights" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ScoringWeights</code><a class="headerlink" href="#promod3.modelling.ScoringWeights" title="Permalink to this definition">¶</a></dt>
<dd><p>Globally accessible set of weights to be used in scoring. This also defines
a consistent naming of keys used for backbone and all atom scorers as set up
by <a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> and <a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>.</p>
@@ -747,145 +816,167 @@ different weights for following lengths: [0,1,2,3,4], [5,6], [7,8], [9,10],
[11,12], [13,14].</p>
<p>If you choose to modify the weights, please ensure to set consistently named
keys in here and to use consistently named scorers and scoring computations!</p>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.GetWeights">
-<em class="property">static </em><code class="sig-name descname">GetWeights</code><span class="sig-paren">(</span><em class="sig-param">with_db=False</em>, <em class="sig-param">with_aa=False</em>, <em class="sig-param">length_dependent=False</em>, <em class="sig-param">loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetWeights" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Named weights to be used when scoring loop candidates. The default
+<em class="property">static </em><code class="descname">GetWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>with_aa=False</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetWeights" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Named weights to be used when scoring loop candidates. The default
weights were optimized to give the best performance when choosing
the loop candidate with the lowest combined score. Each set of
weights includes (different) backbone scoring weights, that are
optionally only trained on a subset of loops with corresponding
loop length.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True to choose a set of weights including DB specific scores
-(stem RMSD and profile scores)</p></li>
-<li><p><strong>with_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True to choose a set of weights including all atom scores</p></li>
-<li><p><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to use general weights or their length
-length dependent counterparts.</p></li>
-<li><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of full loop. If no weights are available for
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True to choose a set of weights including DB specific scores
+(stem RMSD and profile scores)</li>
+<li><strong>with_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True to choose a set of weights including all atom scores</li>
+<li><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to use general weights or their length
+length dependent counterparts.</li>
+<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of full loop. If no weights are available for
this length or when <em>loop_length</em> is -1, the general
-weights are returned.</p></li>
+weights are returned.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.SetWeights">
-<em class="property">static </em><code class="sig-name descname">SetWeights</code><span class="sig-paren">(</span><em class="sig-param">with_db</em>, <em class="sig-param">with_aa</em>, <em class="sig-param">weights</em>, <em class="sig-param">length_dependent=False</em>, <em class="sig-param">loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetWeights" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">SetWeights</code><span class="sig-paren">(</span><em>with_db</em>, <em>with_aa</em>, <em>weights</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetWeights" title="Permalink to this definition">¶</a></dt>
<dd><p>Overwrite a set of weights as returned by <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a>.</p>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.GetBackboneWeights">
-<em class="property">static </em><code class="sig-name descname">GetBackboneWeights</code><span class="sig-paren">(</span><em class="sig-param">with_db=False</em>, <em class="sig-param">with_aa=False</em>, <em class="sig-param">length_dependent=False</em>, <em class="sig-param">loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetBackboneWeights" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Subset of <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a> for backbone scoring as in
+<em class="property">static </em><code class="descname">GetBackboneWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>with_aa=False</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetBackboneWeights" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Subset of <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a> for backbone scoring as in
<code class="xref py py-meth docutils literal notranslate"><span class="pre">scoring.BackboneOverallScorer.CalculateLinearCombination()</span></code>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
-<li><p><strong>with_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
-<li><p><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
-<li><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></li>
+<li><strong>with_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></li>
+<li><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></li>
+<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.GetAllAtomWeights">
-<em class="property">static </em><code class="sig-name descname">GetAllAtomWeights</code><span class="sig-paren">(</span><em class="sig-param">with_db=False</em>, <em class="sig-param">length_dependent=False</em>, <em class="sig-param">loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetAllAtomWeights" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Subset of <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a> for all atom scoring as in
+<em class="property">static </em><code class="descname">GetAllAtomWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetAllAtomWeights" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Subset of <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a> for all atom scoring as in
<code class="xref py py-meth docutils literal notranslate"><span class="pre">scoring.AllAtomOverallScorer.CalculateLinearCombination()</span></code>.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
-<li><p><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
-<li><p><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></li>
+<li><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></li>
+<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetWeights()</span></code></a></li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.GetStemRMSDsKey">
-<em class="property">static </em><code class="sig-name descname">GetStemRMSDsKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetStemRMSDsKey" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetStemRMSDsKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetStemRMSDsKey" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.GetSequenceProfileScoresKey">
-<em class="property">static </em><code class="sig-name descname">GetSequenceProfileScoresKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetSequenceProfileScoresKey" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetSequenceProfileScoresKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetSequenceProfileScoresKey" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.GetStructureProfileScoresKey">
-<em class="property">static </em><code class="sig-name descname">GetStructureProfileScoresKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetStructureProfileScoresKey" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Default key for stem RMSD / sequence profile / structure profile
-scores.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetStructureProfileScoresKey</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetStructureProfileScoresKey" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Default key for stem RMSD / sequence profile / structure profile
+scores.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.SetStemRMSDsKey">
-<em class="property">static </em><code class="sig-name descname">SetStemRMSDsKey</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetStemRMSDsKey" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">SetStemRMSDsKey</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetStemRMSDsKey" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.SetSequenceProfileScoresKey">
-<em class="property">static </em><code class="sig-name descname">SetSequenceProfileScoresKey</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetSequenceProfileScoresKey" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">SetSequenceProfileScoresKey</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetSequenceProfileScoresKey" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.SetStructureProfileScoresKey">
-<em class="property">static </em><code class="sig-name descname">SetStructureProfileScoresKey</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetStructureProfileScoresKey" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New default key for stem RMSD / sequence profile / structure
-profile scores.</p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">SetStructureProfileScoresKey</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetStructureProfileScoresKey" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New default key for stem RMSD / sequence profile / structure
+profile scores.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.GetBackboneScoringKeys">
-<em class="property">static </em><code class="sig-name descname">GetBackboneScoringKeys</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetBackboneScoringKeys" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetBackboneScoringKeys</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetBackboneScoringKeys" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.GetAllAtomScoringKeys">
-<em class="property">static </em><code class="sig-name descname">GetAllAtomScoringKeys</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetAllAtomScoringKeys" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>List of backbone / all-atom scorers to be computed for any set of
-weights defined in here.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">GetAllAtomScoringKeys</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetAllAtomScoringKeys" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">List of backbone / all-atom scorers to be computed for any set of
+weights defined in here.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.SetBackboneScoringKeys">
-<em class="property">static </em><code class="sig-name descname">SetBackboneScoringKeys</code><span class="sig-paren">(</span><em class="sig-param">keys</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetBackboneScoringKeys" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">SetBackboneScoringKeys</code><span class="sig-paren">(</span><em>keys</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetBackboneScoringKeys" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.ScoringWeights.SetAllAtomScoringKeys">
-<em class="property">static </em><code class="sig-name descname">SetAllAtomScoringKeys</code><span class="sig-paren">(</span><em class="sig-param">keys</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetAllAtomScoringKeys" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>keys</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New list of backbone / all-atom scorers to be computed for any
-set of weights defined in here.</p>
-</dd>
-</dl>
+<em class="property">static </em><code class="descname">SetAllAtomScoringKeys</code><span class="sig-paren">(</span><em>keys</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetAllAtomScoringKeys" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>keys</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New list of backbone / all-atom scorers to be computed for any
+set of weights defined in here.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -991,7 +1082,6 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -1012,12 +1102,12 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -1034,7 +1124,7 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="gap_handling.html" title="previous chapter">Handling Gaps</a></li>
<li>Next: <a href="loop_closing.html" title="next chapter">Fitting Loops Into Gaps</a></li>
</ul></li>
@@ -1043,33 +1133,27 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/loop_candidates.rst.txt"
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index eaed142d036c9382c1daaba0f9f6769b56a265d7..dfab8aa39dbb0a60f7f0322aea794238a08ceb65 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Fitting Loops Into Gaps — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Fitting Loops Into Gaps — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="fitting-loops-into-gaps">
@@ -39,8 +38,8 @@
stem residues. ProMod3 implements two algorithms performing this task:</p>
<blockquote>
<div><ul class="simple">
-<li><p>Cyclic coordinate descent (CCD) <a class="reference internal" href="../references.html#canutescu2003" id="id1"><span>[canutescu2003]</span></a></p></li>
-<li><p>Kinematic closure (KIC) <a class="reference internal" href="../references.html#coutsias2005" id="id2"><span>[coutsias2005]</span></a></p></li>
+<li>Cyclic coordinate descent (CCD) <a class="reference internal" href="../references.html#canutescu2003" id="id1">[canutescu2003]</a></li>
+<li>Kinematic closure (KIC) <a class="reference internal" href="../references.html#coutsias2005" id="id2">[coutsias2005]</a></li>
</ul>
</div></blockquote>
<p>In case of small gaps or small issues in the loop you might also consider the
@@ -61,86 +60,94 @@ than a uniform random number in the range [0,1[, the proposed dihedral pair gets
rejected. Please note, that this increases the probability of non-convergence.</p>
<dl class="class">
<dt id="promod3.modelling.CCD">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CCD</code><a class="headerlink" href="#promod3.modelling.CCD" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CCD</code><a class="headerlink" href="#promod3.modelling.CCD" title="Permalink to this definition">¶</a></dt>
<dd><p>Class, that sets up everything you need to perform a particular loop closing
action.</p>
<dl class="method">
<dt id="promod3.modelling.CCD.CCD">
-<code class="sig-name descname">CCD</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">max_steps</em>, <em class="sig-param">rmsd_cutoff</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCD.CCD" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CCD</code><span class="sig-paren">(</span><em>sequence</em>, <em>n_stem</em>, <em>c_stem</em>, <em>torsion_sampler</em>, <em>max_steps</em>, <em>rmsd_cutoff</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCD.CCD" title="Permalink to this definition">¶</a></dt>
<dd><p>All runs with this CCD object will be with application of torsion samplers
to avoid moving into unfavourable regions of the backbone dihedrals.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the backbones to be closed</p></li>
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the backbones to be closed</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
If the residue before <em>n_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
-and phi angle (-1.0472) to evaluate the first angle.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
+and phi angle (-1.0472) to evaluate the first angle.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
If the residue after <em>c_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
-psi angle (-0.7854) to evaluate the last angle.</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
+psi angle (-0.7854) to evaluate the last angle.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – To extract probabilities for the analysis of the
backbone dihedrals. Either a list of torsion
samplers (one for for every residue of the loop to
-be closed) or a single one (used for all residues).</p></li>
-<li><p><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of iterations</p></li>
-<li><p><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
-be closed has RMSD below the <em>c_stem</em></p></li>
-<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed of random number generator to decide whether new phi/psi pair
-should be accepted.</p></li>
+be closed) or a single one (used for all residues).</li>
+<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of iterations</li>
+<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
+be closed has RMSD below the <em>c_stem</em></li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed of random number generator to decide whether new phi/psi pair
+should be accepted.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if a list of torsion samplers is
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if a list of torsion samplers is
given with inconsistent length regarding the sequence. Another
requirement is that all backbone atoms of the stems must be
present.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">CCD</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">max_steps</em>, <em class="sig-param">rmsd_cutoff</em><span class="sig-paren">)</span></dt>
+<code class="descname">CCD</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>max_steps</em>, <em>rmsd_cutoff</em><span class="sig-paren">)</span></dt>
<dd><p>All runs with this CCD object will be without application of torsion samplers.
This is faster but might lead to weird backbone dihedral pairs.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</p></li>
-<li><p><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of iterations</p></li>
-<li><p><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
-be closed has RMSD below the given <em>c_stem</em></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
+<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of iterations</li>
+<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
+be closed has RMSD below the given <em>c_stem</em></li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.CCD.Close">
-<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCD.Close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Close</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCD.Close" title="Permalink to this definition">¶</a></dt>
<dd><p>Closes given <em>bb_list</em> with the settings set at initialization.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Whether <em>rmsd_cutoff</em> has been reached</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the CCD object has been
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether <em>rmsd_cutoff</em> has been reached</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the CCD object has been
initialized with <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> support
and the length of the <em>bb_list</em> is not consistent with the initial
-<em>sequence</em>.</p>
-</dd>
-</dl>
+<em>sequence</em>.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -155,47 +162,55 @@ at these pivot residues. Due to the internal mathematical formalism, up to
16 solutions can be found for a given loop closing problem.</p>
<dl class="class">
<dt id="promod3.modelling.KIC">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">KIC</code><a class="headerlink" href="#promod3.modelling.KIC" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">KIC</code><a class="headerlink" href="#promod3.modelling.KIC" title="Permalink to this definition">¶</a></dt>
<dd><p>Class, that sets up everything you need to perform a particular loop closing
action.</p>
<dl class="method">
<dt id="promod3.modelling.KIC.KIC">
-<code class="sig-name descname">KIC</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KIC.KIC" title="Permalink to this definition">¶</a></dt>
+<code class="descname">KIC</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KIC.KIC" title="Permalink to this definition">¶</a></dt>
<dd><p>All runs of this KIC closing object will adapt the input loops to these
stem residues.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> – Residue describing the stem towards n_ter</p></li>
-<li><p><strong>c_stem</strong> – Residue describing the stem towards c_ter</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_stem</strong> – Residue describing the stem towards n_ter</li>
+<li><strong>c_stem</strong> – Residue describing the stem towards c_ter</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.KIC.Close">
-<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">pivot_one</em>, <em class="sig-param">pivot_two</em>, <em class="sig-param">pivot_three</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KIC.Close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Close</code><span class="sig-paren">(</span><em>bb_list</em>, <em>pivot_one</em>, <em>pivot_two</em>, <em>pivot_three</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KIC.Close" title="Permalink to this definition">¶</a></dt>
<dd><p>Applies KIC algorithm, so that the output loops match the given stem residues</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</p></li>
-<li><p><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of first pivot residue</p></li>
-<li><p><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of second pivot residue</p></li>
-<li><p><strong>pivot_three</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of third pivot residue</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</li>
+<li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of first pivot residue</li>
+<li><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of second pivot residue</li>
+<li><strong>pivot_three</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of third pivot residue</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>List of closed loops (maximum of 16 entries)</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> in case of invalid pivot indices.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">List of closed loops (maximum of 16 entries)</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> in case of invalid pivot indices.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -210,193 +225,230 @@ Once setup, every loop of the same length and sequence can be relaxed by
the relaxer.</p>
<dl class="class">
<dt id="promod3.modelling.BackboneRelaxer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">BackboneRelaxer</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">ff</em>, <em class="sig-param">fix_nterm=True</em>, <em class="sig-param">fix_cterm=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">BackboneRelaxer</code><span class="sig-paren">(</span><em>bb_list</em>, <em>ff</em>, <em>fix_nterm=True</em>, <em>fix_cterm=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up a molecular mechanics topology for given <em>bb_list</em>. Every
<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> of same length and sequence can then be
relaxed. The parametrization is taken from <em>ff</em>, simply neglecting all
interactions to non backbone atoms. The electrostatics get neglected
completely by setting all charges to 0.0.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Basis for topology creation</p></li>
-<li><p><strong>ff</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.ForcefieldLookup</span></code></a>) – Source for parametrization</p></li>
-<li><p><strong>fix_nterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether N-terminal backbone positions (N, CA, CB) should
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Basis for topology creation</li>
+<li><strong>ff</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.ForcefieldLookup</span></code></a>) – Source for parametrization</li>
+<li><strong>fix_nterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether N-terminal backbone positions (N, CA, CB) should
be kept rigid during relaxation
-(C and O are left to move).</p></li>
-<li><p><strong>fix_cterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether C-terminal backbone positions (CA, CB, C, O)
+(C and O are left to move).</li>
+<li><strong>fix_cterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether C-terminal backbone positions (CA, CB, C, O)
should be kept rigid during relaxation
-(N is left to move).</p></li>
+(N is left to move).</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="class">
<dt>
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">BackboneRelaxer</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">density</em>, <em class="sig-param">resolution</em>, <em class="sig-param">fix_nterm=True</em>, <em class="sig-param">fix_cterm=True</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Basis for topology creation</p></li>
-<li><p><strong>fix_nterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether N-terminal backbone positions (N, CA, CB) should
-be kept rigid during relaxation.</p></li>
-<li><p><strong>fix_cterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether C-terminal backbone positions (CA, CB, C, O)
-should be kept rigid during relaxation.</p></li>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">BackboneRelaxer</code><span class="sig-paren">(</span><em>bb_list</em>, <em>density</em>, <em>resolution</em>, <em>fix_nterm=True</em>, <em>fix_cterm=True</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Basis for topology creation</li>
+<li><strong>fix_nterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether N-terminal backbone positions (N, CA, CB) should
+be kept rigid during relaxation.</li>
+<li><strong>fix_cterm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether C-terminal backbone positions (CA, CB, C, O)
+should be kept rigid during relaxation.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if size of <em>bb_list</em> is below 2</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if size of <em>bb_list</em> is below 2</p>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.Run">
-<code class="sig-name descname">Run</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">steps=100</em>, <em class="sig-param">stop_criterion=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.Run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Run</code><span class="sig-paren">(</span><em>bb_list</em>, <em>steps=100</em>, <em>stop_criterion=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.Run" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs steepest descent on given BackboneList. The function possibly fails
if there are particles (almost) on top of each other, resulting in NaN
positions in the OpenMM system. The positions of <strong>bb_list</strong> are not touched
in this case and the function returns an infinit potential energy.
In Python you can check for that with float(“inf”).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – To be relaxed</p></li>
-<li><p><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – number of steepest descent steps</p></li>
-<li><p><strong>stop_criterion</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If maximum force acting on a particle
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – To be relaxed</li>
+<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – number of steepest descent steps</li>
+<li><strong>stop_criterion</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If maximum force acting on a particle
falls below that threshold, the
-relaxation aborts.</p></li>
+relaxation aborts.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Forcefield energy upon relaxation, infinity in case of OpenMM Error</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> has not the same
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Forcefield energy upon relaxation, infinity in case of OpenMM Error</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> has not the same
size or sequence as the initial one.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.AddNRestraint">
-<code class="sig-name descname">AddNRestraint</code><span class="sig-paren">(</span><em class="sig-param">idx</em>, <em class="sig-param">pos</em>, <em class="sig-param">force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddNRestraint" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddNRestraint</code><span class="sig-paren">(</span><em>idx</em>, <em>pos</em>, <em>force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddNRestraint" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds harmonic position restraint for nitrogen atom at specified residue</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
-<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.AddCARestraint">
-<code class="sig-name descname">AddCARestraint</code><span class="sig-paren">(</span><em class="sig-param">idx</em>, <em class="sig-param">pos</em>, <em class="sig-param">force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCARestraint" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddCARestraint</code><span class="sig-paren">(</span><em>idx</em>, <em>pos</em>, <em>force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCARestraint" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds harmonic position restraint for CA atom at specified residue</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
-<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.AddCBRestraint">
-<code class="sig-name descname">AddCBRestraint</code><span class="sig-paren">(</span><em class="sig-param">idx</em>, <em class="sig-param">pos</em>, <em class="sig-param">force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCBRestraint" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddCBRestraint</code><span class="sig-paren">(</span><em>idx</em>, <em>pos</em>, <em>force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCBRestraint" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds harmonic position restraint for CB atom at specified residue,
doesn’t do anything if specified residue is a glycine</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
-<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.AddCRestraint">
-<code class="sig-name descname">AddCRestraint</code><span class="sig-paren">(</span><em class="sig-param">idx</em>, <em class="sig-param">pos</em>, <em class="sig-param">force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCRestraint" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddCRestraint</code><span class="sig-paren">(</span><em>idx</em>, <em>pos</em>, <em>force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddCRestraint" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds harmonic position restraint for C atom at specified residue</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
-<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.AddORestraint">
-<code class="sig-name descname">AddORestraint</code><span class="sig-paren">(</span><em class="sig-param">idx</em>, <em class="sig-param">pos</em>, <em class="sig-param">force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddORestraint" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddORestraint</code><span class="sig-paren">(</span><em>idx</em>, <em>pos</em>, <em>force_constant=100000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.AddORestraint" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds harmonic position restraint for O atom at specified residue</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
-<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>idx</em> is too large</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.SetNonBondedCutoff">
-<code class="sig-name descname">SetNonBondedCutoff</code><span class="sig-paren">(</span><em class="sig-param">nonbonded_cutoff</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.SetNonBondedCutoff" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetNonBondedCutoff</code><span class="sig-paren">(</span><em>nonbonded_cutoff</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.SetNonBondedCutoff" title="Permalink to this definition">¶</a></dt>
<dd><p>Defines cutoff to set for non bonded interactions. By default, all atom-
pairs are compared which is the fastest for small backbones (e.g. in
<a class="reference internal" href="pipeline.html#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>). Otherwise, a cutoff around 5 is reasonable as
we ignore electrostatics.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>nonbonded_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff to set for non bonded interactions. Negative
-means no cutoff.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>nonbonded_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff to set for non bonded interactions. Negative
+means no cutoff.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.GetNonBondedCutoff">
-<code class="sig-name descname">GetNonBondedCutoff</code><span class="sig-paren">(</span><em class="sig-param">nonbonded_cutoff</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.GetNonBondedCutoff" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Cutoff for non bonded interactions.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetNonBondedCutoff</code><span class="sig-paren">(</span><em>nonbonded_cutoff</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.GetNonBondedCutoff" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Cutoff for non bonded interactions.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -440,77 +492,89 @@ quickly relax the loop. The <a class="reference internal" href="#promod3.modelli
</div>
<dl class="class">
<dt id="promod3.modelling.AllAtomRelaxer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">AllAtomRelaxer</code><span class="sig-paren">(</span><em class="sig-param">sc_data</em>, <em class="sig-param">mm_system_creator</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">AllAtomRelaxer</code><span class="sig-paren">(</span><em>sc_data</em>, <em>mm_system_creator</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup relaxer for a given sidechain reconstruction result and a given MM
system creator, which takes care of generating a simulation object.</p>
<p>N/C stems of loop are fixed if they are non-terminal.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a>) – Sidechain reconstruction result</p></li>
-<li><p><strong>mm_system_creator</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a>) – System creator to be used here</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a>) – Sidechain reconstruction result</li>
+<li><strong>mm_system_creator</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a>) – System creator to be used here</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.AllAtomRelaxer.Run">
-<code class="sig-name descname">Run</code><span class="sig-paren">(</span><em class="sig-param">sc_data</em>, <em class="sig-param">steps=100</em>, <em class="sig-param">stop_criterion=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.Run" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Run</code><span class="sig-paren">(</span><em>sc_data</em>, <em>steps=100</em>, <em>stop_criterion=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.Run" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs steepest descent for this system and writes updated positions into
<em>sc_data.env_pos.all_pos</em>. The function possibly fails
if there are particles (almost) on top of each other, resulting in NaN
positions in the OpenMM system. The positions of <em>sc_data.env_pos.all_pos</em>
are not touched in this case and the function returns an infinit potential
energy. In Python you can check for that with float(“inf”).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a>) – Sidechain reconstruction result to be updated</p></li>
-<li><p><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of steepest descent steps</p></li>
-<li><p><strong>stop_criterion</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If maximum force acting on a particle falls below
-that threshold, the relaxation aborts.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a>) – Sidechain reconstruction result to be updated</li>
+<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of steepest descent steps</li>
+<li><strong>stop_criterion</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If maximum force acting on a particle falls below
+that threshold, the relaxation aborts.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Potential energy after relaxation, infinity in case of OpenMM Error</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sc_data</em> is incompatible with
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Potential energy after relaxation, infinity in case of OpenMM Error</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sc_data</em> is incompatible with
the one given in the constructor.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.AllAtomRelaxer.UpdatePositions">
-<code class="sig-name descname">UpdatePositions</code><span class="sig-paren">(</span><em class="sig-param">sc_data</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.UpdatePositions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">UpdatePositions</code><span class="sig-paren">(</span><em>sc_data</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.UpdatePositions" title="Permalink to this definition">¶</a></dt>
<dd><p>Resets simulation positions to a new set of positions. It is assumed that
this <em>sc_data</em> object has the same amino acids as loops and surrounding and
the same disulfid bridges as the one given in the constructor.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a>) – Get new positions from <em>sc_data.env_pos.all_pos</em></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sc_data</em> is incompatible with
-the one given in the constructor.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>sc_data</strong> (<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a>) – Get new positions from <em>sc_data.env_pos.all_pos</em></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>sc_data</em> is incompatible with
+the one given in the constructor.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.AllAtomRelaxer.GetSystemCreator">
-<code class="sig-name descname">GetSystemCreator</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.GetSystemCreator" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>MM system creator passed in the constructor</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetSystemCreator</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.GetSystemCreator" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">MM system creator passed in the constructor</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -520,7 +584,6 @@ the one given in the constructor.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -541,12 +604,12 @@ the one given in the constructor.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -563,7 +626,7 @@ the one given in the constructor.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="loop_candidates.html" title="previous chapter">Handling Loop Candidates</a></li>
<li>Next: <a href="monte_carlo.html" title="next chapter">Generating Loops De Novo</a></li>
</ul></li>
@@ -572,33 +635,27 @@ the one given in the constructor.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
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-
</div>
</div>
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</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/loop_closing.rst.txt"
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 7ecf5c3eda588565d42bc15174a31539d2ad37bf..04ece5d3cd50301e608eaf4d6bde84499b465b51 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Model Checking — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Model Checking — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="model-checking">
@@ -41,85 +40,99 @@ functionality is used within the modelling pipeline.</p>
<h2>Detecting Ring Punches<a class="headerlink" href="#detecting-ring-punches" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.GetRings">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">GetRings</code><span class="sig-paren">(</span><em class="sig-param">ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetRings" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">GetRings</code><span class="sig-paren">(</span><em>ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetRings" title="Permalink to this definition">¶</a></dt>
<dd><p>Get rings for a protein structure.
A ring is only added if all ring-atoms exist or if it is a proline and
three of the atoms exist (center and radii are estimated then).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of rings to perform ring checks. Each ring is a named
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of rings to perform ring checks. Each ring is a named
tuple with:
center (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>),
plane (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Plane</span></code></a>),
radius (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>),
-residue (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</p>
-</dd>
-</dl>
+residue (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.GetRingPunches">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">GetRingPunches</code><span class="sig-paren">(</span><em class="sig-param">rings</em>, <em class="sig-param">ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetRingPunches" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">GetRingPunches</code><span class="sig-paren">(</span><em>rings</em>, <em>ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetRingPunches" title="Permalink to this definition">¶</a></dt>
<dd><p>Get list of residues with rings that are punched by the given structure.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</p></li>
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
have a punched ring.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.HasRingPunches">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">HasRingPunches</code><span class="sig-paren">(</span><em class="sig-param">rings</em>, <em class="sig-param">ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.HasRingPunches" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">HasRingPunches</code><span class="sig-paren">(</span><em>rings</em>, <em>ent</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.HasRingPunches" title="Permalink to this definition">¶</a></dt>
<dd><p>Check if any ring is punched by the given structure.
This check is faster than using <a class="reference internal" href="#promod3.modelling.GetRingPunches" title="promod3.modelling.GetRingPunches"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRingPunches()</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</p></li>
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>True, iff any ring is punched</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">True, iff any ring is punched</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.FilterCandidates">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FilterCandidates</code><span class="sig-paren">(</span><em class="sig-param">candidates</em>, <em class="sig-param">model</em>, <em class="sig-param">gap</em>, <em class="sig-param">orig_indices=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FilterCandidates" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">FilterCandidates</code><span class="sig-paren">(</span><em>candidates</em>, <em>model</em>, <em>gap</em>, <em>orig_indices=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FilterCandidates" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove loop candidates if they cause ring punches.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>candidates</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
-Offending candidates are removed from this list.</p></li>
-<li><p><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</p></li>
-<li><p><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</p></li>
-<li><p><strong>orig_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Mapping to old indexing of candidates. If given, it
-must have as many elements as <em>candidates</em>.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>candidates</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
+Offending candidates are removed from this list.</li>
+<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
+<li><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</li>
+<li><strong>orig_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Mapping to old indexing of candidates. If given, it
+must have as many elements as <em>candidates</em>.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.FilterCandidatesWithSC">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FilterCandidatesWithSC</code><span class="sig-paren">(</span><em class="sig-param">candidates</em>, <em class="sig-param">model</em>, <em class="sig-param">gap</em>, <em class="sig-param">orig_indices=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FilterCandidatesWithSC" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">FilterCandidatesWithSC</code><span class="sig-paren">(</span><em>candidates</em>, <em>model</em>, <em>gap</em>, <em>orig_indices=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FilterCandidatesWithSC" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove loop candidates if they (with sidechain) cause ring punches.
See <a class="reference internal" href="#promod3.modelling.FilterCandidates" title="promod3.modelling.FilterCandidates"><code class="xref py py-func docutils literal notranslate"><span class="pre">FilterCandidates()</span></code></a>.</p>
</dd></dl>
@@ -129,7 +142,7 @@ See <a class="reference internal" href="#promod3.modelling.FilterCandidates" tit
<h2>Model Checking With MolProbity<a class="headerlink" href="#model-checking-with-molprobity" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.RunMolProbity">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RunMolProbity</code><span class="sig-paren">(</span><em class="sig-param">target_pdb</em>, <em class="sig-param">molprobity_bin=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RunMolProbity" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">RunMolProbity</code><span class="sig-paren">(</span><em>target_pdb</em>, <em>molprobity_bin=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RunMolProbity" title="Permalink to this definition">¶</a></dt>
<dd><p>Run <code class="docutils literal notranslate"><span class="pre">MolProbity</span></code> from <code class="docutils literal notranslate"><span class="pre">Phenix</span></code> on a given PDB file.</p>
<p>MolProbity score computation: (formula from molprobity source code)</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">clashscore</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s2">"Clashscore"</span><span class="p">]</span>
@@ -140,62 +153,72 @@ See <a class="reference internal" href="#promod3.modelling.FilterCandidates" tit
<span class="p">(</span> <span class="mf">0.25</span> <span class="o">*</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="nb">max</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">rama_iffy</span> <span class="o">-</span> <span class="mi">2</span><span class="p">))</span> <span class="p">))</span> <span class="o">+</span> <span class="mf">0.5</span>
</pre></div>
</div>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>target_pdb</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to PDB file on which to do analysis.</p></li>
-<li><p><strong>molprobity_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to <code class="docutils literal notranslate"><span class="pre">phenix.molprobity</span></code> executable. If None, it
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>target_pdb</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to PDB file on which to do analysis.</li>
+<li><strong>molprobity_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to <code class="docutils literal notranslate"><span class="pre">phenix.molprobity</span></code> executable. If None, it
searches for it in the <code class="docutils literal notranslate"><span class="pre">PATH</span></code> or (if set) in the
env. variable <code class="docutils literal notranslate"><span class="pre">MOLPROBITY_EXECUTABLE</span></code>.
The function was tested with <code class="docutils literal notranslate"><span class="pre">Phenix</span> <span class="pre">1.9-1692</span></code> and
-with <code class="docutils literal notranslate"><span class="pre">MolProbity</span> <span class="pre">4.2</span></code> which also includes it.</p></li>
+with <code class="docutils literal notranslate"><span class="pre">MolProbity</span> <span class="pre">4.2</span></code> which also includes it.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><p>Dictionary with scores produced by MolProbity. Entries:</p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><p>Dictionary with scores produced by MolProbity. Entries:</p>
<ul class="simple">
-<li><p>”Ramachandran outliers” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
-<li><p>”Ramachandran favored” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
-<li><p>”Rotamer outliers” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
-<li><p>”C-beta deviations” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</p></li>
-<li><p>”Clashscore” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
-<li><p>”MolProbity score” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
-<li><p>”RMS(bonds)” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
-<li><p>”RMS(angles)” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</p></li>
+<li>”Ramachandran outliers” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</li>
+<li>”Ramachandran favored” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</li>
+<li>”Rotamer outliers” (percentage [0,100] as <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</li>
+<li>”C-beta deviations” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>)</li>
+<li>”Clashscore” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</li>
+<li>”MolProbity score” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</li>
+<li>”RMS(bonds)” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</li>
+<li>”RMS(angles)” (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)</li>
</ul>
</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
executable is not found.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.RunMolProbityEntity">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RunMolProbityEntity</code><span class="sig-paren">(</span><em class="sig-param">ost_ent</em>, <em class="sig-param">molprobity_bin=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RunMolProbityEntity" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">RunMolProbityEntity</code><span class="sig-paren">(</span><em>ost_ent</em>, <em>molprobity_bin=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RunMolProbityEntity" title="Permalink to this definition">¶</a></dt>
<dd><p>Run molprobity from phenix on given OST entity.</p>
<p>See <a class="reference internal" href="#promod3.modelling.RunMolProbity" title="promod3.modelling.RunMolProbity"><code class="xref py py-func docutils literal notranslate"><span class="pre">RunMolProbity()</span></code></a> for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.ReportMolProbityScores">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ReportMolProbityScores</code><span class="sig-paren">(</span><em class="sig-param">scores</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReportMolProbityScores" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">ReportMolProbityScores</code><span class="sig-paren">(</span><em>scores</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReportMolProbityScores" title="Permalink to this definition">¶</a></dt>
<dd><p>Print MolProbity score and its components to LogInfo.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>scores</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a>) – MolProbity scores as generated by <a class="reference internal" href="#promod3.modelling.RunMolProbity" title="promod3.modelling.RunMolProbity"><code class="xref py py-func docutils literal notranslate"><span class="pre">RunMolProbity()</span></code></a>.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>scores</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a>) – MolProbity scores as generated by <a class="reference internal" href="#promod3.modelling.RunMolProbity" title="promod3.modelling.RunMolProbity"><code class="xref py py-func docutils literal notranslate"><span class="pre">RunMolProbity()</span></code></a>.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -203,7 +226,6 @@ executable is not found.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -224,12 +246,12 @@ executable is not found.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -246,7 +268,7 @@ executable is not found.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="pipeline.html" title="previous chapter">Modelling Pipeline</a></li>
<li>Next: <a href="gap_handling.html" title="next chapter">Handling Gaps</a></li>
</ul></li>
@@ -255,33 +277,27 @@ executable is not found.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/model_checking.rst.txt"
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index 4a9cf7bbedf72da08008e9c0821ca753f4f9dd7b..e05d228440ebf6a0b28b68d3315ff15fd858cc20 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Generating Loops De Novo — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Generating Loops De Novo — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="generating-loops-de-novo">
@@ -40,11 +39,11 @@ novo structure candidates for loops or N-/C-Termini. Every iteration of the
sampling process consists basically of four steps and we define objects for
each step:</p>
<ul class="simple">
-<li><p><a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>: Propose new conformation</p></li>
-<li><p><a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>: Adapt new conformation to the environment</p></li>
-<li><p><a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>: Score the new conformation</p></li>
-<li><p><a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>: Accept/Reject new conformation based on the score and
-a temperature controlled Metropolis criterion</p></li>
+<li><a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>: Propose new conformation</li>
+<li><a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>: Adapt new conformation to the environment</li>
+<li><a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>: Score the new conformation</li>
+<li><a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>: Accept/Reject new conformation based on the score and
+a temperature controlled Metropolis criterion</li>
</ul>
<p>These steps can be arbitrarily combined to generate custom Monte Carlo sampling
pipelines. This combination either happens manually or by using the convenient
@@ -105,7 +104,7 @@ Carlo sampling to the N-terminal part of crambin:</p>
</div>
<dl class="function">
<dt id="promod3.modelling.SampleMonteCarlo">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SampleMonteCarlo</code><span class="sig-paren">(</span><em class="sig-param">sampler</em>, <em class="sig-param">closer</em>, <em class="sig-param">scorer</em>, <em class="sig-param">cooler</em>, <em class="sig-param">steps</em>, <em class="sig-param">bb_list</em>, <em class="sig-param">initialize</em>, <em class="sig-param">seed=0</em>, <em class="sig-param">lowest_energy_conformation=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SampleMonteCarlo" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">SampleMonteCarlo</code><span class="sig-paren">(</span><em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>steps</em>, <em>bb_list</em>, <em>initialize</em>, <em>seed=0</em>, <em>lowest_energy_conformation=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SampleMonteCarlo" title="Permalink to this definition">¶</a></dt>
<dd><p>A convenient function to perform Monte Carlo sampling using a simulated
annealing scheme. In every iteration, a new loop conformation gets proposed
by the provided <em>sampler</em> and closed by the <em>closer</em>. Upon scoring, this new
@@ -115,28 +114,32 @@ the temperature given by the <em>cooler</em>
The result is stored in <em>bb_list</em> (passed by reference, so NO return value)
and is either the lowest energy conformation ever encountered or the last
accepted proposal.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sampler</strong> (<a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) – Sampler object capable of initializing and altering
-conformations.</p></li>
-<li><p><strong>closer</strong> (<a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Closer object to adapt a new conformation to
-the environment.</p></li>
-<li><p><strong>scorer</strong> (<a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Scorer object to score new loop conformations.</p></li>
-<li><p><strong>cooler</strong> (<a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Cooler object to control the temperature of the
-Monte Carlo trajectory.</p></li>
-<li><p><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of Monte Carlo iterations to be performed.</p></li>
-<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The chosen conformation gets stored here.</p></li>
-<li><p><strong>initialize</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether a new bb_list should be generated as starting
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>sampler</strong> (<a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) – Sampler object capable of initializing and altering
+conformations.</li>
+<li><strong>closer</strong> (<a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Closer object to adapt a new conformation to
+the environment.</li>
+<li><strong>scorer</strong> (<a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Scorer object to score new loop conformations.</li>
+<li><strong>cooler</strong> (<a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Cooler object to control the temperature of the
+Monte Carlo trajectory.</li>
+<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of Monte Carlo iterations to be performed.</li>
+<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The chosen conformation gets stored here.</li>
+<li><strong>initialize</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether a new bb_list should be generated as starting
point, based on the samplers Initialize function.
-The input <em>bb_list</em> gets used otherwise.</p></li>
-<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator.</p></li>
-<li><p><strong>lowest_energy_conformation</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, we choose the lowest scoring
+The input <em>bb_list</em> gets used otherwise.</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random number generator.</li>
+<li><strong>lowest_energy_conformation</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, we choose the lowest scoring
conformation of the trajectory.
-Otherwise, the last accepted proposal.</p></li>
+Otherwise, the last accepted proposal.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<div class="section" id="sampler-object">
@@ -148,172 +151,196 @@ provided samplers or any object that implements the functionality of
<a class="reference internal" href="#promod3.modelling.SamplerBase" title="promod3.modelling.SamplerBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">SamplerBase</span></code></a>.</p>
<dl class="class">
<dt id="promod3.modelling.SamplerBase">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SamplerBase</code><a class="headerlink" href="#promod3.modelling.SamplerBase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">SamplerBase</code><a class="headerlink" href="#promod3.modelling.SamplerBase" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class defining the functions that must be implemented by any
sampler.</p>
<dl class="method">
<dt id="promod3.modelling.SamplerBase.Initialize">
-<code class="sig-name descname">Initialize</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.Initialize" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.Initialize" title="Permalink to this definition">¶</a></dt>
<dd><p>Supposed to initialize structural information from scratch. The sequence
of the generated <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> is taken from <em>bb_list</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to this
-parameter. Sequence / length stay the same.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>None</p>
-</dd>
-</dl>
+parameter. Sequence / length stay the same.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">None</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.SamplerBase.ProposeStep">
-<code class="sig-name descname">ProposeStep</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">proposed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.ProposeStep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ProposeStep</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>proposed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SamplerBase.ProposeStep" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes current positions and proposes a new conformation. There is no
guarantee on maintining any special RT state. The <a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>
is supposed to sort that out.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Starting point, must not change when calling this
-function.</p></li>
-<li><p><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Starting point, must not change when calling this
+function.</li>
+<li><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to
-this parameter.</p></li>
+this parameter.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>None</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">None</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.PhiPsiSampler">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">PhiPsiSampler</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">n_stem_phi=-1.0472</em>, <em class="sig-param">c_stem_psi=-0.78540</em>, <em class="sig-param">prev_aa='A'</em>, <em class="sig-param">next_aa='A'</em>, <em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">PhiPsiSampler</code><span class="sig-paren">(</span><em>sequence</em>, <em>torsion_sampler</em>, <em>n_stem_phi=-1.0472</em>, <em>c_stem_psi=-0.78540</em>, <em>prev_aa='A'</em>, <em>next_aa='A'</em>, <em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>The PhiPsiSampler randomly draws and sets phi/psi dihedral angles from
a distribution provided by the <em>torsion_sampler</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence that should be sampled</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Sampler, from which the phi/psi pairs are drawn. It
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence that should be sampled</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Sampler, from which the phi/psi pairs are drawn. It
is also possible to pass a list of samplers with same
size as the sequence to assign a specific sampler per
-residue.</p></li>
-<li><p><strong>n_stem_phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi angle of the n_stem. This angle is not defined in
+residue.</li>
+<li><strong>n_stem_phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi angle of the n_stem. This angle is not defined in
the sampling region. If the first residue gets selected
for changing the dihedral angles, it draws a psi angle
-given <em>n_stem_phi</em>.</p></li>
-<li><p><strong>c_stem_psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi angle of c_stem. This angle is not defined in
+given <em>n_stem_phi</em>.</li>
+<li><strong>c_stem_psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi angle of c_stem. This angle is not defined in
the sampling region. If the last residue gets selected
for changing the dihedral angles, it draws a phi angle
-given <em>c_stem_psi</em>.</p></li>
-<li><p><strong>prev_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
+given <em>c_stem_psi</em>.</li>
+<li><strong>prev_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
histogram index for the first residue from the
<em>torsion_sampler</em>. (Remember: The torsion sampler
-always considers triplets)</p></li>
-<li><p><strong>next_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
+always considers triplets)</li>
+<li><strong>next_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
histogram index for the last residue from the
<em>torsion_sampler</em>. (Remember: The torsion sampler
-always considers triplets)</p></li>
-<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for the internal random number generators.</p></li>
+always considers triplets)</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for the internal random number generators.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.PhiPsiSampler.Initialize">
-<code class="sig-name descname">Initialize</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler.Initialize" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler.Initialize" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up a new <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> by randomly drawing
phi/psi dihedral angles.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.PhiPsiSampler.ProposeStep">
-<code class="sig-name descname">ProposeStep</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ProposeStep</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PhiPsiSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
<dd><p>Randomly selects one of the residues and resets its phi/psi values
according to a random draw from the internal torsion samplers.
In case of the first residue, only a psi given phi is drawn. Same
principle also applies for the last residue.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</p></li>
-<li><p><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</li>
+<li><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> If size of <em>actual_positions</em>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> If size of <em>actual_positions</em>
is not consistent with the internal sequence. Note, that the
sequence itself doesn’t get checked for efficiency reasons.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.SoftSampler">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SoftSampler</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">max_dev</em>, <em class="sig-param">n_stem_phi=-1.0472</em>, <em class="sig-param">c_stem_psi=-0.78540</em>, <em class="sig-param">prev_aa='A'</em>, <em class="sig-param">next_aa='A'</em>, <em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">SoftSampler</code><span class="sig-paren">(</span><em>sequence</em>, <em>torsion_sampler</em>, <em>max_dev</em>, <em>n_stem_phi=-1.0472</em>, <em>c_stem_psi=-0.78540</em>, <em>prev_aa='A'</em>, <em>next_aa='A'</em>, <em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>Instead of drawing completely new values for a residues phi/psi angles,
only one angle gets altered by a maximum value of <em>max_dev</em> in the
SoftSampler.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence that should be sampled</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Sampler, from which the phi/psi probablities are
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence that should be sampled</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Sampler, from which the phi/psi probablities are
extracted. It is also possible to pass a list of
samplers with same size as the sequence to assign
-a specific sampler per residue.</p></li>
-<li><p><strong>max_dev</strong> – Maximal deviation of dihedral angle from its original
-value per sampling step.</p></li>
-<li><p><strong>n_stem_phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi angle of the n_stem. This angle is not defined in
+a specific sampler per residue.</li>
+<li><strong>max_dev</strong> – Maximal deviation of dihedral angle from its original
+value per sampling step.</li>
+<li><strong>n_stem_phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi angle of the n_stem. This angle is not defined in
the sampling region. If the psi angle of the first
residue gets selected to be changed, <em>n_stem_phi</em> is
used to calculate the phi/psi probability to estimate
-the acceptance probability.</p></li>
-<li><p><strong>c_stem_psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi angle of c_stem. This angle is not defined in
+the acceptance probability.</li>
+<li><strong>c_stem_psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi angle of c_stem. This angle is not defined in
the sampling region. If the phi angle of the last
residue gets selected to be changed, <em>c_stem_psi</em> is
used to calculate the phi/psi probability to estimate
-the acceptance probability.</p></li>
-<li><p><strong>prev_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
+the acceptance probability.</li>
+<li><strong>prev_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
histogram index for the first residue from the
<em>torsion_sampler</em>. (Remember: The torsion sampler
-always considers triplets)</p></li>
-<li><p><strong>next_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
+always considers triplets)</li>
+<li><strong>next_aa</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – This parameter is necessary to extract the according
histogram index for the last residue from the
<em>torsion_sampler</em>. (Remember: The torsion sampler
-always considers triplets)</p></li>
-<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for the internal random number generators.</p></li>
+always considers triplets)</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for the internal random number generators.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.SoftSampler.Initialize">
-<code class="sig-name descname">Initialize</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler.Initialize" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler.Initialize" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up a new <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> by randomly drawing
phi/psi dihedral angles.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.SoftSampler.ProposeStep">
-<code class="sig-name descname">ProposeStep</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ProposeStep</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SoftSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
<dd><p>In an iterative process, the SoftSampler randomly selects one of the
possible dihedral angles in a conformation and changes it by a random value
in [-<em>max_dev</em>, <em>max_dev</em>]. The acceptance probability of this change is
@@ -321,78 +348,93 @@ the fraction of the phi/psi probability before and after changing the
single angle in the particular residue. There is a maximum of 100
iterations. It is therefore theoretically possible, that nothing happens
when a new step should be proposed</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</p></li>
-<li><p><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</li>
+<li><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> If size of <em>actual_positions</em>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> If size of <em>actual_positions</em>
is not consistent with the internal sequence. Note, that the
sequence itself doesn’t get checked for efficiency reasons.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.FragmentSampler">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FragmentSampler</code><span class="sig-paren">(</span><em class="sig-param">sequence</em>, <em class="sig-param">fraggers</em>, <em class="sig-param">init_bb_list=BackboneList(sequence)</em>, <em class="sig-param">sampling_start_index=0</em>, <em class="sig-param">init_fragments=3</em>, <em class="sig-param">seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">FragmentSampler</code><span class="sig-paren">(</span><em>sequence</em>, <em>fraggers</em>, <em>init_bb_list=BackboneList(sequence)</em>, <em>sampling_start_index=0</em>, <em>init_fragments=3</em>, <em>seed=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler" title="Permalink to this definition">¶</a></dt>
<dd><p>The FragmentSampler samples by replacing full fragments originating from a
list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> objects. The region, that actually gets
sampled is determined by <em>sampling_start_index</em> and number of
<a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> objects being available. All parts not covered
by any fragger remain rigid.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Overall sequence</p></li>
-<li><p><strong>fraggers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> objects. The first
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Overall sequence</li>
+<li><strong>fraggers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> objects. The first
fragger covers the region starting at the letter
<em>sampling_start_index</em> of the <em>sequence</em> and so on.
-All fraggers must contain fragments of equal size.</p></li>
-<li><p><strong>init_bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Initial conformation, that serves as a starting point for
+All fraggers must contain fragments of equal size.</li>
+<li><strong>init_bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Initial conformation, that serves as a starting point for
sampling. The default gets constructed using the default
constructor of <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> and
-results in a helix.</p></li>
-<li><p><strong>sampling_start_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Defines the beginning of the region, that actually
-gets sampled.</p></li>
-<li><p><strong>init_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – When calling the Initialize function, the positions get set
+results in a helix.</li>
+<li><strong>sampling_start_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Defines the beginning of the region, that actually
+gets sampled.</li>
+<li><strong>init_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – When calling the Initialize function, the positions get set
to the ones of <em>init_bb_list</em>. This is the number of
-fragments that gets randomly selected and inserted.</p></li>
-<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for the internal random number generators</p></li>
+fragments that gets randomly selected and inserted.</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for the internal random number generators</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.FragmentSampler.Initialize">
-<code class="sig-name descname">Initialize</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler.Initialize" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler.Initialize" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets up a new <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a> by setting the setting
bb_list = <em>init_bb_list</em> and randomly replace n fragments
with n = <em>init_fragments</em></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The newly created conformation gets stored in here</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.FragmentSampler.ProposeStep">
-<code class="sig-name descname">ProposeStep</code><span class="sig-paren">(</span><em class="sig-param">actual_step</em>, <em class="sig-param">proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ProposeStep</code><span class="sig-paren">(</span><em>actual_step</em>, <em>proposed_position</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FragmentSampler.ProposeStep" title="Permalink to this definition">¶</a></dt>
<dd><p>Randomly selects a position and selects a random fragment from the according
fragger object to alter the conformation.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</p></li>
-<li><p><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</li>
+<li><strong>proposed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -409,217 +451,259 @@ use any of the provided closers or any object that implements the
functionality of <a class="reference internal" href="#promod3.modelling.CloserBase" title="promod3.modelling.CloserBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">CloserBase</span></code></a>.</p>
<dl class="class">
<dt id="promod3.modelling.CloserBase">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CloserBase</code><a class="headerlink" href="#promod3.modelling.CloserBase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CloserBase</code><a class="headerlink" href="#promod3.modelling.CloserBase" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class defining the functions that must be implemented by any
closer.</p>
<dl class="method">
<dt id="promod3.modelling.CloserBase.Close">
-<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloserBase.Close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloserBase.Close" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes current positions and proposes a new conformation that fits to a
given environment.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Starting point, must not change when calling this
-function.</p></li>
-<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Starting point, must not change when calling this
+function.</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Passed by reference, so the resulting
<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> is assigned to
-this parameter.</p></li>
+this parameter.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Whether closing procedure was successful</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Whether closing procedure was successful</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.CCDCloser">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CCDCloser</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">sequence</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCDCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CCDCloser</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>sequence</em>, <em>torsion_sampler</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCDCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>The CCDCloser applies the CCD algorithm to the sampled conformation
to enforce the match between the conformations stem residue and
the stems given by the closer. The <em>torsion_sampler</em> is used to
avoid moving into unfavourable phi/psi ranges.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
-should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
-should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the conformation to be closed.</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</li>
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the conformation to be closed.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – To enforce valid phi/psi ranges. Alternatively, you
can also pass a list of sampler objects to assign a
unique torsion sampler to every residue of the
-conformation to be closed.</p></li>
-<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random generators.</p></li>
+conformation to be closed.</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random generators.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.CCDCloser.Close">
-<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCDCloser.Close" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</p></li>
-<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</p></li>
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CCDCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Whether CCD converged</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether CCD converged</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.DirtyCCDCloser">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">DirtyCCDCloser</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DirtyCCDCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">DirtyCCDCloser</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DirtyCCDCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>The DirtyCCDCloser applies the CCD algorithm to the sampled conformation
to enforce the match between the conformations stem residue and
the stems given by the closer. There is no check for reasonable backbone
dihedral angles as it is the case for the <a class="reference internal" href="#promod3.modelling.CCDCloser" title="promod3.modelling.CCDCloser"><code class="xref py py-class docutils literal notranslate"><span class="pre">CCDCloser</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
-should adapt.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
-should adapt.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+should adapt.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+should adapt.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.DirtyCCDCloser.Close">
-<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DirtyCCDCloser.Close" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</p></li>
-<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</p></li>
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DirtyCCDCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Whether CCD converged</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether CCD converged</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.KICCloser">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">KICCloser</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em>, <em class="sig-param">c_stem</em>, <em class="sig-param">seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KICCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">KICCloser</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KICCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>The KIC closer randomly picks three pivot residues in the conformation
to be closed and applies the KIC algorithm. KIC gives up to 16 possible
solutions. The KICCloser simply picks the first one.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
-adapt.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
-adapt.</p></li>
-<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random generators.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+adapt.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+adapt.</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random generators.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.KICCloser.Close">
-<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KICCloser.Close" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</p></li>
-<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</p></li>
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.KICCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed.</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed conformation gets stored in here.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Whether KIC found a solution</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether KIC found a solution</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.NTerminalCloser">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">NTerminalCloser</code><span class="sig-paren">(</span><em class="sig-param">c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">NTerminalCloser</code><span class="sig-paren">(</span><em>c_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>The <a class="reference internal" href="#promod3.modelling.NTerminalCloser" title="promod3.modelling.NTerminalCloser"><code class="xref py py-class docutils literal notranslate"><span class="pre">NTerminalCloser</span></code></a> simply takes the conformation and closes by
superposing the c_stem with the desired positions.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
-adapt.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+adapt.</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.NTerminalCloser.Close">
-<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed (or in this case
-transformed in space).</p></li>
-<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed (transformed) conformation gets stored in
-here.</p></li>
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.NTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed (or in this case
+transformed in space).</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed (transformed) conformation gets stored in
+here.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Whether closing was successful</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether closing was successful</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.CTerminalCloser">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CTerminalCloser</code><span class="sig-paren">(</span><em class="sig-param">n_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CTerminalCloser</code><span class="sig-paren">(</span><em>n_stem</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>The <a class="reference internal" href="#promod3.modelling.CTerminalCloser" title="promod3.modelling.CTerminalCloser"><code class="xref py py-class docutils literal notranslate"><span class="pre">CTerminalCloser</span></code></a> simply takes the conformation and closes by
superposing the n_stem with the desired positions.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
-adapt.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+adapt.</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.CTerminalCloser.Close">
-<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed (or in this case
-transformed in space).</p></li>
-<li><p><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed (transformed) conformation gets stored in
-here.</p></li>
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CTerminalCloser.Close" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>actual_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Conformation to be closed (or in this case
+transformed in space).</li>
+<li><strong>closed_positions</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Closed (transformed) conformation gets stored in
+here.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Whether closing was successful</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Whether closing was successful</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.DeNovoCloser">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">DeNovoCloser</code><a class="headerlink" href="#promod3.modelling.DeNovoCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">DeNovoCloser</code><a class="headerlink" href="#promod3.modelling.DeNovoCloser" title="Permalink to this definition">¶</a></dt>
<dd><p>In case of sampling a full stretch, you dont have external constraints. The
closer has a rather boring job in this case.</p>
<dl class="method">
<dt id="promod3.modelling.DeNovoCloser.Close">
-<code class="sig-name descname">Close</code><span class="sig-paren">(</span><em class="sig-param">actual_positions</em>, <em class="sig-param">closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DeNovoCloser.Close" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Close</code><span class="sig-paren">(</span><em>actual_positions</em>, <em>closed_positions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DeNovoCloser.Close" title="Permalink to this definition">¶</a></dt>
<dd><p>Does absolutely nothing, except copying over the coordinates from
<em>actual_positions</em> to <em>closed_positions</em> and return true.</p>
</dd></dl>
@@ -634,76 +718,82 @@ energy, the lower the better. You can either use the provided scorer or any
object implementing the functionality defined in <a class="reference internal" href="#promod3.modelling.ScorerBase" title="promod3.modelling.ScorerBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScorerBase</span></code></a>.</p>
<dl class="class">
<dt id="promod3.modelling.ScorerBase">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ScorerBase</code><a class="headerlink" href="#promod3.modelling.ScorerBase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ScorerBase</code><a class="headerlink" href="#promod3.modelling.ScorerBase" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class defining the functions that must be implemented by any
scorer.</p>
<dl class="method">
<dt id="promod3.modelling.ScorerBase.GetScore">
-<code class="sig-name descname">GetScore</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScorerBase.GetScore" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScorerBase.GetScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes coordinates and spits out a score given some internal structural
environment.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Coordinates to be scored</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The score</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a>) – Coordinates to be scored</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The score</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.LinearScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">LinearScorer</code><span class="sig-paren">(</span><em class="sig-param">scorer</em>, <em class="sig-param">scorer_env</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx</em>, <em class="sig-param">linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">LinearScorer</code><span class="sig-paren">(</span><em>scorer</em>, <em>scorer_env</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx</em>, <em>linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>The LinearScorer allows to combine the scores available from
<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a> in a linear manner. See
<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="promod3.scoring.BackboneOverallScorer.CalculateLinearCombination"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CalculateLinearCombination()</span></code></a> for a
detailed description of the arguments.</p>
<div class="admonition warning">
-<p class="admonition-title">Warning</p>
-<p>The provided <em>scorer_env</em> will be altered in every
+<p class="first admonition-title">Warning</p>
+<p class="last">The provided <em>scorer_env</em> will be altered in every
<a class="reference internal" href="#promod3.modelling.LinearScorer.GetScore" title="promod3.modelling.LinearScorer.GetScore"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetScore()</span></code></a> call.
You might consider the Stash / Pop mechanism of the
<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> to restore to the
original state once the sampling is done.</p>
</div>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a>) – Scorer Object with set environment for the particular loop
-modelling problem.</p></li>
-<li><p><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – The environment that is linked to the <em>scorer</em></p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES.</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues to score</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belong to.</p></li>
-<li><p><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
-values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)) – Weights for each desired scorer.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a>) – Scorer Object with set environment for the particular loop
+modelling problem.</li>
+<li><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – The environment that is linked to the <em>scorer</em></li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES.</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues to score</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belong to.</li>
+<li><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
+values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)) – Weights for each desired scorer.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
which no scorer exists</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.LinearScorer.GetScore">
-<code class="sig-name descname">GetScore</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer.GetScore" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to be scored.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A linear combination of the scores</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer.GetScore" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to be scored.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A linear combination of the scores</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -718,25 +808,27 @@ or any object implementing the functionality defined in
<a class="reference internal" href="#promod3.modelling.CoolerBase" title="promod3.modelling.CoolerBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">CoolerBase</span></code></a>.</p>
<dl class="class">
<dt id="promod3.modelling.CoolerBase">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CoolerBase</code><a class="headerlink" href="#promod3.modelling.CoolerBase" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">CoolerBase</code><a class="headerlink" href="#promod3.modelling.CoolerBase" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class defining the functions that must be implemented by any
cooler.</p>
<dl class="method">
<dt id="promod3.modelling.CoolerBase.GetTemperature">
-<code class="sig-name descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.GetTemperature" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The Temperature</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.GetTemperature" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The Temperature</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.CoolerBase.Reset">
-<code class="sig-name descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.Reset" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CoolerBase.Reset" title="Permalink to this definition">¶</a></dt>
<dd><p>Resets to original state, so a new Monte Carlo trajectory can be generated</p>
</dd></dl>
@@ -744,33 +836,40 @@ cooler.</p>
<dl class="class">
<dt id="promod3.modelling.ExponentialCooler">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ExponentialCooler</code><span class="sig-paren">(</span><em class="sig-param">change_frequency</em>, <em class="sig-param">start_temperature</em>, <em class="sig-param">cooling_factor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ExponentialCooler</code><span class="sig-paren">(</span><em>change_frequency</em>, <em>start_temperature</em>, <em>cooling_factor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler" title="Permalink to this definition">¶</a></dt>
<dd><p>The exponential cooler starts with a given <em>start_temperature</em> and counts the
calls to its <a class="reference internal" href="#promod3.modelling.ExponentialCooler.GetTemperature" title="promod3.modelling.ExponentialCooler.GetTemperature"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetTemperature()</span></code></a> function. According to the
<em>change_frequency</em>, the returned temperature gets multiplied by the
<em>cooling_factor</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>change_frequency</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Frequency to change temperature</p></li>
-<li><p><strong>start_temperature</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – temperature to start with</p></li>
-<li><p><strong>cooling_factor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor to decrease temperature</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>change_frequency</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Frequency to change temperature</li>
+<li><strong>start_temperature</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – temperature to start with</li>
+<li><strong>cooling_factor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor to decrease temperature</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.ExponentialCooler.GetTemperature">
-<code class="sig-name descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler.GetTemperature" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>current temperature</p>
-</dd>
-</dl>
+<code class="descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler.GetTemperature" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">current temperature</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ExponentialCooler.Reset">
-<code class="sig-name descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler.Reset" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ExponentialCooler.Reset" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets current temperature back to <em>start_temperature</em> and the
internal counter to 0</p>
</dd></dl>
@@ -782,7 +881,6 @@ internal counter to 0</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -803,12 +901,12 @@ internal counter to 0</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -825,7 +923,7 @@ internal counter to 0</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="loop_closing.html" title="previous chapter">Fitting Loops Into Gaps</a></li>
<li>Next: <a href="sidechain_reconstruction.html" title="next chapter">Sidechain Reconstruction</a></li>
</ul></li>
@@ -834,33 +932,27 @@ internal counter to 0</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
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-
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</div>
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</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/monte_carlo.rst.txt"
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index 59e416f6890acd8b8e90a74b7c38d802c2d44d7a..184688346f49e5b7d8d9cfdeec85da76417ef6d5 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Modelling Pipeline — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Modelling Pipeline — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,24 +30,22 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="modelling-pipeline">
<h1>Modelling Pipeline<a class="headerlink" href="#modelling-pipeline" title="Permalink to this headline">¶</a></h1>
<p>A protein homology modelling pipeline has the following main steps:</p>
<ul class="simple">
-<li><p>Build a raw model from the template (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a> function)</p></li>
-<li><p>Perform loop modelling to close (or remove) all gaps (see functions
+<li>Build a raw model from the template (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a> function)</li>
+<li>Perform loop modelling to close (or remove) all gaps (see functions
<a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>, <a class="reference internal" href="#promod3.modelling.RemoveTerminalGaps" title="promod3.modelling.RemoveTerminalGaps"><code class="xref py py-func docutils literal notranslate"><span class="pre">RemoveTerminalGaps()</span></code></a>,
<a class="reference internal" href="#promod3.modelling.MergeGapsByDistance" title="promod3.modelling.MergeGapsByDistance"><code class="xref py py-func docutils literal notranslate"><span class="pre">MergeGapsByDistance()</span></code></a>, <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>,
<a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByMonteCarlo()</span></code></a>, <a class="reference internal" href="#promod3.modelling.CloseLargeDeletions" title="promod3.modelling.CloseLargeDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseLargeDeletions()</span></code></a> or
<a class="reference internal" href="#promod3.modelling.CloseGaps" title="promod3.modelling.CloseGaps"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseGaps()</span></code></a> that calls all these functions using predefined
-heuristics)</p></li>
-<li><p>Build sidechains (see <a class="reference internal" href="#promod3.modelling.BuildSidechains" title="promod3.modelling.BuildSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildSidechains()</span></code></a> function)</p></li>
-<li><p>Minimize energy of final model using molecular mechanics
-(see <a class="reference internal" href="#promod3.modelling.MinimizeModelEnergy" title="promod3.modelling.MinimizeModelEnergy"><code class="xref py py-func docutils literal notranslate"><span class="pre">MinimizeModelEnergy()</span></code></a> function)</p></li>
+heuristics)</li>
+<li>Build sidechains (see <a class="reference internal" href="#promod3.modelling.BuildSidechains" title="promod3.modelling.BuildSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildSidechains()</span></code></a> function)</li>
+<li>Minimize energy of final model using molecular mechanics
+(see <a class="reference internal" href="#promod3.modelling.MinimizeModelEnergy" title="promod3.modelling.MinimizeModelEnergy"><code class="xref py py-func docutils literal notranslate"><span class="pre">MinimizeModelEnergy()</span></code></a> function)</li>
</ul>
<p>The last steps to go from a raw model to a final model can easily be executed
with the <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a> function. If you want to run and tweak the
@@ -93,190 +92,229 @@ purposes:</p>
<h2>Build Raw Modelling Handle<a class="headerlink" href="#build-raw-modelling-handle" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.modelling.ModellingHandle">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ModellingHandle</code><a class="headerlink" href="#promod3.modelling.ModellingHandle" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ModellingHandle</code><a class="headerlink" href="#promod3.modelling.ModellingHandle" title="Permalink to this definition">¶</a></dt>
<dd><p>Handles the result for structure model building and provides high-level methods
to turn an initial raw model (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a>)
into a complete protein model by removing any existing gaps.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.model">
-<code class="sig-name descname">model</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.model" title="Permalink to this definition">¶</a></dt>
+<code class="descname">model</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.model" title="Permalink to this definition">¶</a></dt>
<dd><p>The resulting model. This includes one chain per target chain (in the same
order as the sequences in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>) and (if they were included) a
chain named ‘_’ for ligands. You can therefore access <cite>model.chains</cite> items
and <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a> items with the same indexing and the optional ligand
chain follows afterwards.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.gaps">
-<code class="sig-name descname">gaps</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.gaps" title="Permalink to this definition">¶</a></dt>
+<code class="descname">gaps</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.gaps" title="Permalink to this definition">¶</a></dt>
<dd><p>List of gaps in the model that could not be copied from the template. These
gaps may be the result of insertions/deletions in the alignment or due to
missing or incomplete backbone coordinates in the template structure.
Gaps of different chains are appended one after another.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGapList" title="promod3.modelling.StructuralGapList"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGapList</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGapList" title="promod3.modelling.StructuralGapList"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGapList</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.seqres">
-<code class="sig-name descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
+<code class="descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain
of the target protein.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.profiles">
-<code class="sig-name descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
+<code class="descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>). Please note, that this
attribute won’t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>. You have
to fill it manually or even better by the convenient function
<a class="reference internal" href="#promod3.modelling.SetSequenceProfiles" title="promod3.modelling.SetSequenceProfiles"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetSequenceProfiles()</span></code></a>, to ensure consistency with the seqres.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.psipred_predictions">
-<code class="sig-name descname">psipred_predictions</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.psipred_predictions" title="Permalink to this definition">¶</a></dt>
+<code class="descname">psipred_predictions</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.psipred_predictions" title="Permalink to this definition">¶</a></dt>
<dd><p>List of predictions with one <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a> for
each chain of the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>). Please
note, that this attribute won’t be set by simply calling
<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>. You have to fill it manually or even better by
the convenient function <a class="reference internal" href="#promod3.modelling.SetPsipredPredictions" title="promod3.modelling.SetPsipredPredictions"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetPsipredPredictions()</span></code></a>, to ensure
consistency with the seqres.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.backbone_scorer_env">
-<code class="sig-name descname">backbone_scorer_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="Permalink to this definition">¶</a></dt>
+<code class="descname">backbone_scorer_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="Permalink to this definition">¶</a></dt>
<dd><p>Backbone score environment attached to this handle. A default environment is
set with <a class="reference internal" href="#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> when needed. Additional
information can be added to the environment before running the pipeline
steps.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.backbone_scorer">
-<code class="sig-name descname">backbone_scorer</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">backbone_scorer</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Backbone scorer container attached to this handle. A default set of scorers
is initialized with <a class="reference internal" href="#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> when needed.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.all_atom_scorer_env">
-<code class="sig-name descname">all_atom_scorer_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="Permalink to this definition">¶</a></dt>
+<code class="descname">all_atom_scorer_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="Permalink to this definition">¶</a></dt>
<dd><p>All atom environment attached to this handle for scoring. A default
environment is set with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when needed. This
environment is for temporary work only and is only updated to score loops.
It is not to be updated when loops are chosen and added to the final model.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.all_atom_scorer">
-<code class="sig-name descname">all_atom_scorer</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">all_atom_scorer</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="Permalink to this definition">¶</a></dt>
<dd><p>All atom scorer container attached to this handle. A default set of scorers
is initialized with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when needed.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer" title="promod3.scoring.AllAtomOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomOverallScorer</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomOverallScorer" title="promod3.scoring.AllAtomOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomOverallScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.all_atom_sidechain_env">
-<code class="sig-name descname">all_atom_sidechain_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="Permalink to this definition">¶</a></dt>
+<code class="descname">all_atom_sidechain_env</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="Permalink to this definition">¶</a></dt>
<dd><p>All atom environment attached to this handle for sidechain reconstruction. A
default environment is set with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when
needed.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.sidechain_reconstructor">
-<code class="sig-name descname">sidechain_reconstructor</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sidechain_reconstructor</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>A sidechain reconstructor to add sidechains to loops prior to all atom
scoring. A default one is set with <a class="reference internal" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a> when
needed.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.fragger_handles">
-<code class="sig-name descname">fragger_handles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.fragger_handles" title="Permalink to this definition">¶</a></dt>
+<code class="descname">fragger_handles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.fragger_handles" title="Permalink to this definition">¶</a></dt>
<dd><p>Optional attribute which is set in <a class="reference internal" href="#promod3.modelling.SetFraggerHandles" title="promod3.modelling.SetFraggerHandles"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetFraggerHandles()</span></code></a>. Use
<code class="xref py py-meth docutils literal notranslate"><span class="pre">hasattr()</span></code> to check if it’s available. If it’s set, it is used in
<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.modelling_issues">
-<code class="sig-name descname">modelling_issues</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.modelling_issues" title="Permalink to this definition">¶</a></dt>
+<code class="descname">modelling_issues</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.modelling_issues" title="Permalink to this definition">¶</a></dt>
<dd><p>Optional attribute which is set in <a class="reference internal" href="#promod3.modelling.AddModellingIssue" title="promod3.modelling.AddModellingIssue"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddModellingIssue()</span></code></a>. Use
<code class="xref py py-meth docutils literal notranslate"><span class="pre">hasattr()</span></code> to check if it’s available. If it’s set, it can be used to
check issues which occurred in <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a> (see
<a class="reference internal" href="#promod3.modelling.MinimizeModelEnergy" title="promod3.modelling.MinimizeModelEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">MinimizeModelEnergy()</span></code></a> and <a class="reference internal" href="#promod3.modelling.CheckFinalModel" title="promod3.modelling.CheckFinalModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CheckFinalModel()</span></code></a> for details).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ModellingIssue" title="promod3.modelling.ModellingIssue"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingIssue</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.modelling.ModellingIssue" title="promod3.modelling.ModellingIssue"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingIssue</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.ModellingHandle.Copy">
-<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingHandle.Copy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingHandle.Copy" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates a deep copy. Everything will be copied over to the returned
<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>, except the potentially set scoring members
<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="promod3.modelling.ModellingHandle.backbone_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer</span></code></a>,
@@ -285,21 +323,23 @@ check issues which occurred in <a class="reference internal" href="#promod3.mode
<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="promod3.modelling.ModellingHandle.all_atom_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer</span></code></a>,
<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="promod3.modelling.ModellingHandle.all_atom_sidechain_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_sidechain_env</span></code></a> and
<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sidechain_reconstructor</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>A deep copy of the current handle</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A deep copy of the current handle</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.BuildRawModel">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">BuildRawModel</code><span class="sig-paren">(</span><em class="sig-param">aln</em>, <em class="sig-param">chain_names=None</em>, <em class="sig-param">include_ligands=False</em>, <em class="sig-param">spdbv_style=False</em>, <em class="sig-param">aln_preprocessing='default'</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildRawModel" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">BuildRawModel</code><span class="sig-paren">(</span><em>aln</em>, <em>chain_names=None</em>, <em>include_ligands=False</em>, <em>spdbv_style=False</em>, <em>aln_preprocessing='default'</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildRawModel" title="Permalink to this definition">¶</a></dt>
<dd><p>Builds a raw (pseudo) model from the alignment. Can either take a single
alignment handle or an alignment handle list. Every list item is treated as a
single chain in the final raw model.</p>
@@ -316,9 +356,9 @@ deuterium atoms are not copied into the model.</p>
residues are treated as follows:</p>
<blockquote>
<div><ul class="simple">
-<li><p>Selenium methionine residues are converted to methionine</p></li>
-<li><p>Side chains which contain all atoms of the parent amino acid, e.g.
-phosphoserine are copied as a whole with the modifications stripped off.</p></li>
+<li>Selenium methionine residues are converted to methionine</li>
+<li>Side chains which contain all atoms of the parent amino acid, e.g.
+phosphoserine are copied as a whole with the modifications stripped off.</li>
</ul>
</div></blockquote>
<p>Residues with missing backbone atoms and D-peptides are generally skipped and
@@ -330,19 +370,21 @@ subsequent loop modelling can insert new residues without having to renumber.
<strong>The numbering of residues starts for every chain with the value 1</strong>.</p>
<p>The returned <a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a> stores the obtained raw model as well
as information about insertions and deletions in the gaps list.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
-list of alignment handles for raw model with multiple chains.</p></li>
-<li><p><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if we wish to include ligands in the model. This
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
+list of alignment handles for raw model with multiple chains.</li>
+<li><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if we wish to include ligands in the model. This
searches for ligands in all OST handles of the views
attached to the alignments. Ligands are identified
with the <cite>ligand</cite> property in the handle (set by OST
based on HET records) or by the chain name ‘_’ (as set
in SMTL). All ligands are added to a new chain named
-‘_’.</p></li>
-<li><p><strong>chain_names</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – If set, this overrides the default chain naming
+‘_’.</li>
+<li><strong>chain_names</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – If set, this overrides the default chain naming
(chains are consecutively named according to
characters in
‘ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz’).
@@ -352,33 +394,35 @@ If <em>aln</em> is of type <code class="xref py py-class docutils literal notran
<em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> of same size as <em>aln</em> or a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>.
For the latter case, chains will consecutively named
-according to characters in <em>chain_names</em>.</p></li>
-<li><p><strong>spdbv_style</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if we need a model in the old SPDBV style.</p></li>
-<li><p><strong>aln_preprocessing</strong> – Calls <a class="reference internal" href="#promod3.modelling.PullTerminalDeletions" title="promod3.modelling.PullTerminalDeletions"><code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.modelling.PullTerminalDeletions()</span></code></a>
+according to characters in <em>chain_names</em>.</li>
+<li><strong>spdbv_style</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if we need a model in the old SPDBV style.</li>
+<li><strong>aln_preprocessing</strong> – Calls <a class="reference internal" href="#promod3.modelling.PullTerminalDeletions" title="promod3.modelling.PullTerminalDeletions"><code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.modelling.PullTerminalDeletions()</span></code></a>
if set to ‘default’. Can be disabled when set
-to False.</p></li>
+to False.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Raw (pseudo) model from the alignment.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> when:</p>
-<ul class="simple">
-<li><p>the alignments do not have two sequences</p></li>
-<li><p>the second sequence does not have an attached structure</p></li>
-<li><p>the residues of the template structure do not match with the
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Raw (pseudo) model from the alignment.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first">A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> when:</p>
+<ul class="last simple">
+<li>the alignments do not have two sequences</li>
+<li>the second sequence does not have an attached structure</li>
+<li>the residues of the template structure do not match with the
alignment sequence (note that you can set an “offset” (see
<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetSequenceOffset()</span></code></a>) for the
-template sequence (but not for the target))</p></li>
-<li><p>the target sequence has a non-zero offset (cannot be honored as
-the resulting model will always start its residue numbering at 1)</p></li>
+template sequence (but not for the target))</li>
+<li>the target sequence has a non-zero offset (cannot be honored as
+the resulting model will always start its residue numbering at 1)</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -386,7 +430,7 @@ the resulting model will always start its residue numbering at 1)</p></li>
<h2>The Default Pipeline<a class="headerlink" href="#the-default-pipeline" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.BuildFromRawModel">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">BuildFromRawModel</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">use_amber_ff=False</em>, <em class="sig-param">extra_force_fields=[]</em>, <em class="sig-param">model_termini=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildFromRawModel" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">BuildFromRawModel</code><span class="sig-paren">(</span><em>mhandle</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em>, <em>model_termini=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildFromRawModel" title="Permalink to this definition">¶</a></dt>
<dd><p>Build a model starting with a raw model (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a>).</p>
<p>This function implements a recommended pipeline to generate complete models
from a raw model. The steps are shown in detail in the code example
@@ -406,23 +450,25 @@ attached using <a class="reference internal" href="#promod3.modelling.SetFragger
But be aware of increased runtime due to the fragment search step.</p>
<p>If the function fails to close all gaps, it will produce a warning and
return an incomplete model.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
-alignment.</p></li>
-<li><p><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
+alignment.</li>
+<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
and <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
Both do a similarly good job without ligands (CHARMM
slightly better), but you will want to be consistent
-with the optional force fields in <cite>extra_force_fields</cite>.</p></li>
-<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
+with the optional force fields in <cite>extra_force_fields</cite>.</li>
+<li><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
(ligand) residue cannot be parametrized with the
default force field. The force fields are tried
in the order as given and ligands without an
-existing parametrization are skipped.</p></li>
-<li><p><strong>model_termini</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – The default modelling pipeline in ProMod3 is optimized
+existing parametrization are skipped.</li>
+<li><strong>model_termini</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – The default modelling pipeline in ProMod3 is optimized
to generate a gap-free model of the region in the
target sequence(s) that is covered with template
information. Terminal extensions without template
@@ -431,16 +477,18 @@ You can activate this flag to enforce a model of the
full target sequence(s). The terminal parts will be
modelled with a crude Monte Carlo approach. Be aware
that the accuracy of those termini is likely to be
-limited. Termini of length 1 won’t be modelled.</p></li>
+limited.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Delivers the model as an OST entity.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Delivers the model as an OST entity.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -448,128 +496,141 @@ limited. Termini of length 1 won’t be modelled.</p></li>
<h2>Modelling Steps<a class="headerlink" href="#modelling-steps" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.SetupDefaultBackboneScoring">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SetupDefaultBackboneScoring</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetupDefaultBackboneScoring" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">SetupDefaultBackboneScoring</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetupDefaultBackboneScoring" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup scorers and environment for meddling with backbones.
This one is already tailored towards a certain modelling job.
The scorers added (with their respective keys) are:</p>
<ul class="simple">
-<li><p>“cb_packing”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a></p></li>
-<li><p>“cbeta”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a></p></li>
-<li><p>“reduced”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a></p></li>
-<li><p>“clash”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.ClashScorer" title="promod3.scoring.ClashScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ClashScorer</span></code></a></p></li>
-<li><p>“hbond”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a></p></li>
-<li><p>“torsion”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a></p></li>
-<li><p>“pairwise”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer" title="promod3.scoring.PairwiseScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseScorer</span></code></a></p></li>
+<li>“cb_packing”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a></li>
+<li>“cbeta”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a></li>
+<li>“reduced”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a></li>
+<li>“clash”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.ClashScorer" title="promod3.scoring.ClashScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ClashScorer</span></code></a></li>
+<li>“hbond”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a></li>
+<li>“torsion”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a></li>
+<li>“pairwise”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer" title="promod3.scoring.PairwiseScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseScorer</span></code></a></li>
</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The modelling handle. This will set the properties
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The modelling handle. This will set the properties
<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="promod3.modelling.ModellingHandle.backbone_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer</span></code></a> and
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="promod3.modelling.ModellingHandle.backbone_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer_env</span></code></a> of <cite>mhandle</cite>.</p>
-</dd>
-</dl>
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="promod3.modelling.ModellingHandle.backbone_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer_env</span></code></a> of <cite>mhandle</cite>.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.IsBackboneScoringSetUp">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">IsBackboneScoringSetUp</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.IsBackboneScoringSetUp" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if <a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="promod3.modelling.ModellingHandle.backbone_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer</span></code></a> and
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="promod3.modelling.ModellingHandle.backbone_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer_env</span></code></a> of <cite>mhandle</cite> are set.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle to check.</p>
-</dd>
-</dl>
+<code class="descclassname">promod3.modelling.</code><code class="descname">IsBackboneScoringSetUp</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.IsBackboneScoringSetUp" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if <a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer" title="promod3.modelling.ModellingHandle.backbone_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer</span></code></a> and
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.backbone_scorer_env" title="promod3.modelling.ModellingHandle.backbone_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">backbone_scorer_env</span></code></a> of <cite>mhandle</cite> are set.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle to check.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.SetupDefaultAllAtomScoring">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SetupDefaultAllAtomScoring</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">SetupDefaultAllAtomScoring</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetupDefaultAllAtomScoring" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup scorers and environment to perform all atom scoring.
This one is already tailored towards a certain modelling job, where we
reconstruct sidechains for loop candidates and score them.
The scorers added (with their respective keys) are:</p>
<ul class="simple">
-<li><p>“aa_interaction”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a></p></li>
-<li><p>“aa_packing”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a></p></li>
-<li><p>“aa_clash”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer" title="promod3.scoring.AllAtomClashScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomClashScorer</span></code></a></p></li>
+<li>“aa_interaction”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a></li>
+<li>“aa_packing”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a></li>
+<li>“aa_clash”: <a class="reference internal" href="../scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer" title="promod3.scoring.AllAtomClashScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomClashScorer</span></code></a></li>
</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The modelling handle. This will set the properties
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The modelling handle. This will set the properties
<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer_env</span></code></a>,
<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="promod3.modelling.ModellingHandle.all_atom_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer</span></code></a>,
<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="promod3.modelling.ModellingHandle.all_atom_sidechain_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_sidechain_env</span></code></a> and
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sidechain_reconstructor</span></code></a>.</p>
-</dd>
-</dl>
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sidechain_reconstructor</span></code></a>.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.IsAllAtomScoringSetUp">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">IsAllAtomScoringSetUp</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.IsAllAtomScoringSetUp" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if <a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer_env</span></code></a>,
+<code class="descclassname">promod3.modelling.</code><code class="descname">IsAllAtomScoringSetUp</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.IsAllAtomScoringSetUp" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if <a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer_env</span></code></a>,
<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer" title="promod3.modelling.ModellingHandle.all_atom_scorer"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer</span></code></a>,
<a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_sidechain_env" title="promod3.modelling.ModellingHandle.all_atom_sidechain_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_sidechain_env</span></code></a> and
-<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sidechain_reconstructor</span></code></a> of <cite>mhandle</cite> are set.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle to check.</p>
-</dd>
-</dl>
+<a class="reference internal" href="#promod3.modelling.ModellingHandle.sidechain_reconstructor" title="promod3.modelling.ModellingHandle.sidechain_reconstructor"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sidechain_reconstructor</span></code></a> of <cite>mhandle</cite> are set.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle to check.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.InsertLoop">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">InsertLoop</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">bb_list</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.InsertLoop" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">InsertLoop</code><span class="sig-paren">(</span><em>mhandle</em>, <em>bb_list</em>, <em>start_resnum</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.InsertLoop" title="Permalink to this definition">¶</a></dt>
<dd><p>Insert loop into model and ensure consistent updating of scoring environments.
Note that we do not update <a class="reference internal" href="#promod3.modelling.ModellingHandle.all_atom_scorer_env" title="promod3.modelling.ModellingHandle.all_atom_scorer_env"><code class="xref py py-attr docutils literal notranslate"><span class="pre">all_atom_scorer_env</span></code></a> as
that one is meant to be updated only while scoring. To clear a gap while
inserting a loop, use the simpler <a class="reference internal" href="gap_handling.html#promod3.modelling.InsertLoopClearGaps" title="promod3.modelling.InsertLoopClearGaps"><code class="xref py py-meth docutils literal notranslate"><span class="pre">InsertLoopClearGaps()</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to insert (backbone only).</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the start position in the SEQRES.</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop belongs to.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Loop to insert (backbone only).</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop belongs to.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.RemoveTerminalGaps">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">RemoveTerminalGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RemoveTerminalGaps" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">RemoveTerminalGaps</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RemoveTerminalGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes terminal gaps without modelling them (just removes them from the list
of gaps). This is useful for pipelines which lack the possibility to properly
model loops at the termini.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Number of gaps which were removed.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Number of gaps which were removed.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.ReorderGaps">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ReorderGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReorderGaps" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">ReorderGaps</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReorderGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Reorders all gaps to ensure sequential order by performing lexicographical
comparison on the sequence formed by chain index of the gap and
start residue number.</p>
@@ -577,7 +638,7 @@ start residue number.</p>
<dl class="function">
<dt id="promod3.modelling.MergeMHandle">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MergeMHandle</code><span class="sig-paren">(</span><em class="sig-param">source_mhandle</em>, <em class="sig-param">target_mhandle</em>, <em class="sig-param">source_chain_idx</em>, <em class="sig-param">target_chain_idx</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">end_resnum</em>, <em class="sig-param">transform</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeMHandle" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">MergeMHandle</code><span class="sig-paren">(</span><em>source_mhandle</em>, <em>target_mhandle</em>, <em>source_chain_idx</em>, <em>target_chain_idx</em>, <em>start_resnum</em>, <em>end_resnum</em>, <em>transform</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeMHandle" title="Permalink to this definition">¶</a></dt>
<dd><p>Merges the specified stretch of <strong>source_mhandle</strong> into <strong>target_mhandle</strong> by
replacing all structural information and gaps in the stretch
<strong>start_resnum</strong> and <strong>end_resnum</strong> (inclusive). The residues specified by
@@ -587,144 +648,164 @@ i.e. not be enclosed by a gap. If a gap encloses <strong>start_resnum</strong> o
shortened version not including the part overlapping with the defined stretch.
If there is any scoring set up (backbone or all atom), the according
environments get updated in <strong>target_mhandle</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>source_mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Source of structural information and gaps</p></li>
-<li><p><strong>target_mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Structural information and gaps will be copied in here</p></li>
-<li><p><strong>source_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – This is the chain where the info comes from</p></li>
-<li><p><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – This is the chain where the info goes to</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue of the copied stretch</p></li>
-<li><p><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Last residue of the copied stretch</p></li>
-<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
-they’re copied over</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>source_mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Source of structural information and gaps</li>
+<li><strong>target_mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Structural information and gaps will be copied in here</li>
+<li><strong>source_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – This is the chain where the info comes from</li>
+<li><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – This is the chain where the info goes to</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue of the copied stretch</li>
+<li><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Last residue of the copied stretch</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
+they’re copied over</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> when:</p>
-<ul class="simple">
-<li><p>the chain indices are invalid</p></li>
-<li><p>the SEQRES of the specified chains do not match</p></li>
-<li><p>the start and end residue numbers are invalid or when the residues
-at the specified positions in the <strong>source_mhandle</strong> do not exist</p></li>
-<li><p>a gap in the <strong>source_mhandle</strong> encloses the residues specified by
-<strong>start_resnum</strong> and <strong>end_resnum</strong></p></li>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first">A <a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#RuntimeError" title="(in Python v3.7)"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code></a> when:</p>
+<ul class="last simple">
+<li>the chain indices are invalid</li>
+<li>the SEQRES of the specified chains do not match</li>
+<li>the start and end residue numbers are invalid or when the residues
+at the specified positions in the <strong>source_mhandle</strong> do not exist</li>
+<li>a gap in the <strong>source_mhandle</strong> encloses the residues specified by
+<strong>start_resnum</strong> and <strong>end_resnum</strong></li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.SetSequenceProfiles">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SetSequenceProfiles</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">profiles</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetSequenceProfiles" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">SetSequenceProfiles</code><span class="sig-paren">(</span><em>mhandle</em>, <em>profiles</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetSequenceProfiles" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets the <a class="reference internal" href="#promod3.modelling.ModellingHandle.profiles" title="promod3.modelling.ModellingHandle.profiles"><code class="xref py py-attr docutils literal notranslate"><span class="pre">sequence</span> <span class="pre">profiles</span></code></a> of <strong>mhandle</strong>
while ensuring consistency with the <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</p></li>
-<li><p><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</li>
+<li><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#ValueError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ValueError</span></code></a> when the given <strong>profiles</strong> are not consistent
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#ValueError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ValueError</span></code></a> when the given <strong>profiles</strong> are not consistent
with seqres in <strong>mhandle</strong></p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.SetPsipredPredictions">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SetPsipredPredictions</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">predictions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetPsipredPredictions" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">SetPsipredPredictions</code><span class="sig-paren">(</span><em>mhandle</em>, <em>predictions</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetPsipredPredictions" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets the <a class="reference internal" href="#promod3.modelling.ModellingHandle.psipred_predictions" title="promod3.modelling.ModellingHandle.psipred_predictions"><code class="xref py py-attr docutils literal notranslate"><span class="pre">predictions</span></code></a> of
<strong>mhandle</strong> while ensuring consistency with the
<a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the predictions attached afterwards</p></li>
-<li><p><strong>predictions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a>) – The predictions to attach</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the predictions attached afterwards</li>
+<li><strong>predictions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code></a>) – The predictions to attach</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#ValueError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ValueError</span></code></a> when the given <strong>predictions</strong> are not consistent
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#ValueError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ValueError</span></code></a> when the given <strong>predictions</strong> are not consistent
with seqres in <strong>mhandle</strong></p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.SetFraggerHandles">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SetFraggerHandles</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">fragger_handles</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetFraggerHandles" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">SetFraggerHandles</code><span class="sig-paren">(</span><em>mhandle</em>, <em>fragger_handles</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SetFraggerHandles" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets <a class="reference internal" href="#promod3.modelling.ModellingHandle.fragger_handles" title="promod3.modelling.ModellingHandle.fragger_handles"><code class="xref py py-attr docutils literal notranslate"><span class="pre">fragger_handles</span></code></a> in <em>mhandle</em> while
ensuring consistency with the <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingHandle.seqres</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the fragger handles attached afterwards</p></li>
-<li><p><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a>) – The fragger handles to attach</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the fragger handles attached afterwards</li>
+<li><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a>) – The fragger handles to attach</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#ValueError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ValueError</span></code></a> when the given <em>fragger_handles</em> are not
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/exceptions.html#ValueError" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ValueError</span></code></a> when the given <em>fragger_handles</em> are not
consistent with seqres in <em>mhandle</em></p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.CloseGaps">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CloseGaps</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">merge_distance=4</em>, <em class="sig-param">fragment_db=None</em>, <em class="sig-param">structure_db=None</em>, <em class="sig-param">torsion_sampler=None</em>, <em class="sig-param">fragger_handles=None</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em>, <em class="sig-param">length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseGaps" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">CloseGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>merge_distance=4</em>, <em>fragment_db=None</em>, <em>structure_db=None</em>, <em>torsion_sampler=None</em>, <em>fragger_handles=None</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to close all gaps in a model, except termini. It will go through
following steps:</p>
<ul class="simple">
-<li><p>Try to close small deletions by relaxing them
-(see <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>)</p></li>
-<li><p>Iteratively merge gaps up to a distance <strong>merge_distance</strong>
+<li>Try to close small deletions by relaxing them
+(see <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>)</li>
+<li>Iteratively merge gaps up to a distance <strong>merge_distance</strong>
(see <a class="reference internal" href="#promod3.modelling.MergeGapsByDistance" title="promod3.modelling.MergeGapsByDistance"><code class="xref py py-func docutils literal notranslate"><span class="pre">MergeGapsByDistance()</span></code></a>) and try to fill them with a database
-approach (see <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>)</p></li>
-<li><p>Try to fill remaining gaps using a Monte Carlo approach
-(see <a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByMonteCarlo()</span></code></a>)</p></li>
-<li><p>Large deletions get closed using a last resort approach
-(see <a class="reference internal" href="#promod3.modelling.CloseLargeDeletions" title="promod3.modelling.CloseLargeDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseLargeDeletions()</span></code></a>)</p></li>
+approach (see <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>)</li>
+<li>Try to fill remaining gaps using a Monte Carlo approach
+(see <a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByMonteCarlo()</span></code></a>)</li>
+<li>Large deletions get closed using a last resort approach
+(see <a class="reference internal" href="#promod3.modelling.CloseLargeDeletions" title="promod3.modelling.CloseLargeDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseLargeDeletions()</span></code></a>)</li>
</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>merge_distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. merge distance when performing the database
-approach</p></li>
-<li><p><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – Database for searching fragments in database
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>merge_distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. merge distance when performing the database
+approach</li>
+<li><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – Database for searching fragments in database
approach, must be consistent with provided
-<strong>structure_db</strong>. A default is loaded if None.</p></li>
-<li><p><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Structure db from which the <strong>fragment_db</strong> gets
+<strong>structure_db</strong>. A default is loaded if None.</li>
+<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Structure db from which the <strong>fragment_db</strong> gets
it’s structural information. A default is loaded
-if None.</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
+if None.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.TorsionSampler</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
and <a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByMonteCarlo()</span></code></a> A default one is
-loaded if None.</p></li>
-<li><p><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>
+loaded if None.</li>
+<li><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.FraggerHandle</span></code></a>
objects for each chain in <strong>mhandle</strong>.
If provided, fragments will be used for
sampling when the <a class="reference internal" href="#promod3.modelling.FillLoopsByMonteCarlo" title="promod3.modelling.FillLoopsByMonteCarlo"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByMonteCarlo()</span></code></a>
-gets executed.</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</p></li>
-<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
-processed.</p></li>
-<li><p><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a> provides different sets
+gets executed.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</li>
+<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
+processed.</li>
+<li><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a> provides different sets
of weights that have been trained on different
loop subsets. If this flag is true, the length
dependent weights are used to close loops with
-database / Monte Carlo.</p></li>
+database / Monte Carlo.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.CloseSmallDeletions">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CloseSmallDeletions</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">max_extension=9</em>, <em class="sig-param">clash_thresh=1.0</em>, <em class="sig-param">e_thresh=200</em>, <em class="sig-param">use_scoring_extender=True</em>, <em class="sig-param">use_full_extender=True</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em>, <em class="sig-param">ff_lookup=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseSmallDeletions" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">CloseSmallDeletions</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_extension=9</em>, <em>clash_thresh=1.0</em>, <em>e_thresh=200</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>ff_lookup=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseSmallDeletions" title="Permalink to this definition">¶</a></dt>
<dd><p>Close small deletions by relaxing neighbouring residues.</p>
<p>Small deletions in the template from the target-template alignment have a
good chance to be bridged just by relaxing neighbours around a tiny gap.
@@ -747,16 +828,18 @@ solution is stereochemically sensible.</p>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
</pre></div>
</div>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>max_extension</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of gap extension steps to perform
-(see <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>)</p></li>
-<li><p><strong>clash_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold for the backbone clash score. Acceptance
-means being lower than this.</p></li>
-<li><p><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Potential energy should be lower than this.</p></li>
-<li><p><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>max_extension</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of gap extension steps to perform
+(see <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>)</li>
+<li><strong>clash_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Threshold for the backbone clash score. Acceptance
+means being lower than this.</li>
+<li><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Potential energy should be lower than this.</li>
+<li><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
The gap is penalized according as
0.8*length + sum(helices) + sum(sheets).
@@ -764,30 +847,32 @@ For the scondary-structure-penalty to work,
the model-template must have the appropriate
information before <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a> is
called (e.g. with
-<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</p></li>
-<li><p><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
+<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>. Also works in combination
with <cite>use_scoring_extender</cite>. This allows the gap
extender to skip neighboring gaps and to correctly
-handle gaps close to termini.</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</p></li>
-<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
-processed.</p></li>
-<li><p><strong>ff_lookup</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.ForcefieldLookup</span></code></a>) – Forcefield to parametrize
+handle gaps close to termini.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</li>
+<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
+processed.</li>
+<li><strong>ff_lookup</strong> (<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.ForcefieldLookup</span></code></a>) – Forcefield to parametrize
<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> in
<a class="reference internal" href="loop_closing.html#promod3.modelling.BackboneRelaxer" title="promod3.modelling.BackboneRelaxer"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.modelling.BackboneRelaxer</span></code></a>.
If set to None, the one returned by
<a class="reference internal" href="../loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetDefault" title="promod3.loop.ForcefieldLookup.GetDefault"><code class="xref py py-func docutils literal notranslate"><span class="pre">promod3.loop.ForcefieldLookup.GetDefault()</span></code></a>
-gets used.</p></li>
+gets used.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.MergeGapsByDistance">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MergeGapsByDistance</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">distance</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeGapsByDistance" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">MergeGapsByDistance</code><span class="sig-paren">(</span><em>mhandle</em>, <em>distance</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MergeGapsByDistance" title="Permalink to this definition">¶</a></dt>
<dd><p>Merge 2 neighbouring gaps by deleting residues in-between.</p>
<p>Check if two neighbouring gaps are at max. <em>distance</em> residues apart from
each other. Then delete the residues and store a new gap spanning the whole
@@ -812,24 +897,28 @@ Non-sequential gaps are ignored!</p>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
</pre></div>
</div>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The max. no. of residues between two gaps up to which
-merge happens.</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</p></li>
-<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, two gaps only get merged if they’re
-both in this resnum range.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The max. no. of residues between two gaps up to which
+merge happens.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</li>
+<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, two gaps only get merged if they’re
+both in this resnum range.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.FillLoopsByDatabase">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FillLoopsByDatabase</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">fragment_db</em>, <em class="sig-param">structure_db</em>, <em class="sig-param">torsion_sampler=None</em>, <em class="sig-param">max_loops_to_search=40</em>, <em class="sig-param">min_loops_required=4</em>, <em class="sig-param">max_res_extension=-1</em>, <em class="sig-param">extended_search=True</em>, <em class="sig-param">use_scoring_extender=True</em>, <em class="sig-param">use_full_extender=True</em>, <em class="sig-param">score_variant=0</em>, <em class="sig-param">ring_punch_detection=1</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em>, <em class="sig-param">max_num_all_atom=0</em>, <em class="sig-param">clash_thresh=-1</em>, <em class="sig-param">length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByDatabase" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByDatabase</code><span class="sig-paren">(</span><em>mhandle</em>, <em>fragment_db</em>, <em>structure_db</em>, <em>torsion_sampler=None</em>, <em>max_loops_to_search=40</em>, <em>min_loops_required=4</em>, <em>max_res_extension=-1</em>, <em>extended_search=True</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>max_num_all_atom=0</em>, <em>clash_thresh=-1</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByDatabase" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to fill up loops from a structural database.</p>
<p>Usually this will extend the gaps a bit to match candidates from the
database. Do not expect a gap being filled in between its actual stem
@@ -854,81 +943,85 @@ This function cannot fill gaps at C- or N-terminal.</p>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
</pre></div>
</div>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – A fragment database coupled to the <em>structure_db</em>.</p></li>
-<li><p><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Backbone/profile data.</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. A default one is
-loaded if None.</p></li>
-<li><p><strong>max_loops_to_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – A fragment database coupled to the <em>structure_db</em>.</li>
+<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Backbone/profile data.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. A default one is
+loaded if None.</li>
+<li><strong>max_loops_to_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
evaluated per loop. The actual found candidates
may be more (if we found ‘enough’) or less (if
-not enough candidates exist) of this number.</p></li>
-<li><p><strong>min_loops_required</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Define how many candidates we require to close
+not enough candidates exist) of this number.</li>
+<li><strong>min_loops_required</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Define how many candidates we require to close
the loop. If we did not find at least this number
of candidates for a gap, we skip it without
closing. Can be set to <code class="docutils literal notranslate"><span class="pre">max_loops_to_search</span></code>
(or equivalently to -1) to enforce that we only
-close gaps for which we found enough candidates.</p></li>
-<li><p><strong>max_res_extension</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Only allow this number of residues to be added to
+close gaps for which we found enough candidates.</li>
+<li><strong>max_res_extension</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Only allow this number of residues to be added to
the gaps when extending. If set to <strong>-1</strong>, any
number of residues can be added (as long as the
-<cite>fragment_db</cite> allows it).</p></li>
-<li><p><strong>extended_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = more loop candidates are considered.
+<cite>fragment_db</cite> allows it).</li>
+<li><strong>extended_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = more loop candidates are considered.
The candidate search is done less precisely (see
<a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a>).
The candidates are still scored and evaluated the
-same though (only more of them considered).</p></li>
-<li><p><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
+same though (only more of them considered).</li>
+<li><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
-<li><p><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
+<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
<a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
-<li><p><strong>score_variant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <p>How to score loop candidates. Options:</p>
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
+<li><strong>score_variant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <p>How to score loop candidates. Options:</p>
<ul>
-<li><p><strong>0</strong>: put frame of backbone residues enclosing all
+<li><strong>0</strong>: put frame of backbone residues enclosing all
candidates and score frame. This will also “score”
-non-modelled residues!</p></li>
-<li><p><strong>1</strong>: score candidates directly</p></li>
-<li><p><strong>2</strong>: like <strong>1</strong> but penalize length of candidate</p></li>
+non-modelled residues!</li>
+<li><strong>1</strong>: score candidates directly</li>
+<li><strong>2</strong>: like <strong>1</strong> but penalize length of candidate</li>
</ul>
-</p></li>
-<li><p><strong>ring_punch_detection</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <p>How to deal with ring punchings. Options:</p>
+</li>
+<li><strong>ring_punch_detection</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <p>How to deal with ring punchings. Options:</p>
<ul>
-<li><p><strong>0</strong>: not at all (fastest)</p></li>
-<li><p><strong>1</strong>: check for punchings with existing rings</p></li>
-<li><p><strong>2</strong>: check incl. sidechain for loop cand.</p></li>
+<li><strong>0</strong>: not at all (fastest)</li>
+<li><strong>1</strong>: check for punchings with existing rings</li>
+<li><strong>2</strong>: check incl. sidechain for loop cand.</li>
</ul>
-</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</p></li>
-<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
-processed</p></li>
-<li><p><strong>max_num_all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If > 0, we prefilter loop candidates based on
+</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</li>
+<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
+processed</li>
+<li><strong>max_num_all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If > 0, we prefilter loop candidates based on
non-all-atom-scores and apply all atom scoring to
the best <em>max_num_all_atom</em> candidates. If desired,
<em>5</em> is a good value here (larger values give only
numerical improvement). With <em>5</em>, this will be
approx. 2x slower than without and will give a
-slight improvement in loop selection.</p></li>
-<li><p><strong>clash_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If > 0, we only keep loop candidates which have a
-backbone clash score lower than this.</p></li>
-<li><p><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a> provides different sets
+slight improvement in loop selection.</li>
+<li><strong>clash_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If > 0, we only keep loop candidates which have a
+backbone clash score lower than this.</li>
+<li><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a> provides different sets
of weights that have been trained on different
loop subsets. If this flag is true, the length
dependent weights are used to select the final
-loops.</p></li>
+loops.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.FillLoopsByMonteCarlo">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">FillLoopsByMonteCarlo</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">torsion_sampler=None</em>, <em class="sig-param">max_loops_to_search=6</em>, <em class="sig-param">max_extension=30</em>, <em class="sig-param">mc_num_loops=2</em>, <em class="sig-param">mc_steps=5000</em>, <em class="sig-param">use_scoring_extender=True</em>, <em class="sig-param">use_full_extender=True</em>, <em class="sig-param">score_variant=0</em>, <em class="sig-param">ring_punch_detection=1</em>, <em class="sig-param">fragger_handles=None</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em>, <em class="sig-param">length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByMonteCarlo" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByMonteCarlo</code><span class="sig-paren">(</span><em>mhandle</em>, <em>torsion_sampler=None</em>, <em>max_loops_to_search=6</em>, <em>max_extension=30</em>, <em>mc_num_loops=2</em>, <em>mc_steps=5000</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>fragger_handles=None</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FillLoopsByMonteCarlo" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to fill up loops with Monte Carlo sampling.</p>
<p>This is meant as a “last-resort” approach when it is not possible to fill
the loops from the database with <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>.
@@ -956,89 +1049,96 @@ is only used if the gap length is >= the length of fragments stored.</p>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
</pre></div>
</div>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. A default one is
-loaded if None.</p></li>
-<li><p><strong>max_loops_to_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
-evaluated per loop.</p></li>
-<li><p><strong>max_extension</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of gap extension steps to perform
-(see <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>)</p></li>
-<li><p><strong>mc_num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of loop candidates to consider for each extended gap
-(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</p></li>
-<li><p><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
-(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</p></li>
-<li><p><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles. A default one is
+loaded if None.</li>
+<li><strong>max_loops_to_search</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Define how many candidates are ‘enough’ to be
+evaluated per loop.</li>
+<li><strong>max_extension</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of gap extension steps to perform
+(see <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>)</li>
+<li><strong>mc_num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of loop candidates to consider for each extended gap
+(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</li>
+<li><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
+(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</li>
+<li><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
-<li><p><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
+<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
<a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
-<li><p><strong>score_variant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – How to score loop candidates (AllAtom not supported).
-See <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>.</p></li>
-<li><p><strong>ring_punch_detection</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – How to deal with ring punchings.
-See <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>.</p></li>
-<li><p><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a>) – Either None (no fragger sampling used) or one
-fragger handle for each chain in <em>mhandle</em>.</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</p></li>
-<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
-processed</p></li>
-<li><p><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a> provides different sets
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
+<li><strong>score_variant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – How to score loop candidates (AllAtom not supported).
+See <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>.</li>
+<li><strong>ring_punch_detection</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – How to deal with ring punchings.
+See <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>.</li>
+<li><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a>) – Either None (no fragger sampling used) or one
+fragger handle for each chain in <em>mhandle</em>.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</li>
+<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
+processed</li>
+<li><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a> provides different sets
of weights that have been trained on different
loop subsets. If this flag is true, the length
dependent weights are used to select the final
-loops.</p></li>
+loops.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.CloseLargeDeletions">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CloseLargeDeletions</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">structure_db</em>, <em class="sig-param">linker_length=8</em>, <em class="sig-param">num_fragments=500</em>, <em class="sig-param">use_scoring_extender=True</em>, <em class="sig-param">use_full_extender=True</em>, <em class="sig-param">chain_idx=None</em>, <em class="sig-param">resnum_range=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseLargeDeletions" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">CloseLargeDeletions</code><span class="sig-paren">(</span><em>mhandle</em>, <em>structure_db</em>, <em>linker_length=8</em>, <em>num_fragments=500</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CloseLargeDeletions" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to close large deletions.</p>
<p>This is meant as a “last-resort” approach. In some cases you cannot
close very large deletions simply because the two parts separated
by a deletion are too far apart. The idea is to sample a linker region
and always move the whole chain towards the n-terminus.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – The database from which to extract fragments for
-the linker region.</p></li>
-<li><p><strong>linker_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Desired length (in residues w/o stems) for the
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – The database from which to extract fragments for
+the linker region.</li>
+<li><strong>linker_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Desired length (in residues w/o stems) for the
linker. This may be shorter if extender cannot
-extend further.</p></li>
-<li><p><strong>num_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to sample the linker.</p></li>
-<li><p><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
+extend further.</li>
+<li><strong>num_fragments</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to sample the linker.</li>
+<li><strong>use_scoring_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.ScoringGapExtender" title="promod3.modelling.ScoringGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringGapExtender</span></code></a> instead
of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
-<li><p><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
+<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
<a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>.
-See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
-processed</p></li>
-<li><p><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
-processed</p></li>
+See <a class="reference internal" href="#promod3.modelling.CloseSmallDeletions" title="promod3.modelling.CloseSmallDeletions"><code class="xref py py-func docutils literal notranslate"><span class="pre">CloseSmallDeletions()</span></code></a>.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps from chain with given index get
+processed</li>
+<li><strong>resnum_range</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
+processed</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.ModelTermini">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ModelTermini</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">torsion_sampler</em>, <em class="sig-param">fragger_handles=None</em>, <em class="sig-param">mc_num_loops=20</em>, <em class="sig-param">mc_steps=5000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModelTermini" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">ModelTermini</code><span class="sig-paren">(</span><em>mhandle</em>, <em>torsion_sampler</em>, <em>fragger_handles=None</em>, <em>mc_num_loops=20</em>, <em>mc_steps=5000</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModelTermini" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to model termini with Monte Carlo sampling.</p>
<p>Use with care! This is an experimental feature which will increase coverage
but we do not assume that the resulting termini are of high quality!</p>
<p>The termini are modelled by either sampling the dihedral angles or (if
<em>fragger_handles</em> is given) <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal notranslate"><span class="pre">Fragger</span></code></a> lists. The latter
is only used if the gap length is >= the length of fragments stored.</p>
-<p>Terminal gaps of length 1 are ignored by this function!</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
@@ -1057,65 +1157,73 @@ is only used if the gap length is >= the length of fragments stored.</p>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
</pre></div>
</div>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles.</p></li>
-<li><p><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a>) – Either None (no fragger sampling used) or one
-fragger handle for each chain in <em>mhandle</em>.</p></li>
-<li><p><strong>mc_num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of loop candidates to consider for each terminal gap
-(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</p></li>
-<li><p><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
-(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A sampler for torsion angles.</li>
+<li><strong>fragger_handles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="algorithms.html#promod3.modelling.FraggerHandle" title="promod3.modelling.FraggerHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">FraggerHandle</span></code></a>) – Either None (no fragger sampling used) or one
+fragger handle for each chain in <em>mhandle</em>.</li>
+<li><strong>mc_num_loops</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of loop candidates to consider for each terminal gap
+(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</li>
+<li><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
+(see <a class="reference internal" href="loop_candidates.html#promod3.modelling.LoopCandidates.FillFromMonteCarloSampler" title="promod3.modelling.LoopCandidates.FillFromMonteCarloSampler"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromMonteCarloSampler()</span></code></a>)</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.BuildSidechains">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">BuildSidechains</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">merge_distance=4</em>, <em class="sig-param">fragment_db=None</em>, <em class="sig-param">structure_db=None</em>, <em class="sig-param">torsion_sampler=None</em>, <em class="sig-param">rotamer_library=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildSidechains" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">BuildSidechains</code><span class="sig-paren">(</span><em>mhandle</em>, <em>merge_distance=4</em>, <em>fragment_db=None</em>, <em>structure_db=None</em>, <em>torsion_sampler=None</em>, <em>rotamer_library=None</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BuildSidechains" title="Permalink to this definition">¶</a></dt>
<dd><p>Build sidechains for model.</p>
<p>This is a wrapper for <a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a>,
followed by a check for ring punches. If ring punches are found it
introduces gaps for the residues with punched rings and tries to fill them
with <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a> with <em>ring_punch_detection=2</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>merge_distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.MergeGapsByDistance" title="promod3.modelling.MergeGapsByDistance"><code class="xref py py-func docutils literal notranslate"><span class="pre">MergeGapsByDistance()</span></code></a>
-if ring punches are found.</p></li>
-<li><p><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>merge_distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.MergeGapsByDistance" title="promod3.modelling.MergeGapsByDistance"><code class="xref py py-func docutils literal notranslate"><span class="pre">MergeGapsByDistance()</span></code></a>
+if ring punches are found.</li>
+<li><strong>fragment_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
if ring punches are found. A default one is loaded
-if None.</p></li>
-<li><p><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
+if None.</li>
+<li><strong>structure_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
if ring punches are found. A default one is loaded
-if None.</p></li>
-<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
+if None.</li>
+<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – Used as parameter for <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal notranslate"><span class="pre">FillLoopsByDatabase()</span></code></a>
if ring punches are found. A default one is loaded
-if None.</p></li>
-<li><p><strong>rotamer_library</strong> (<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a> or
+if None.</li>
+<li><strong>rotamer_library</strong> (<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a> or
<a class="reference internal" href="../sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a>) – Used as parameter for
<code class="xref py py-func docutils literal notranslate"><span class="pre">modelling.ReconstructSidechains()</span></code>, a default
-one is loaded if None.</p></li>
+one is loaded if None.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.MinimizeModelEnergy">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">max_iterations=12</em>, <em class="sig-param">max_iter_sd=20</em>, <em class="sig-param">max_iter_lbfgs=10</em>, <em class="sig-param">use_amber_ff=False</em>, <em class="sig-param">extra_force_fields=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_iterations=12</em>, <em>max_iter_sd=20</em>, <em>max_iter_lbfgs=10</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Minimize energy of final model using molecular mechanics.</p>
<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
It will iteratively (at most <em>max_iterations</em> times):</p>
<ul class="simple">
-<li><p>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</p></li>
-<li><p>run up to <em>max_iter_lbfgs</em> minimization iter. of a Limited-memory
-Broyden-Fletcher-Goldfarb-Shanno method</p></li>
-<li><p>abort if no stereochemical problems found</p></li>
+<li>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</li>
+<li>run up to <em>max_iter_lbfgs</em> minimization iter. of a Limited-memory
+Broyden-Fletcher-Goldfarb-Shanno method</li>
+<li>abort if no stereochemical problems found</li>
</ul>
<p>The idea is that we don’t want to minimize “too much”. So, we iteratively
minimize until there are no stereochemical problems and not more.</p>
@@ -1126,113 +1234,133 @@ If the variable is not set, 1 thread will be used by default.</p>
(happens if atoms are on top of each other or almost), the energy
minimization is aborted. This issue is logged and added as a major issue to
<a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal notranslate"><span class="pre">modelling_issues</span></code></a> of <em>mhandle</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</p></li>
-<li><p><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations for SD+LBFGS</p></li>
-<li><p><strong>max_iter_sd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within SD method</p></li>
-<li><p><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within LBFGS method</p></li>
-<li><p><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
-CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</p></li>
-<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
-<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle on which to apply change.</li>
+<li><strong>max_iterations</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations for SD+LBFGS</li>
+<li><strong>max_iter_sd</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within SD method</li>
+<li><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within LBFGS method</li>
+<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
+CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
+<li><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
+<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The model including all oxygens as used in the minimizer.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The model including all oxygens as used in the minimizer.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.CheckFinalModel">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">CheckFinalModel</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CheckFinalModel" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">CheckFinalModel</code><span class="sig-paren">(</span><em>mhandle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.CheckFinalModel" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs samity checks on final models and reports problems.</p>
<p>Issues are logged and tracked in <a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal notranslate"><span class="pre">modelling_issues</span></code></a>
of <em>mhandle</em>. Major issues:</p>
<ul class="simple">
-<li><p>Chains with less than 3 residues (usually due to bad templates).</p></li>
-<li><p>Incomplete models (i.e. some gaps couldn’t be closed). One issue is
-created per unclosed gap and the stems of the gap are added to the issue.</p></li>
-<li><p>Complete models with sequence mismatches (should never happen).</p></li>
-<li><p>Residues with rings which have been punched by another bond.</p></li>
+<li>Chains with less than 3 residues (usually due to bad templates).</li>
+<li>Incomplete models (i.e. some gaps couldn’t be closed). One issue is
+created per unclosed gap and the stems of the gap are added to the issue.</li>
+<li>Complete models with sequence mismatches (should never happen).</li>
+<li>Residues with rings which have been punched by another bond.</li>
</ul>
<p>Minor issues:</p>
<ul class="simple">
-<li><p>Remaining stereo-chemical problems after energy minimization. The affected
+<li>Remaining stereo-chemical problems after energy minimization. The affected
residues will have the boolean property “stereo_chemical_problem_backbone”
-set to True, if the problem affects backbone atoms.</p></li>
+set to True, if the problem affects backbone atoms.</li>
</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle for which to perform checks.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle for which to perform checks.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.ModellingIssue">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ModellingIssue</code><span class="sig-paren">(</span><em class="sig-param">text</em>, <em class="sig-param">severity</em>, <em class="sig-param">residue_list=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingIssue" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>text</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.text" title="promod3.modelling.ModellingIssue.text"><code class="xref py py-attr docutils literal notranslate"><span class="pre">text</span></code></a>.</p></li>
-<li><p><strong>severity</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.severity" title="promod3.modelling.ModellingIssue.severity"><code class="xref py py-attr docutils literal notranslate"><span class="pre">severity</span></code></a>.</p></li>
-<li><p><strong>residue_list</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.residue_list" title="promod3.modelling.ModellingIssue.residue_list"><code class="xref py py-attr docutils literal notranslate"><span class="pre">residue_list</span></code></a>.</p></li>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">ModellingIssue</code><span class="sig-paren">(</span><em>text</em>, <em>severity</em>, <em>residue_list=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingIssue" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>text</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.text" title="promod3.modelling.ModellingIssue.text"><code class="xref py py-attr docutils literal notranslate"><span class="pre">text</span></code></a>.</li>
+<li><strong>severity</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.severity" title="promod3.modelling.ModellingIssue.severity"><code class="xref py py-attr docutils literal notranslate"><span class="pre">severity</span></code></a>.</li>
+<li><strong>residue_list</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.residue_list" title="promod3.modelling.ModellingIssue.residue_list"><code class="xref py py-attr docutils literal notranslate"><span class="pre">residue_list</span></code></a>.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="attribute">
<dt id="promod3.modelling.ModellingIssue.text">
-<code class="sig-name descname">text</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.text" title="Permalink to this definition">¶</a></dt>
+<code class="descname">text</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.text" title="Permalink to this definition">¶</a></dt>
<dd><p>Description of issue.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingIssue.severity">
-<code class="sig-name descname">severity</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.severity" title="Permalink to this definition">¶</a></dt>
+<code class="descname">severity</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.severity" title="Permalink to this definition">¶</a></dt>
<dd><p>Severity of issue.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.ModellingIssue.Severity" title="promod3.modelling.ModellingIssue.Severity"><code class="xref py py-class docutils literal notranslate"><span class="pre">Severity</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="#promod3.modelling.ModellingIssue.Severity" title="promod3.modelling.ModellingIssue.Severity"><code class="xref py py-class docutils literal notranslate"><span class="pre">Severity</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingIssue.residue_list">
-<code class="sig-name descname">residue_list</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.residue_list" title="Permalink to this definition">¶</a></dt>
+<code class="descname">residue_list</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.residue_list" title="Permalink to this definition">¶</a></dt>
<dd><p>List of residues affected by issue (or empty list if global issue).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="class">
<dt id="promod3.modelling.ModellingIssue.Severity">
-<em class="property">class </em><code class="sig-name descname">Severity</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descname">Severity</code><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates severities.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingIssue.Severity.MAJOR">
-<code class="sig-name descname">MAJOR</code><em class="property"> = 10</em><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity.MAJOR" title="Permalink to this definition">¶</a></dt>
+<code class="descname">MAJOR</code><em class="property"> = 10</em><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity.MAJOR" title="Permalink to this definition">¶</a></dt>
<dd><p>Major issues like MM-failures, incomplete models and ring punches.</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.ModellingIssue.Severity.MINOR">
-<code class="sig-name descname">MINOR</code><em class="property"> = 0</em><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity.MINOR" title="Permalink to this definition">¶</a></dt>
+<code class="descname">MINOR</code><em class="property"> = 0</em><a class="headerlink" href="#promod3.modelling.ModellingIssue.Severity.MINOR" title="Permalink to this definition">¶</a></dt>
<dd><p>Minor issues like remaining stereo-chemistry problems after MM.</p>
</dd></dl>
@@ -1240,36 +1368,42 @@ set to True, if the problem affects backbone atoms.</p></li>
<dl class="method">
<dt id="promod3.modelling.ModellingIssue.is_major">
-<code class="sig-name descname">is_major</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingIssue.is_major" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True if this is a major issue.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">is_major</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ModellingIssue.is_major" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True if this is a major issue.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.AddModellingIssue">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">AddModellingIssue</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">text</em>, <em class="sig-param">severity</em>, <em class="sig-param">residue_list=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AddModellingIssue" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">AddModellingIssue</code><span class="sig-paren">(</span><em>mhandle</em>, <em>text</em>, <em>severity</em>, <em>residue_list=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AddModellingIssue" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds a new <a class="reference internal" href="#promod3.modelling.ModellingIssue" title="promod3.modelling.ModellingIssue"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingIssue</span></code></a> to
<a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal notranslate"><span class="pre">modelling_issues</span></code></a> in <em>mhandle</em>.</p>
<p>If <em>mhandle</em> doesn’t contain the <a class="reference internal" href="#promod3.modelling.ModellingHandle.modelling_issues" title="promod3.modelling.ModellingHandle.modelling_issues"><code class="xref py py-attr docutils literal notranslate"><span class="pre">modelling_issues</span></code></a>
attribute yet, it is added.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the issue added to.</p></li>
-<li><p><strong>text</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.text" title="promod3.modelling.ModellingIssue.text"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingIssue.text</span></code></a>.</p></li>
-<li><p><strong>severity</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.severity" title="promod3.modelling.ModellingIssue.severity"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingIssue.severity</span></code></a>.</p></li>
-<li><p><strong>residue_list</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.residue_list" title="promod3.modelling.ModellingIssue.residue_list"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingIssue.residue_list</span></code></a>.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the issue added to.</li>
+<li><strong>text</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.text" title="promod3.modelling.ModellingIssue.text"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingIssue.text</span></code></a>.</li>
+<li><strong>severity</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.severity" title="promod3.modelling.ModellingIssue.severity"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingIssue.severity</span></code></a>.</li>
+<li><strong>residue_list</strong> – Sets <a class="reference internal" href="#promod3.modelling.ModellingIssue.residue_list" title="promod3.modelling.ModellingIssue.residue_list"><code class="xref py py-attr docutils literal notranslate"><span class="pre">ModellingIssue.residue_list</span></code></a>.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -1277,29 +1411,30 @@ attribute yet, it is added.</p>
<h2>Alignment Fiddling<a class="headerlink" href="#alignment-fiddling" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.DeleteGapCols">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">DeleteGapCols</code><span class="sig-paren">(</span><em class="sig-param">aln</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DeleteGapCols" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">DeleteGapCols</code><span class="sig-paren">(</span><em>aln</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.DeleteGapCols" title="Permalink to this definition">¶</a></dt>
<dd><p>Deletes alignment columns that only contain gaps.</p>
<p>Columns that only contain gaps (‘-‘) are removed. If no such column can be
identified, the input alignment gets returned. A new alignment gets
constructed otherwise. The sequences of the new alignment retain name, offset
and the potentially attached <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original
sequences.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The processed alignment</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The processed alignment</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.modelling.PullTerminalDeletions">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">PullTerminalDeletions</code><span class="sig-paren">(</span><em class="sig-param">aln</em>, <em class="sig-param">min_terminal_anchor_size=4</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PullTerminalDeletions" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">PullTerminalDeletions</code><span class="sig-paren">(</span><em>aln</em>, <em>min_terminal_anchor_size=4</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.PullTerminalDeletions" title="Permalink to this definition">¶</a></dt>
<dd><p>Fixes deletions close to termini.</p>
<p>Some alignment tools may produce alignments with deletions close to the
termini. For example:</p>
@@ -1334,17 +1469,18 @@ ATOMSEQ: ABCDEFGHI...
input alignment gets returned. A new alignment gets constructed otherwise.
The sequences of the new alignment retain name, offset and the potentially
attached <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original sequences.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The processed alignment</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The processed alignment</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -1352,7 +1488,6 @@ attached <a class="reference external" href="https://www.openstructure.org/docs/
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -1373,12 +1508,12 @@ attached <a class="reference external" href="https://www.openstructure.org/docs/
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -1395,8 +1530,8 @@ attached <a class="reference external" href="https://www.openstructure.org/docs/
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
<li>Next: <a href="model_checking.html" title="next chapter">Model Checking</a></li>
</ul></li>
</ul></li>
@@ -1404,33 +1539,27 @@ attached <a class="reference external" href="https://www.openstructure.org/docs/
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
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-
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</div>
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- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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<a href="../_sources/modelling/pipeline.rst.txt"
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index cf1a4a3d2e32e1bf2da14921995031cdaff486f6..980622fd937d01d81b7fc7169cbaa996af57c06d 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Sidechain Reconstruction — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Sidechain Reconstruction — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,18 +30,16 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="sidechain-reconstruction">
<h1>Sidechain Reconstruction<a class="headerlink" href="#sidechain-reconstruction" title="Permalink to this headline">¶</a></h1>
<p>Two methods are provided to fully reconstruct sidechains of residues:</p>
<ul class="simple">
-<li><p>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
-<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p></li>
-<li><p>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
-and used to reconstruct sidechains of single loops</p></li>
+<li>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></li>
+<li>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
+and used to reconstruct sidechains of single loops</li>
</ul>
<p>Example usage:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">mol</span>
@@ -86,40 +85,44 @@ and used to reconstruct sidechains of single loops</p></li>
<h2>Reconstruct Function<a class="headerlink" href="#reconstruct-function" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.modelling.ReconstructSidechains">
-<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">ReconstructSidechains</code><span class="sig-paren">(</span><em class="sig-param">ent</em>, <em class="sig-param">keep_sidechains=False</em>, <em class="sig-param">build_disulfids=True</em>, <em class="sig-param">rotamer_model='frm'</em>, <em class="sig-param">consider_ligands=True</em>, <em class="sig-param">rotamer_library=None</em>, <em class="sig-param">optimize_subrotamers=True</em>, <em class="sig-param">graph_max_complexity=100000000</em>, <em class="sig-param">graph_initial_epsilon=0.02</em>, <em class="sig-param">energy_function='SCWRL4'</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReconstructSidechains" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">ReconstructSidechains</code><span class="sig-paren">(</span><em>ent</em>, <em>keep_sidechains=False</em>, <em>build_disulfids=True</em>, <em>rotamer_model='frm'</em>, <em>consider_ligands=True</em>, <em>rotamer_library=None</em>, <em>optimize_subrotamers=True</em>, <em>graph_max_complexity=100000000</em>, <em>graph_initial_epsilon=0.02</em>, <em>energy_function='SCWRL4'</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ReconstructSidechains" title="Permalink to this definition">¶</a></dt>
<dd><p>Reconstruct sidechains for the given structure.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
-reconstruction gets directly applied on the structure itself.</p></li>
-<li><p><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in <em>ent</em> (i.e.
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
+reconstruction gets directly applied on the structure itself.</li>
+<li><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in <em>ent</em> (i.e.
containing all required atoms) should be kept rigid
-and directly be added to the frame.</p></li>
-<li><p><strong>build_disulfids</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether possible disulfid bonds should be
+and directly be added to the frame.</li>
+<li><strong>build_disulfids</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether possible disulfid bonds should be
searched. If a disulfid bond is found, the two
participating cysteins are fixed and added to
-the frame.</p></li>
-<li><p><strong>rotamer_model</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Rotamer model to be used, can either be “frm” or “rrm”</p></li>
-<li><p><strong>consider_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether to add ligands (anything in chain
-‘_’) as static objects.</p></li>
-<li><p><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code>) – A rotamer library to extract the rotamers from. The
-default is to call <code class="xref py py-meth docutils literal notranslate"><span class="pre"><LoadBBDepLib>()</span></code>.</p></li>
-<li><p><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Only considered when <em>rotamer_model</em>
+the frame.</li>
+<li><strong>rotamer_model</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Rotamer model to be used, can either be “frm” or “rrm”</li>
+<li><strong>consider_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether to add ligands (anything in chain
+‘_’) as static objects.</li>
+<li><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code>) – A rotamer library to extract the rotamers from. The
+default is to call <code class="xref py py-meth docutils literal notranslate"><span class="pre"><LoadBBDepLib>()</span></code>.</li>
+<li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Only considered when <em>rotamer_model</em>
is “frm”.
If set to True, the FRM solution undergoes
some postprocessing by calling
<code class="xref py py-func docutils literal notranslate"><span class="pre">SubrotamerOptimizer()</span></code> with default
-parametrization.</p></li>
-<li><p><strong>graph_max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. complexity for
-<code class="xref py py-meth docutils literal notranslate"><span class="pre">RotamerGraph.TreeSolve()</span></code>.</p></li>
-<li><p><strong>graph_intial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Initial epsilon for
-<code class="xref py py-meth docutils literal notranslate"><span class="pre">RotamerGraph.TreeSolve()</span></code>.</p></li>
-<li><p><strong>energy_function</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – What energy function to use can be any in
-[“SCWRL4”, “SCWRL3”]</p></li>
+parametrization.</li>
+<li><strong>graph_max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. complexity for
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">RotamerGraph.TreeSolve()</span></code>.</li>
+<li><strong>graph_intial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Initial epsilon for
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">RotamerGraph.TreeSolve()</span></code>.</li>
+<li><strong>energy_function</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – What energy function to use can be any in
+[“SCWRL4”, “SCWRL3”]</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -127,7 +130,7 @@ parametrization.</p></li>
<h2>SidechainReconstructor Class<a class="headerlink" href="#sidechainreconstructor-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.modelling.SidechainReconstructor">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SidechainReconstructor</code><span class="sig-paren">(</span><em class="sig-param">keep_sidechains=True</em>, <em class="sig-param">build_disulfids=True</em>, <em class="sig-param">optimize_subrotamers=False</em>, <em class="sig-param">remodel_cutoff=20</em>, <em class="sig-param">rigid_frame_cutoff=0</em>, <em class="sig-param">graph_max_complexity=100000000</em>, <em class="sig-param">graph_intial_epsilon=0.02</em>, <em class="sig-param">disulfid_score_thresh=45</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">SidechainReconstructor</code><span class="sig-paren">(</span><em>keep_sidechains=True</em>, <em>build_disulfids=True</em>, <em>optimize_subrotamers=False</em>, <em>remodel_cutoff=20</em>, <em>rigid_frame_cutoff=0</em>, <em>graph_max_complexity=100000000</em>, <em>graph_intial_epsilon=0.02</em>, <em>disulfid_score_thresh=45</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>Reconstruct sidechains for single loops or residues. Must be linked to an
all atom env. (<a class="reference internal" href="#promod3.modelling.SidechainReconstructor.AttachEnvironment" title="promod3.modelling.SidechainReconstructor.AttachEnvironment"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AttachEnvironment()</span></code></a>) containing the structural data.
Residues are identified as N- or C-terminal according to the seqres in the
@@ -142,23 +145,25 @@ will be considered for remodelling. Everything further away than 20A but
within 20A + 10A = 30A will also be considered as rigid frame (all
backbone atoms and the sidechain if present). The distance criteria is the
CB atom distance between residues (CA in case of glycine).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in env. (i.e.
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in env. (i.e.
containing all required atoms) should be kept rigid
-and directly be added to the result.</p></li>
-<li><p><strong>build_disulfids</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether possible disulfid bonds should be
+and directly be added to the result.</li>
+<li><strong>build_disulfids</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether possible disulfid bonds should be
searched. If a disulfid bond is found, the two
participating cysteins are fixed and added to
-the result.</p></li>
-<li><p><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether the
+the result.</li>
+<li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether the
<a class="reference internal" href="../sidechain/subrotamer_optimizer.html#promod3.sidechain.SubrotamerOptimizer" title="promod3.sidechain.SubrotamerOptimizer"><code class="xref py py-func docutils literal notranslate"><span class="pre">SubrotamerOptimizer()</span></code></a>
with default parametrization should be called
-if we’re dealing with FRM rotamers.</p></li>
-<li><p><strong>remodel_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff to identify all residues that need to be
-remodelled.</p></li>
-<li><p><strong>rigid_frame_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff to control the visibility of the rigid
+if we’re dealing with FRM rotamers.</li>
+<li><strong>remodel_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff to identify all residues that need to be
+remodelled.</li>
+<li><strong>rigid_frame_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Cutoff to control the visibility of the rigid
frame to the reconstruction procedure.
Everything within
[<em>remodel_cutoff</em>,
@@ -167,22 +172,24 @@ will be considered as ridig frame. Small sidenote:
if the <em>keep_sidechains</em> flag is true and all
residues within <em>remodel_cutoff</em> already have a
sidechain, the <em>rigid_frame_cutoff</em> won’t have any
-effect.</p></li>
-<li><p><strong>graph_max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. complexity for
-<code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code>.</p></li>
-<li><p><strong>graph_intial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Initial epsilon for
-<code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code>.</p></li>
-<li><p><strong>disulfid_score_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If <code class="xref py py-meth docutils literal notranslate"><span class="pre">DisulfidScore()</span></code> between two CYS is
+effect.</li>
+<li><strong>graph_max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. complexity for
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code>.</li>
+<li><strong>graph_intial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Initial epsilon for
+<code class="xref py py-meth docutils literal notranslate"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code>.</li>
+<li><strong>disulfid_score_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – If <code class="xref py py-meth docutils literal notranslate"><span class="pre">DisulfidScore()</span></code> between two CYS is
below this threshold, we consider them to be
-disulfid-bonded.</p></li>
+disulfid-bonded.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.modelling.SidechainReconstructor.Reconstruct">
-<code class="sig-name descname">Reconstruct</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor.Reconstruct" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Reconstruct</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor.Reconstruct" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">Reconstruct</code><span class="sig-paren">(</span><em class="sig-param">start_resnum_list</em>, <em class="sig-param">num_residues_list</em>, <em class="sig-param">chain_idx_list</em><span class="sig-paren">)</span></dt>
+<code class="descname">Reconstruct</code><span class="sig-paren">(</span><em>start_resnum_list</em>, <em>num_residues_list</em>, <em>chain_idx_list</em><span class="sig-paren">)</span></dt>
<dd><p>Reconstruct sidechains for one or several loops extracted from environment.
Overlapping loops are merged and 0-length loops are removed. All residues in
the loop(s) are expected to contain valid CB positions (or CA for GLY),
@@ -192,62 +199,70 @@ loop(s) and in the surrounding with all backbone and sidechain heavy atom
positions set.</p>
<p>Note that the structural data of the loop(s) is expected to be in the linked
environment before calling this!</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop.</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the loop belongs to.</p></li>
-<li><p><strong>start_resnum_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Starts of loops.</p></li>
-<li><p><strong>num_residues_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Lengths of loops.</p></li>
-<li><p><strong>chain_idx_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chains the loops belong to.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the loop belongs to.</li>
+<li><strong>start_resnum_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Starts of loops.</li>
+<li><strong>num_residues_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Lengths of loops.</li>
+<li><strong>chain_idx_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chains the loops belong to.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A helper object with all the reconstruction results.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if reconstructor was never attached
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">A helper object with all the reconstruction results.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.modelling.SidechainReconstructionData" title="promod3.modelling.SidechainReconstructionData"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructionData</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if reconstructor was never attached
to an environment or if parameters lead to invalid / unset
positions in environment.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.modelling.SidechainReconstructor.AttachEnvironment">
-<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em>, <em class="sig-param">use_frm=True</em>, <em class="sig-param">use_bbdep_lib=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em>, <em>use_frm=True</em>, <em>use_bbdep_lib=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.SidechainReconstructor.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em>, <em class="sig-param">use_frm</em>, <em class="sig-param">rotamer_library</em><span class="sig-paren">)</span></dt>
+<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em>, <em>use_frm</em>, <em>rotamer_library</em><span class="sig-paren">)</span></dt>
<dd><p>Link reconstructor to given <em>env</em>. A helper class is used in the background
to provide sidechain-objects for the environment. As this class is reused by
every reconstructor linked to <em>env</em>, the used parameters must be consistent
if multiple reconstructors are used (or you must use a distinct <em>env</em>).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>) – Link to this environment.</p></li>
-<li><p><strong>use_frm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, use flexible rotamer model, else rigid.</p></li>
-<li><p><strong>use_bbdep_lib</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, use default backbone dependent rot. library
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>) – Link to this environment.</li>
+<li><strong>use_frm</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, use flexible rotamer model, else rigid.</li>
+<li><strong>use_bbdep_lib</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If True, use default backbone dependent rot. library
(<code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadBBDepLib()</span></code>), else use
backbone independent one
-(<code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadLib()</span></code>).</p></li>
-<li><p><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code>) – Custom rotamer library to be used.</p></li>
+(<code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadLib()</span></code>).</li>
+<li><strong>rotamer_library</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code> / <code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code>) – Custom rotamer library to be used.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>env</em> was already linked to
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>env</em> was already linked to
another reconstructor with inconsistent parameters. Acceptable
changes:</p>
-<ul class="simple">
-<li><p><em>keep_sidechains</em> = True, if previously False</p></li>
-<li><p><em>build_disulfids</em> = False, if previously True</p></li>
+<ul class="last simple">
+<li><em>keep_sidechains</em> = True, if previously False</li>
+<li><em>build_disulfids</em> = False, if previously True</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -257,27 +272,30 @@ changes:</p>
<h2>The SidechainReconstructionData class<a class="headerlink" href="#the-sidechainreconstructiondata-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.modelling.SidechainReconstructionData">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">SidechainReconstructionData</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">SidechainReconstructionData</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData" title="Permalink to this definition">¶</a></dt>
<dd><p>Contains the results of a sidechain reconstruction
(<a class="reference internal" href="#promod3.modelling.SidechainReconstructor.Reconstruct" title="promod3.modelling.SidechainReconstructor.Reconstruct"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SidechainReconstructor.Reconstruct()</span></code></a>). All attributes are read only!</p>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.env_pos">
-<code class="sig-name descname">env_pos</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.env_pos" title="Permalink to this definition">¶</a></dt>
+<code class="descname">env_pos</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.env_pos" title="Permalink to this definition">¶</a></dt>
<dd><p>Container for structural data and mapping to the internal residue indices
of the used <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>. Useful for scoring and env.
updates.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.loop_start_indices">
-<code class="sig-name descname">loop_start_indices</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.loop_start_indices" title="Permalink to this definition">¶</a></dt>
+<code class="descname">loop_start_indices</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.loop_start_indices" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.modelling.SidechainReconstructionData.loop_lengths">
-<code class="sig-name descname">loop_lengths</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.loop_lengths" title="Permalink to this definition">¶</a></dt>
+<code class="descname">loop_lengths</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.loop_lengths" title="Permalink to this definition">¶</a></dt>
<dd><p>The first <em>sum(loop_lengths)</em> residues in
<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnvPositions.res_indices" title="promod3.loop.AllAtomEnvPositions.res_indices"><code class="xref py py-attr docutils literal notranslate"><span class="pre">res_indices</span></code></a> of <em>env_pos</em> are
guaranteed to belong to the actual input, all the rest comes from the close
@@ -288,59 +306,74 @@ entry in <em>loop_start_indices</em> and <em>loop_lengths</em>. For loop <em>i_l
<em>res_indices[loop_start_indices[i_loop] + loop_lengths[i_loop] - 1]</em> is the
C-stem of the loop. The loop indices are contiguous in <em>res_indices</em> between
the stems.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.rotamer_res_indices">
-<code class="sig-name descname">rotamer_res_indices</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.rotamer_res_indices" title="Permalink to this definition">¶</a></dt>
+<code class="descname">rotamer_res_indices</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.rotamer_res_indices" title="Permalink to this definition">¶</a></dt>
<dd><p>Indices of residues within <em>env_pos</em> for which we generated a new sidechain
(in [<em>0, len(env_pos.res_indices)-1</em>]).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.disulfid_bridges">
-<code class="sig-name descname">disulfid_bridges</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.disulfid_bridges" title="Permalink to this definition">¶</a></dt>
+<code class="descname">disulfid_bridges</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.disulfid_bridges" title="Permalink to this definition">¶</a></dt>
<dd><p>Pairs of residue indices within <em>env_pos</em> for which we generated a disulfid
bridge (indices in [<em>0, len(env_pos.res_indices)-1</em>]).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with two <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.is_n_ter">
-<code class="sig-name descname">is_n_ter</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.is_n_ter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">is_n_ter</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.is_n_ter" title="Permalink to this definition">¶</a></dt>
<dd><p>True/False depending on whether a given residue in <em>env_pos</em> is N-terminal
in the environment (same length as <em>env_pos.res_indices</em>)</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.SidechainReconstructionData.is_c_ter">
-<code class="sig-name descname">is_c_ter</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.is_c_ter" title="Permalink to this definition">¶</a></dt>
+<code class="descname">is_c_ter</code><a class="headerlink" href="#promod3.modelling.SidechainReconstructionData.is_c_ter" title="Permalink to this definition">¶</a></dt>
<dd><p>True/False depending on whether a given residue in <em>env_pos</em> is C-terminal
in the environment (same length as <em>env_pos.res_indices</em>)</p>
-<dl class="field-list simple">
-<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -350,7 +383,6 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -371,12 +403,12 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -393,7 +425,7 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li>Previous: <a href="monte_carlo.html" title="previous chapter">Generating Loops De Novo</a></li>
<li>Next: <a href="algorithms.html" title="next chapter">Modelling Algorithms</a></li>
</ul></li>
@@ -402,33 +434,27 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/sidechain_reconstruction.rst.txt"
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 18ab416e6de12e24f5323a72ac410ca1e282bbd4..4629e19fb62e0b1865a01acd2115ca59fdadce24 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index 84ec5377cf7cefde90c2f61eecd82ab2517e53a8..53ee73f38cf93faae4a3eaef0a682ed27f29dc3c 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Using Binary Files In ProMod3 — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Using Binary Files In ProMod3 — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="using-binary-files-in-project">
@@ -47,10 +46,10 @@ though that <code class="docutils literal notranslate"><span class="pre">sizeof(
memory. Everything else (e.g. <code class="docutils literal notranslate"><span class="pre">sizeof(int)</span></code>, endianness, padding of structs)
can vary. Two approaches can be used:</p>
<ol class="arabic simple">
-<li><p>Raw binary data files which are very fast to load, but assume a certain
-memory-layout for the internal representation of data</p></li>
-<li><p>Portable binary data files which are slow to load, but do not assume a given
-memory-layout for the internal representation of data</p></li>
+<li>Raw binary data files which are very fast to load, but assume a certain
+memory-layout for the internal representation of data</li>
+<li>Portable binary data files which are slow to load, but do not assume a given
+memory-layout for the internal representation of data</li>
</ol>
<p>Portable I/O should always be provided for binary files. If this is too slow
for your needs, you can provide functionality for raw binary files. In that
@@ -72,12 +71,12 @@ SavePortable).</p>
<code class="file docutils literal notranslate"><span class="pre">promod3/core/check_io.hh</span></code>. The header is written/read before the data
itself and is structured as follows:</p>
<ul class="simple">
-<li><p>a “magic number” (ensures that we can read <code class="docutils literal notranslate"><span class="pre">uint32_t</span></code> which is needed for
-the following fields)</p></li>
-<li><p>a version number (allows for backwards-compatibility)</p></li>
-<li><p>sizes for all types which are treated as raw memory (i.e. casted to a byte
-(<code class="docutils literal notranslate"><span class="pre">char</span></code>) array and written either to memory or to a stream)</p></li>
-<li><p>example values for the used base-types (ensures we can e.g. read an <code class="docutils literal notranslate"><span class="pre">int</span></code>)</p></li>
+<li>a “magic number” (ensures that we can read <code class="docutils literal notranslate"><span class="pre">uint32_t</span></code> which is needed for
+the following fields)</li>
+<li>a version number (allows for backwards-compatibility)</li>
+<li>sizes for all types which are treated as raw memory (i.e. casted to a byte
+(<code class="docutils literal notranslate"><span class="pre">char</span></code>) array and written either to memory or to a stream)</li>
+<li>example values for the used base-types (ensures we can e.g. read an <code class="docutils literal notranslate"><span class="pre">int</span></code>)</li>
</ul>
<p>For portable I/O (see below), we only write/read fixed-width fundamental
data-types (e.g. <code class="docutils literal notranslate"><span class="pre">int32_t</span></code>, <code class="docutils literal notranslate"><span class="pre">float</span></code>). Hence, we only check if we can
@@ -97,8 +96,8 @@ header file <code class="file docutils literal notranslate"><span class="pre">pr
Generally, we store any data-structure value-by-value as fixed-width types!</p>
<p>Writing and reading is performed by the following classes:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">PortableBinaryDataSink</span></code> to write files (opened as <code class="docutils literal notranslate"><span class="pre">std::ofstream</span></code>)</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">PortableBinaryDataSource</span></code> to read files (opened as <code class="docutils literal notranslate"><span class="pre">std::ifstream</span></code>)</p></li>
+<li><code class="docutils literal notranslate"><span class="pre">PortableBinaryDataSink</span></code> to write files (opened as <code class="docutils literal notranslate"><span class="pre">std::ofstream</span></code>)</li>
+<li><code class="docutils literal notranslate"><span class="pre">PortableBinaryDataSource</span></code> to read files (opened as <code class="docutils literal notranslate"><span class="pre">std::ifstream</span></code>)</li>
</ul>
<p>Each serializable class must define a <code class="docutils literal notranslate"><span class="pre">Serialize</span></code> function that accepts sinks
and sources, such as:</p>
@@ -116,21 +115,21 @@ global functions such as:</p>
</div>
<p>Given a sink or source object <code class="docutils literal notranslate"><span class="pre">ds</span></code>, we read/write an object <code class="docutils literal notranslate"><span class="pre">v</span></code> as:</p>
<ul class="simple">
-<li><p><code class="docutils literal notranslate"><span class="pre">ds</span> <span class="pre">&</span> <span class="pre">v</span></code>, if <code class="docutils literal notranslate"><span class="pre">v</span></code> is an instance of a class, a <code class="docutils literal notranslate"><span class="pre">bool</span></code> or any
-fixed-width type (e.g. <code class="docutils literal notranslate"><span class="pre">char</span></code>, <code class="docutils literal notranslate"><span class="pre">int_32_t</span></code>, <code class="docutils literal notranslate"><span class="pre">float</span></code>)</p></li>
-<li><p><code class="docutils literal notranslate"><span class="pre">core::ConvertBaseType<T>(ds,</span> <span class="pre">v)</span></code>, where <code class="docutils literal notranslate"><span class="pre">T</span></code> is a fixed-width type.
+<li><code class="docutils literal notranslate"><span class="pre">ds</span> <span class="pre">&</span> <span class="pre">v</span></code>, if <code class="docutils literal notranslate"><span class="pre">v</span></code> is an instance of a class, a <code class="docutils literal notranslate"><span class="pre">bool</span></code> or any
+fixed-width type (e.g. <code class="docutils literal notranslate"><span class="pre">char</span></code>, <code class="docutils literal notranslate"><span class="pre">int_32_t</span></code>, <code class="docutils literal notranslate"><span class="pre">float</span></code>)</li>
+<li><code class="docutils literal notranslate"><span class="pre">core::ConvertBaseType<T>(ds,</span> <span class="pre">v)</span></code>, where <code class="docutils literal notranslate"><span class="pre">T</span></code> is a fixed-width type.
<code class="docutils literal notranslate"><span class="pre">v</span></code> will then be converted to/from <code class="docutils literal notranslate"><span class="pre">T</span></code>. This is needed for any non-fixed
-fundamental type (e.g. <code class="docutils literal notranslate"><span class="pre">uint</span></code>, <code class="docutils literal notranslate"><span class="pre">short</span></code>, <code class="docutils literal notranslate"><span class="pre">Real</span></code>).</p></li>
+fundamental type (e.g. <code class="docutils literal notranslate"><span class="pre">uint</span></code>, <code class="docutils literal notranslate"><span class="pre">short</span></code>, <code class="docutils literal notranslate"><span class="pre">Real</span></code>).</li>
</ul>
<p>Implementation notes:</p>
<ul class="simple">
-<li><p>the <code class="docutils literal notranslate"><span class="pre">Serialize</span></code> function for fundamental types takes care of endianness
-(all written as little endian and converted from/to native endianness)</p></li>
-<li><p>custom <code class="docutils literal notranslate"><span class="pre">Serialize</span></code> functions exist for <code class="docutils literal notranslate"><span class="pre">String</span></code> (= <code class="docutils literal notranslate"><span class="pre">std::string</span></code>),
+<li>the <code class="docutils literal notranslate"><span class="pre">Serialize</span></code> function for fundamental types takes care of endianness
+(all written as little endian and converted from/to native endianness)</li>
+<li>custom <code class="docutils literal notranslate"><span class="pre">Serialize</span></code> functions exist for <code class="docutils literal notranslate"><span class="pre">String</span></code> (= <code class="docutils literal notranslate"><span class="pre">std::string</span></code>),
<code class="docutils literal notranslate"><span class="pre">std::vector<T></span></code> and <code class="docutils literal notranslate"><span class="pre">std::pair<T,T2></span></code>. It will throw an error if the
used type <code class="docutils literal notranslate"><span class="pre">T</span></code> or <code class="docutils literal notranslate"><span class="pre">T2</span></code> is a fundamental type. In that case, you have to
-serialize the values manually and convert each element appropriately.</p></li>
-<li><p>you can use <code class="docutils literal notranslate"><span class="pre">ds.IsSource()</span></code> to distinguish sources and sinks.</p></li>
+serialize the values manually and convert each element appropriately.</li>
+<li>you can use <code class="docutils literal notranslate"><span class="pre">ds.IsSource()</span></code> to distinguish sources and sinks.</li>
</ul>
</div>
<div class="section" id="code-example">
@@ -363,50 +362,47 @@ and non-portable I/O:</p>
<h2>Exisiting Binary Files<a class="headerlink" href="#exisiting-binary-files" title="Permalink to this headline">¶</a></h2>
<p>The following binary files are currently in ProMod3:</p>
<ul class="simple">
-<li><p>module <code class="docutils literal notranslate"><span class="pre">loop</span></code>:</p>
-<ul>
-<li><p><code class="file docutils literal notranslate"><span class="pre">frag_db.dat</span></code>
-(<a class="reference internal" href="loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">structure_db.dat</span></code>
-(<a class="reference internal" href="loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">torsion_sampler_coil.dat</span></code>
-(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">torsion_sampler.dat</span></code>
-(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">torsion_sampler_extended.dat</span></code>
-(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">torsion_sampler_helical.dat</span></code>
-(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">ff_lookup_charmm.dat</span></code>
-(<a class="reference internal" href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>)</p></li>
+<li>module <code class="docutils literal notranslate"><span class="pre">loop</span></code>:<ul>
+<li><code class="file docutils literal notranslate"><span class="pre">frag_db.dat</span></code>
+(<a class="reference internal" href="loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">structure_db.dat</span></code>
+(<a class="reference internal" href="loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">torsion_sampler_coil.dat</span></code>
+(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">torsion_sampler.dat</span></code>
+(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">torsion_sampler_extended.dat</span></code>
+(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">torsion_sampler_helical.dat</span></code>
+(<a class="reference internal" href="loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">ff_lookup_charmm.dat</span></code>
+(<a class="reference internal" href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>)</li>
</ul>
</li>
-<li><p>module <code class="docutils literal notranslate"><span class="pre">scoring</span></code>:</p>
-<ul>
-<li><p><code class="file docutils literal notranslate"><span class="pre">cbeta_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">cb_packing_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">hbond_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">reduced_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">ss_agreement_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SSAgreementScorer</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">torsion_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">aa_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">aa_packing_scorer.dat</span></code>
-(<a class="reference internal" href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a>)</p></li>
+<li>module <code class="docutils literal notranslate"><span class="pre">scoring</span></code>:<ul>
+<li><code class="file docutils literal notranslate"><span class="pre">cbeta_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">cb_packing_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">hbond_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">reduced_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">ss_agreement_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SSAgreementScorer</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">torsion_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">aa_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">aa_packing_scorer.dat</span></code>
+(<a class="reference internal" href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a>)</li>
</ul>
</li>
-<li><p>module <code class="docutils literal notranslate"><span class="pre">sidechain</span></code>:</p>
-<ul>
-<li><p><code class="file docutils literal notranslate"><span class="pre">bb_dep_lib.dat</span></code>
-(<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a>)</p></li>
-<li><p><code class="file docutils literal notranslate"><span class="pre">lib.dat</span></code>
-(<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a>)</p></li>
+<li>module <code class="docutils literal notranslate"><span class="pre">sidechain</span></code>:<ul>
+<li><code class="file docutils literal notranslate"><span class="pre">bb_dep_lib.dat</span></code>
+(<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a>)</li>
+<li><code class="file docutils literal notranslate"><span class="pre">lib.dat</span></code>
+(<a class="reference internal" href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a>)</li>
</ul>
</li>
</ul>
@@ -425,7 +421,6 @@ in the <code class="file docutils literal notranslate"><span class="pre">extras/
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -462,33 +457,27 @@ in the <code class="file docutils literal notranslate"><span class="pre">extras/
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/portableIO.rst.txt"
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 6ddff087213a19145e54caa4d81778254493b245..06632bdef08109eb6898181cc0df6a7ebb72ba1c 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Python Module Index — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Python Module Index — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -19,7 +21,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
@@ -30,8 +31,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
@@ -99,7 +98,6 @@
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -132,33 +130,27 @@
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/references.html b/doc/html/references.html
index ba8c49687f2c8cd175676f134fe85c2cf46afe25..c5cfde451fc538649c62098da9c73dc3434b22f5 100644
--- a/doc/html/references.html
+++ b/doc/html/references.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>References — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>References — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,107 +30,153 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="references">
<h1>References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h1>
-<dl class="citation">
-<dt class="label" id="biasini2013"><span class="brackets">biasini2013</span></dt>
-<dd><p>Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J,
+<table class="docutils citation" frame="void" id="biasini2013" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[biasini2013]</td><td>Biasini M, Schmidt T, Bienert S, Mariani V, Studer G, Haas J,
Johner N, Schenk AD, Philippsen A and Schwede T (2013).
OpenStructure: an integrated software framework for
-computational structural biology. Acta Cryst.</p>
-</dd>
-<dt class="label" id="canutescu2003"><span class="brackets">canutescu2003</span></dt>
-<dd><p>Canutescu AA and Dunbrack RL Jr. (2003).
+computational structural biology. Acta Cryst.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="canutescu2003" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[canutescu2003]</td><td>Canutescu AA and Dunbrack RL Jr. (2003).
Cyclic coordinate descent: A robotics algorithm for protein
-loop closure. Protein Sci.</p>
-</dd>
-<dt class="label" id="canutescu2003b"><span class="brackets">canutescu2003b</span></dt>
-<dd><p>Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003).
+loop closure. Protein Sci.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="canutescu2003b" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[canutescu2003b]</td><td>Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003).
A graph-theory algorithm for rapid protein side-chain
-prediction. Protein Sci.</p>
-</dd>
-<dt class="label" id="coutsias2005"><span class="brackets">coutsias2005</span></dt>
-<dd><p>Coutsias EA, Seok C, Wester MJ, Dill KA (2005).
+prediction. Protein Sci.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="coutsias2005" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[coutsias2005]</td><td>Coutsias EA, Seok C, Wester MJ, Dill KA (2005).
Resultants and loop closure. International Journal of Quantum
-Chemistry.</p>
-</dd>
-<dt class="label" id="chakravarty1999"><span class="brackets">chakravarty1999</span></dt>
-<dd><p>Chakravarty S, Varadarajan R (1999).
+Chemistry.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="chakravarty1999" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[chakravarty1999]</td><td>Chakravarty S, Varadarajan R (1999).
Residue depth: a novel parameter for the analysis of
-protein structure and stability. Structure.</p>
-</dd>
-<dt class="label" id="davis2006"><span class="brackets">davis2006</span></dt>
-<dd><p>Davis IW, Arendall WB, Richardson DC, Richardson JS (2006).
+protein structure and stability. Structure.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="davis2006" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[davis2006]</td><td>Davis IW, Arendall WB, Richardson DC, Richardson JS (2006).
The backrub motion: how protein backbone shrugs when a sidechain
-dances. Structure.</p>
-</dd>
-<dt class="label" id="goldstein1994"><span class="brackets">goldstein1994</span></dt>
-<dd><p>Goldstein RF (1994).
+dances. Structure.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="goldstein1994" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[goldstein1994]</td><td>Goldstein RF (1994).
Efficient rotamer elimination applied to protein side-chains
-and related spin glasses. Biophys J.</p>
-</dd>
-<dt class="label" id="jones1999"><span class="brackets">Jones1999</span></dt>
-<dd><p>Jones DT (1999).
+and related spin glasses. Biophys J.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="jones1999" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[Jones1999]</td><td>Jones DT (1999).
Protein secondary structure prediction based on position-specific
-scoring matrices. J. Mol. Biol.</p>
-</dd>
-<dt class="label" id="kabsch1983"><span class="brackets">kabsch1983</span></dt>
-<dd><p>Kabsch W, Sander C (1983).
+scoring matrices. J. Mol. Biol.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="kabsch1983" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[kabsch1983]</td><td>Kabsch W, Sander C (1983).
Dictionary of protein secondary structure: pattern recognition of
-hydrogen-bonded and geometrical features. Biopolymers.</p>
-</dd>
-<dt class="label" id="krivov2009"><span class="brackets">krivov2009</span></dt>
-<dd><p>Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009).
+hydrogen-bonded and geometrical features. Biopolymers.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="krivov2009" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[krivov2009]</td><td>Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009).
Improved prediction of protein side-chain conformations with
-SCWRL4. Proteins.</p>
-</dd>
-<dt class="label" id="leach1998"><span class="brackets">leach1998</span></dt>
-<dd><p>Leach AR, Lemon AP (1998).
+SCWRL4. Proteins.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="leach1998" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[leach1998]</td><td>Leach AR, Lemon AP (1998).
Exploring the conformational space of protein side chains using
-dead-end elimination and the A* algorithm. Proteins.</p>
-</dd>
-<dt class="label" id="nussinov1991"><span class="brackets">nussinov1991</span></dt>
-<dd><p>Nussinov R and Wolfson HJ (1991).
+dead-end elimination and the A* algorithm. Proteins.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="nussinov1991" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[nussinov1991]</td><td>Nussinov R and Wolfson HJ (1991).
Efficient detection of three-dimensional structural motifs in
-biological macromolecules by computer vision techniques. PNAS.</p>
-</dd>
-<dt class="label" id="shapovalov2011"><span class="brackets">shapovalov2011</span></dt>
-<dd><p>Shapovalov MV and Dunbrack RL Jr. (2011).
+biological macromolecules by computer vision techniques. PNAS.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="shapovalov2011" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[shapovalov2011]</td><td>Shapovalov MV and Dunbrack RL Jr. (2011).
A smoothed backbone-dependent rotamer library for proteins
derived from adaptive kernel density estimates and
-regressions. Structure.</p>
-</dd>
-<dt class="label" id="soding2005"><span class="brackets">soding2005</span></dt>
-<dd><p>Söding J (2005).
+regressions. Structure.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="soding2005" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[soding2005]</td><td>Söding J (2005).
Protein homology detection by HMM-HMM comparison.
-Bioinformatics.</p>
-</dd>
-<dt class="label" id="solis2006"><span class="brackets">solis2006</span></dt>
-<dd><p>Solis AD, Rackovsky S (2006). Improvement of statistical
+Bioinformatics.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="solis2006" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[solis2006]</td><td>Solis AD, Rackovsky S (2006). Improvement of statistical
potentials and threading score functions using information
-maximization. Proteins.</p>
-</dd>
-<dt class="label" id="trott2010"><span class="brackets">trott2010</span></dt>
-<dd><p>Trott O, Olson AJ (2010). AutoDock Vina: improving the speed and
+maximization. Proteins.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="trott2010" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[trott2010]</td><td>Trott O, Olson AJ (2010). AutoDock Vina: improving the speed and
accuracy of docking with a new scoring function, efficient
-optimization and multithreading. J Comput Chem</p>
-</dd>
-<dt class="label" id="zhou2005"><span class="brackets">zhou2005</span></dt>
-<dd><p>Zhou H, Zhou Y (2005).
+optimization and multithreading. J Comput Chem</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="zhou2005" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[zhou2005]</td><td>Zhou H, Zhou Y (2005).
Fold Recognition by Combining Sequence Profiles Derived From
Evolution and From Depth-Dependent Structural Alignment of
-Fragments. Proteins.</p>
-</dd>
-</dl>
+Fragments. Proteins.</td></tr>
+</tbody>
+</table>
</div>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -164,33 +211,27 @@ Fragments. Proteins.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
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- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 7724c7078731bdeee33cc4350fadb20f7697559d..3e3d467e790f5bf411b0328dc7ff1466db12cd59 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>All Atom Scorers — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>All Atom Scorers — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="all-atom-scorers">
@@ -39,119 +38,132 @@
<h2>AllAtomOverallScorer class<a class="headerlink" href="#allatomoverallscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.AllAtomOverallScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">AllAtomOverallScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomOverallScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Container that allows for the storage of multiple scorers identified by a key
(<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) and the computation of combined scores.</p>
<p>Scorers need to be individually set or loaded by
<a class="reference internal" href="#promod3.scoring.LoadDefaultAllAtomOverallScorer" title="promod3.scoring.LoadDefaultAllAtomOverallScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadDefaultAllAtomOverallScorer()</span></code></a></p>
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.Contains">
-<code class="sig-name descname">Contains</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.Contains" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if a scorer object for this key was already added.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
-</dd>
-</dl>
+<code class="descname">Contains</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.Contains" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if a scorer object for this key was already added.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.Get">
-<code class="sig-name descname">Get</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.Get" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Scorer with the given <em>key</em> (read-only access).</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomScorer</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there is no scorer with that
-<em>key</em>.</p>
-</dd>
-</dl>
+<code class="descname">Get</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.Get" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Scorer with the given <em>key</em> (read-only access).</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomScorer</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there is no scorer with that
+<em>key</em>.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.AttachEnvironment">
-<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>) – Link all scorers to this score environment.</p>
-</dd>
-</dl>
+<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>) – Link all scorers to this score environment.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination">
-<code class="sig-name descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em class="sig-param">linear_weights</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em>linear_weights</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate linear combination of scores for the desired loop(s) (extracted
from environment) against the set environment (see
<a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AllAtomScorer.CalculateScore()</span></code></a>).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)) – Weights for each desired scorer. You can add a
constant value to each score by defining a weight
-with key “intercept”.</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop(s).</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
+with key “intercept”.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop(s).</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Score for the given set of atoms.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score for the given set of atoms.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
which no scorer exists or anything raised in
<a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AllAtomScorer.CalculateScore()</span></code></a> for any of the used scorers.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.__getitem__">
-<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.__getitem__" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.AllAtomOverallScorer.__setitem__">
-<code class="sig-name descname">__setitem__</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.__setitem__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__setitem__</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.__setitem__" title="Permalink to this definition">¶</a></dt>
<dd><p>Allow read/write access (with [<em>key</em>]) to scorer object with given key.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadDefaultAllAtomOverallScorer">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadDefaultAllAtomOverallScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadDefaultAllAtomOverallScorer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Loads or creates the default scorers accessible through
+<code class="descclassname">promod3.scoring.</code><code class="descname">LoadDefaultAllAtomOverallScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadDefaultAllAtomOverallScorer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Loads or creates the default scorers accessible through
following keys:
-“aa_interaction”, “aa_packing”, “aa_clash”</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.AllAtomOverallScorer" title="promod3.scoring.AllAtomOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomOverallScorer</span></code></a></p>
-</dd>
-</dl>
+“aa_interaction”, “aa_packing”, “aa_clash”</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomOverallScorer" title="promod3.scoring.AllAtomOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomOverallScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -159,75 +171,86 @@ following keys:
<h2>AllAtomScorer base class<a class="headerlink" href="#allatomscorer-base-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.AllAtomScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">AllAtomScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Base class for all the all atom scorers listed below.</p>
<dl class="method">
<dt id="promod3.scoring.AllAtomScorer.AttachEnvironment">
-<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>) – Link scorer to this score environment.</p>
-</dd>
-</dl>
+<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a>) – Link scorer to this score environment.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomScorer.CalculateScore">
-<code class="sig-name descname">CalculateScore</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateScore</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates score for the desired loop(s) (extracted from environment) against
the set environment. Unless otherwise noted in the scorer, a lower “score”
is better!</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop(s).</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop(s).</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Score for the given set of atoms.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>(for most scorers) <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if scorer was
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score for the given set of atoms.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">(for most scorers) <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if scorer was
never attached to a score environment, if scorer has never been
properly initialized or if <em>chain_index</em> / <em>start_resnum</em> lead to
invalid positions.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomScorer.CalculateScoreProfile">
-<code class="sig-name descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates per residue scores for the desired loop(s) (extracted from
environment) against the set environment.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop(s).</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
-(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop(s).</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
+(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Scores for the given loop(s), one for each residue.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Scores for the given loop(s), one for each residue.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>same <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> as <a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CalculateScore()</span></code></a>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">same <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> as <a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CalculateScore()</span></code></a>.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -237,7 +260,7 @@ of <a class="reference external" href="https://docs.python.org/3.7/library/funct
<h2>AllAtomInteractionScorer class<a class="headerlink" href="#allatominteractionscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.AllAtomInteractionScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">AllAtomInteractionScorer</code><span class="sig-paren">(</span><em class="sig-param">cutoff</em>, <em class="sig-param">bins</em>, <em class="sig-param">seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomInteractionScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>bins</em>, <em>seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomScorer</span></code></a>. Evaluates a pairwise
pseudo interaction energy between all atoms which are located within a
<em>cutoff</em> and which are at least <em>seq_sep</em> residues apart. An energy is
@@ -250,133 +273,154 @@ in the input loops. You can change this behaviour with the according
functions.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadAllAtomInteractionScorer" title="promod3.scoring.LoadAllAtomInteractionScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadAllAtomInteractionScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer.SetEnergy" title="promod3.scoring.AllAtomInteractionScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other atoms are counted.</p></li>
-<li><p><strong>bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
-of [0,*cutoff*]).</p></li>
-<li><p><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Minimal separation in sequence two residues must have to
-be considered.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other atoms are counted.</li>
+<li><strong>bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
+of [0,*cutoff*]).</li>
+<li><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Minimal separation in sequence two residues must have to
+be considered.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>bins</em> < 1 or
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>bins</em> < 1 or
<em>seq_sep</em> < 1.</p>
-</dd>
-</dl>
-<dl class="method">
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.scoring.AllAtomInteractionScorer.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.AllAtomInteractionScorer.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer.Save" title="promod3.scoring.AllAtomInteractionScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer.SavePortable" title="promod3.scoring.AllAtomInteractionScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded scorer</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.AllAtomInteractionScorer.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.SetEnergy">
-<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">aaa1</em>, <em class="sig-param">aaa2</em>, <em class="sig-param">bin</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aaa1</em>, <em>aaa2</em>, <em>bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of heavy atom types and for every <em>bin</em> < <em>bins</em>.
Internal symmetry is enforced => Calling SetEnergy(aaa1, aaa2, bin, energy) is
equivalent to calling SetEnergy(aaa1, aaa2, bin, energy) AND
SetEnergy(aaa2, aaa1, bin, energy).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aaa1</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for first interaction partner.</p></li>
-<li><p><strong>aaa2</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for second interaction partner.</p></li>
-<li><p><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</p></li>
-<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aaa1</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for first interaction partner.</li>
+<li><strong>aaa2</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for second interaction partner.</li>
+<li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.DoInternalScores">
-<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions within the
-loop. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions within the
+loop. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.DoExternalScores">
-<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions towards the
-environment. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions towards the
+environment. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomInteractionScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues in the input loop. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues in the input loop. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadAllAtomInteractionScorer">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadAllAtomInteractionScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadAllAtomInteractionScorer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The default predefined AllAtomInteractionScorer (loaded from disk)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a></p>
-</dd>
-</dl>
+<code class="descclassname">promod3.scoring.</code><code class="descname">LoadAllAtomInteractionScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadAllAtomInteractionScorer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined AllAtomInteractionScorer (loaded from disk)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomInteractionScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -384,111 +428,126 @@ of residues in the input loop. True by default.</p>
<h2>AllAtomPackingScorer class<a class="headerlink" href="#allatompackingscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.AllAtomPackingScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">AllAtomPackingScorer</code><span class="sig-paren">(</span><em class="sig-param">cutoff</em>, <em class="sig-param">max_count</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomPackingScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>max_count</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomScorer</span></code></a>. Evaluates pseudo
energies by counting surrounding atoms within a certain <em>cutoff</em> radius around
all heavy atoms not belonging to the assessed residue itself.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadAllAtomPackingScorer" title="promod3.scoring.LoadAllAtomPackingScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadAllAtomPackingScorer()</span></code></a>) or by setting all energies (see
<a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer.SetEnergy" title="promod3.scoring.AllAtomPackingScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other atoms are counted.</p></li>
-<li><p><strong>max_count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If number of other atoms exceeds <em>max_count</em>, it will
-be set to this number.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other atoms are counted.</li>
+<li><strong>max_count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If number of other atoms exceeds <em>max_count</em>, it will
+be set to this number.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>max_count</em> < 1.</p>
-</dd>
-</dl>
-<dl class="method">
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>max_count</em> < 1.</p>
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.scoring.AllAtomPackingScorer.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.AllAtomPackingScorer.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer.Save" title="promod3.scoring.AllAtomPackingScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer.SavePortable" title="promod3.scoring.AllAtomPackingScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded scorer</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomPackingScorer.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.AllAtomPackingScorer.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomPackingScorer.SetEnergy">
-<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">aaa</em>, <em class="sig-param">count</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aaa</em>, <em>count</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every heavy atom type and for every <em>count</em> <= <em>max_count</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aaa</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for which to set energy.</p></li>
-<li><p><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of surrounding atoms for which to set energy.</p></li>
-<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aaa</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) – Heavy atom type for which to set energy.</li>
+<li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of surrounding atoms for which to set energy.</li>
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomPackingScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues in the input loop. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues in the input loop. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadAllAtomPackingScorer">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadAllAtomPackingScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadAllAtomPackingScorer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The default predefined AllAtomPackingScorer (loaded from disk)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a></p>
-</dd>
-</dl>
+<code class="descclassname">promod3.scoring.</code><code class="descname">LoadAllAtomPackingScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadAllAtomPackingScorer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined AllAtomPackingScorer (loaded from disk)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPackingScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -496,45 +555,54 @@ of residues in the input loop. True by default.</p>
<h2>AllAtomClashScorer class<a class="headerlink" href="#allatomclashscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.AllAtomClashScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">AllAtomClashScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomClashScorer</code><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomScorer</span></code></a>. Calculates a simple
clash score of all atoms against the environment. There is no need to define
any parameters here as all interaction energies are fixed (see Eq. (11) in
-<a class="reference internal" href="../references.html#canutescu2003b" id="id1"><span>[canutescu2003b]</span></a>). By default, the scorer calculates the scores by
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>). By default, the scorer calculates the scores by
including everything, the stuff set in the environment and the coordinates
in the input loops. You can change this behaviour with the according
functions.</p>
<dl class="method">
<dt id="promod3.scoring.AllAtomClashScorer.DoInternalScores">
-<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions within the
-loop. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions within the
+loop. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomClashScorer.DoExternalScores">
-<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions towards the
-environment. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions towards the
+environment. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.AllAtomClashScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues in the input loop. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues in the input loop. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -544,7 +612,6 @@ of residues in the input loop. True by default.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -565,12 +632,12 @@ of residues in the input loop. True by default.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -587,7 +654,7 @@ of residues in the input loop. True by default.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
<li>Previous: <a href="backbone_scorers.html" title="previous chapter">Backbone Scorers</a></li>
<li>Next: <a href="other_scoring_functions.html" title="next chapter">Other Scoring Functions</a></li>
</ul></li>
@@ -596,33 +663,27 @@ of residues in the input loop. True by default.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
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- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/scoring/all_atom_scorers.rst.txt"
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index 145b8ca99c90a973d9ebe0c83a959427d2c4dc14..ab4bc1a2ce98e5afc7b5073c5ed553defd7fa3ca 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Backbone Score Environment — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Backbone Score Environment — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="backbone-score-environment">
@@ -39,7 +38,7 @@
<h2>BackboneScoreEnv class<a class="headerlink" href="#backbonescoreenv-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.BackboneScoreEnv">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">BackboneScoreEnv</code><span class="sig-paren">(</span><em class="sig-param">seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">BackboneScoreEnv</code><span class="sig-paren">(</span><em>seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv" title="Permalink to this definition">¶</a></dt>
<dd><p>The backbone score environment contains and handles all model-specific data
used by the scorers. It is linked to a (list of) seqres (one per chain) at
construction. The idea is to initialize it at the beginning of the modelling
@@ -48,202 +47,233 @@ prediction, etc). All scorers attached to that environment will see that data
and can calculate scores accordingly.
Scoring with this setup is a two step process:</p>
<ul class="simple">
-<li><p>Set the positions you want to score in the environment to make it available
-to all attached scorers</p></li>
-<li><p>Call the scorers to get the desired scores</p></li>
+<li>Set the positions you want to score in the environment to make it available
+to all attached scorers</li>
+<li>Call the scorers to get the desired scores</li>
</ul>
<p>One problem that might occur is that you mess around with the environment and
at some point you want to restore the original state. The
<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> provides a Stash / Pop mechanism to perform this
task.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
-chain). Whenever setting structural data, consistency with this SEQRES is enforced.</p>
-</dd>
-</dl>
+chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
+</tr>
+</tbody>
+</table>
<p>To access parts of the environment there are two key arguments to consider:</p>
<ul class="simple">
-<li><p><em>chain_idx</em>: Index of chain as it occurs in <em>seqres</em> (0 for single sequence)</p></li>
-<li><p><em>start_resnum</em>: Residue number defining the position in the SEQRES of chain
+<li><em>chain_idx</em>: Index of chain as it occurs in <em>seqres</em> (0 for single sequence)</li>
+<li><em>start_resnum</em>: Residue number defining the position in the SEQRES of chain
with index <em>chain_idx</em>. <strong>The numbering starts for every chain with the
-value 1</strong>.</p></li>
+value 1</strong>.</li>
</ul>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.Copy">
-<code class="sig-name descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Copy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>A copy of the current <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> without any scorers
-attached</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">Copy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Copy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A copy of the current <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> without any scorers
+attached</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.SetInitialEnvironment">
-<code class="sig-name descname">SetInitialEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env_structure</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetInitialEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetInitialEnvironment</code><span class="sig-paren">(</span><em>env_structure</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetInitialEnvironment" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets structural environment with which loops to be scored interact. If
structural data was already set, all the existing data gets cleared first.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
-order as the SEQRES items provided in constructor.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>env</em> is inconsistent with
+order as the SEQRES items provided in constructor.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>env</em> is inconsistent with
SEQRES set in constructor. This can be because of corrupt residue
-numbers or sequence mismatches.</p>
-</dd>
-</dl>
+numbers or sequence mismatches.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.SetEnvironment">
-<code class="sig-name descname">SetEnvironment</code><span class="sig-paren">(</span><em class="sig-param">bb_list</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetEnvironment</code><span class="sig-paren">(</span><em>bb_list</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetEnvironment" title="Permalink to this definition">¶</a></dt>
<dd><p>Add/update structural information in environment. If structural data for
specific residues is already set, the data gets resetted for these
positions.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if sequence of <em>bb_list</em> is
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if sequence of <em>bb_list</em> is
inconsistent with previously SEQRES set in constructor or when
either <em>start_resnum</em> or <em>chain_idx</em> point to invalid positions in
the SEQRES.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.ClearEnvironment">
-<code class="sig-name descname">ClearEnvironment</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.ClearEnvironment" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ClearEnvironment</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.ClearEnvironment" title="Permalink to this definition">¶</a></dt>
<dd><p>Clears a stretch of length <em>num_residues</em> in the environment in chain
with idx <em>chain_idx</em> starting from residue number <em>start_resnum</em></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start of stretch to clear</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of stretch to clear</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start of stretch to clear</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of stretch to clear</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the stretch belongs to</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when either <em>start_resnum</em> or
<em>chain_idx</em> point to invalid positions in the SEQRES.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.SetPsipredPrediction">
-<code class="sig-name descname">SetPsipredPrediction</code><span class="sig-paren">(</span><em class="sig-param">pred</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetPsipredPrediction" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetPsipredPrediction</code><span class="sig-paren">(</span><em>pred</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetPsipredPrediction" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the psipred prediction, which is necessary to calculate some scores.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>pred</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code>) – Psipred prediction to set (one per chain).</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the number of predictions is
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>pred</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<code class="xref py py-class docutils literal notranslate"><span class="pre">PsipredPrediction</span></code>) – Psipred prediction to set (one per chain).</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the number of predictions is
inconsistent with the number of internal chains or when one of the
-predictions’ sizes is inconsistent with the internal SEQRES size.</p>
-</dd>
-</dl>
+predictions’ sizes is inconsistent with the internal SEQRES size.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.AddPairwiseFunction">
-<code class="sig-name descname">AddPairwiseFunction</code><span class="sig-paren">(</span><em class="sig-param">function</em>, <em class="sig-param">function_type</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddPairwiseFunction</code><span class="sig-paren">(</span><em>function</em>, <em>function_type</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds a pairwise function that can be used in <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ApplyPairwiseFunction()</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>function</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunction</span></code></a>) – Pairwise function to be added.</p></li>
-<li><p><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – What distances should be looked at for this function.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>function</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunction</span></code></a>) – Pairwise function to be added.</li>
+<li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – What distances should be looked at for this function.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Function index to be used in <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ApplyPairwiseFunction()</span></code></a>.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Function index to be used in <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ApplyPairwiseFunction()</span></code></a>.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction">
-<code class="sig-name descname">ApplyPairwiseFunction</code><span class="sig-paren">(</span><em class="sig-param">chain_idx_one</em>, <em class="sig-param">resnum_one</em>, <em class="sig-param">chain_idx_two</em>, <em class="sig-param">resnum_two</em>, <em class="sig-param">f_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplyPairwiseFunction</code><span class="sig-paren">(</span><em>chain_idx_one</em>, <em>resnum_one</em>, <em>chain_idx_two</em>, <em>resnum_two</em>, <em>f_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>Define two residues to be evaluated with a given pairwise function. This
data can then be used by scorers. Note that the pairs are symmetric and so
there is no need to add them twice with switched residues.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>chain_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain index of first residue</p></li>
-<li><p><strong>resnum_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number of first residue</p></li>
-<li><p><strong>chain_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain index of second residue</p></li>
-<li><p><strong>resnum_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number of second residue</p></li>
-<li><p><strong>f_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of pairwise function (as returned by
-<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.AddPairwiseFunction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddPairwiseFunction()</span></code></a>)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>chain_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain index of first residue</li>
+<li><strong>resnum_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number of first residue</li>
+<li><strong>chain_idx_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain index of second residue</li>
+<li><strong>resnum_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number of second residue</li>
+<li><strong>f_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of pairwise function (as returned by
+<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.AddPairwiseFunction"><code class="xref py py-meth docutils literal notranslate"><span class="pre">AddPairwiseFunction()</span></code></a>)</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any of the chain indices or
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if any of the chain indices or
res. numbers is invalid, the interaction partners are the same
residue or when <em>f_idx</em> is an invalid index.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.Stash">
-<code class="sig-name descname">Stash</code><span class="sig-paren">(</span><em class="sig-param">start_rnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Stash" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Stash</code><span class="sig-paren">(</span><em>start_rnum</em>, <em>num_residues</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Stash" title="Permalink to this definition">¶</a></dt>
<dd><p>FILO style stashing. You can perform up to 100 stash operations to save
the current state of certain stretches in the environment. This state can
be restored by calling <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.Pop" title="promod3.scoring.BackboneScoreEnv.Pop"><code class="xref py py-func docutils literal notranslate"><span class="pre">Pop()</span></code></a>. In one stash operation you can either
stash one stretch by providing integers as input or several stretches by
providing lists of integers.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_rnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – start rnum of stretch to stash</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – length of stretch to stash</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – chain idx of stretch to stash</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>start_rnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – start rnum of stretch to stash</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – length of stretch to stash</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – chain idx of stretch to stash</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.Pop">
-<code class="sig-name descname">Pop</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Pop" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Pop</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Pop" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove and apply the the last stash operation.</p>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.GetSeqres">
-<code class="sig-name descname">GetSeqres</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.GetSeqres" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>SEQRES that was set in constructor (one sequence per chain).</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetSeqres</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.GetSeqres" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -253,75 +283,84 @@ providing lists of integers.</p>
<h2>Pairwise function classes<a class="headerlink" href="#pairwise-function-classes" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.PairwiseFunctionType">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">PairwiseFunctionType</code><a class="headerlink" href="#promod3.scoring.PairwiseFunctionType" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">PairwiseFunctionType</code><a class="headerlink" href="#promod3.scoring.PairwiseFunctionType" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the pairwise function types. Possible values:</p>
<ul class="simple">
-<li><p><em>CA_PAIRWISE_FUNCTION</em> - Evaluate CA atoms distances.</p></li>
-<li><p><em>CB_PAIRWISE_FUNCTION</em> - Evaluate CB atoms distances.</p></li>
+<li><em>CA_PAIRWISE_FUNCTION</em> - Evaluate CA atoms distances.</li>
+<li><em>CB_PAIRWISE_FUNCTION</em> - Evaluate CB atoms distances.</li>
</ul>
</dd></dl>
<dl class="class">
<dt id="promod3.scoring.PairwiseFunction">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">PairwiseFunction</code><a class="headerlink" href="#promod3.scoring.PairwiseFunction" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">PairwiseFunction</code><a class="headerlink" href="#promod3.scoring.PairwiseFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>Base class for any pairwise function.</p>
<dl class="method">
<dt id="promod3.scoring.PairwiseFunction.Score">
-<code class="sig-name descname">Score</code><span class="sig-paren">(</span><em class="sig-param">distance</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseFunction.Score" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Score for a given pairwise distance</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Pairwise distance</p>
-</dd>
-</dl>
+<code class="descname">Score</code><span class="sig-paren">(</span><em>distance</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseFunction.Score" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Score for a given pairwise distance</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>distance</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Pairwise distance</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.scoring.ConstraintFunction">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">ConstraintFunction</code><span class="sig-paren">(</span><em class="sig-param">min_dist</em>, <em class="sig-param">max_dist</em>, <em class="sig-param">values</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ConstraintFunction" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ConstraintFunction</code><span class="sig-paren">(</span><em>min_dist</em>, <em>max_dist</em>, <em>values</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ConstraintFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunction</span></code></a>.
Defines a constraint function. The score for a distance between <em>min_dist</em> and
<em>max_dist</em> is determined by linear interpolation assuming the first and last
value exactly lying on <em>min_dist</em> and <em>max_dist</em>. For distances outside the
range defined by <em>min_dist</em> and <em>max_dist</em>, the returned score is 0.0.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>min_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal distance to be considered</p></li>
-<li><p><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance to be considered</p></li>
-<li><p><strong>values</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The possible values that get returned when the distance is
-between <em>min_dist</em> and <em>max_dist</em></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>min_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal distance to be considered</li>
+<li><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance to be considered</li>
+<li><strong>values</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The possible values that get returned when the distance is
+between <em>min_dist</em> and <em>max_dist</em></li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>min_dist</em> >= <em>max_dist</em> or when
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>min_dist</em> >= <em>max_dist</em> or when
<em>min_dist</em> or <em>max_dist</em> are negative or when <em>values</em> contains no
elements</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="class">
<dt id="promod3.scoring.ContactFunction">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">ContactFunction</code><span class="sig-paren">(</span><em class="sig-param">max_dist</em>, <em class="sig-param">score</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ContactFunction" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ContactFunction</code><span class="sig-paren">(</span><em>max_dist</em>, <em>score</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ContactFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunction</span></code></a>.
Defines a simple contact function. The score value is <em>score</em> if
distance < <em>max_dist</em> and 0.0 otherwise.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance to be in contact</p></li>
-<li><p><strong>score</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Value that gets returned if in contact</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>max_dist</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal distance to be in contact</li>
+<li><strong>score</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Value that gets returned if in contact</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -329,39 +368,45 @@ distance < <em>max_dist</em> and 0.0 otherwise.</p>
<h2>Convenient construction of pairwise functions<a class="headerlink" href="#convenient-construction-of-pairwise-functions" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.DiscoContainer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">DiscoContainer</code><span class="sig-paren">(</span><em class="sig-param">seqres</em><span class="optional">[</span>, <em class="sig-param">function_type = CA_PAIRWISE_FUNCTION</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">DiscoContainer</code><span class="sig-paren">(</span><em>seqres</em><span class="optional">[</span>, <em>function_type = CA_PAIRWISE_FUNCTION</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer" title="Permalink to this definition">¶</a></dt>
<dd><p>A container collecting structural information until it can be added in form
of <a class="reference internal" href="#promod3.scoring.ConstraintFunction" title="promod3.scoring.ConstraintFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">ConstraintFunction</span></code></a> to a <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> .
The constraint functions are built after the principle of QMEANDisCo.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</p></li>
-<li><p><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
-or CB atoms</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
+<li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
+or CB atoms</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="function">
<dt id="promod3.scoring.DiscoContainer.AddStructuralInfo">
-<code class="sig-name descname">AddStructuralInfo</code><span class="sig-paren">(</span><em class="sig-param">aln</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer.AddStructuralInfo" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
+<code class="descname">AddStructuralInfo</code><span class="sig-paren">(</span><em>aln</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer.AddStructuralInfo" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
SEQRES and the second sequence the actual structural
-info. The second sequence must have a view attached.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if number of sequences in <em>aln</em> is
+info. The second sequence must have a view attached.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if number of sequences in <em>aln</em> is
not two, the SEQRES does not match or when the second sequence in
-<em>aln</em> has no view attached.</p>
-</dd>
-</dl>
+<em>aln</em> has no view attached.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.DiscoContainer.AttachConstraints">
-<code class="sig-name descname">AttachConstraints</code><span class="sig-paren">(</span><em class="sig-param">env</em>, <em class="sig-param">chain_indices</em><span class="optional">[</span>, <em class="sig-param">cluster_thresh = 0.5</em>, <em class="sig-param">gamma = 70.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer.AttachConstraints" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AttachConstraints</code><span class="sig-paren">(</span><em>env</em>, <em>chain_indices</em><span class="optional">[</span>, <em>cluster_thresh = 0.5</em>, <em>gamma = 70.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer.AttachConstraints" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates distance constraints and adds it to <em>env</em>.
It first clusters the added sequences with a pairwise normalised sequence
similarity based on BLOSUM62. It’s a hierarchical clustering with with an
@@ -373,25 +418,29 @@ target SEQRES. How fast this influence vanishes gets controlled by gamma.
The higher it is, the faster vanishes the influence of structural info
from distant clusters. The final pairwise cluster functions get then
directly added to the scoring <em>env</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>env</strong> (<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – The scoring env to which the constraint
-should be added</p></li>
-<li><p><strong>chain_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Indices of chains for which the constraints should
-be added</p></li>
-<li><p><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Controls the clustering behaviour at the initial
-stage of constraint construction</p></li>
-<li><p><strong>gamma</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Controls how fast the influence of constraint
-functions of distant clusters vanishes</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>env</strong> (<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – The scoring env to which the constraint
+should be added</li>
+<li><strong>chain_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Indices of chains for which the constraints should
+be added</li>
+<li><strong>cluster_thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Controls the clustering behaviour at the initial
+stage of constraint construction</li>
+<li><strong>gamma</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Controls how fast the influence of constraint
+functions of distant clusters vanishes</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if one of the <em>chain_indices</em> is
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if one of the <em>chain_indices</em> is
invalid or the SEQRES set in <em>env</em> for specified chain is
inconsistent with SEQRES you initialized the DiscoContainer with</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -401,7 +450,6 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -422,12 +470,12 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -444,8 +492,8 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
<li>Next: <a href="backbone_scorers.html" title="next chapter">Backbone Scorers</a></li>
</ul></li>
</ul></li>
@@ -453,33 +501,27 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/scoring/backbone_score_env.rst.txt"
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index aebb68b2beed7d10b16c167114ff95fa9d2da67a..ff76e572ea550aa83438163d2af9440503f6bfbe 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Backbone Scorers — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Backbone Scorers — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="backbone-scorers">
@@ -39,148 +38,165 @@
<h2>BackboneOverallScorer class<a class="headerlink" href="#backboneoverallscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.BackboneOverallScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">BackboneOverallScorer</code><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">BackboneOverallScorer</code><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Container that allows for the storage of multiple scorers identified by a key
(<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) and the computation of combined scores.</p>
<p>Scorers need to be individually set or loaded by
<a class="reference internal" href="#promod3.scoring.LoadDefaultBackboneOverallScorer" title="promod3.scoring.LoadDefaultBackboneOverallScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadDefaultBackboneOverallScorer()</span></code></a></p>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.Contains">
-<code class="sig-name descname">Contains</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Contains" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>True, if a scorer object for this key was already added.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
-</dd>
-</dl>
+<code class="descname">Contains</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Contains" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">True, if a scorer object for this key was already added.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.Get">
-<code class="sig-name descname">Get</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Get" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Scorer with the given <em>key</em> (read-only access).</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a></p>
-</dd>
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there is no scorer with that
-<em>key</em>.</p>
-</dd>
-</dl>
+<code class="descname">Get</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Get" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Scorer with the given <em>key</em> (read-only access).</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there is no scorer with that
+<em>key</em>.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.AttachEnvironment">
-<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>env</strong> (<a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – Link all scorers to this score environment.</p>
-</dd>
-</dl>
+<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env</strong> (<a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – Link all scorers to this score environment.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.Calculate">
-<code class="sig-name descname">Calculate</code><span class="sig-paren">(</span><em class="sig-param">key</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Calculate" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Calculate</code><span class="sig-paren">(</span><em>key</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Calculate" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate score for one or several stretches of amino acids given the
current scoring environment.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Score calculated with the desired scorer for the given stretch(es).</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there is no scorer with that
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score calculated with the desired scorer for the given stretch(es).</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if there is no scorer with that
<em>key</em> or anything raised in <a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BackboneScorer.CalculateScore()</span></code></a>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.CalculateLinearCombination">
-<code class="sig-name descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em class="sig-param">linear_weights</em>, <em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em>linear_weights</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate linear combination of scores for one or several stretches of
amino acids given the current scoring environment.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>,
values: <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>)) – Weights for each desired scorer. You can add a
constant value to each score by defining a weight
-with key “intercept”.</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
+with key “intercept”.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Linear combination of the scores calculated with the desired
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Linear combination of the scores calculated with the desired
scorers for the given stretch(es)</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>linear_weights</em> has a <em>key</em> for
which no scorer exists or anything raised in
<a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BackboneScorer.CalculateScore()</span></code></a> for any of the used scorers.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.__getitem__">
-<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.__getitem__" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.BackboneOverallScorer.__setitem__">
-<code class="sig-name descname">__setitem__</code><span class="sig-paren">(</span><em class="sig-param">key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.__setitem__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__setitem__</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.__setitem__" title="Permalink to this definition">¶</a></dt>
<dd><p>Allow read/write access (with [<em>key</em>]) to scorer object with given key.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>key</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Key for desired scorer.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadDefaultBackboneOverallScorer">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadDefaultBackboneOverallScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadDefaultBackboneOverallScorer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Loads or creates the default scorers accessible through
+<code class="descclassname">promod3.scoring.</code><code class="descname">LoadDefaultBackboneOverallScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadDefaultBackboneOverallScorer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Loads or creates the default scorers accessible through
following keys:
-“cb_packing”, “cbeta”, “reduced”, “clash”, “hbond”, “ss_agreement”,”torsion”, “pairwise”</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a></p>
-</dd>
-</dl>
+“cb_packing”, “cbeta”, “reduced”, “clash”, “hbond”, “ss_agreement”,”torsion”, “pairwise”</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneOverallScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -188,75 +204,86 @@ following keys:
<h2>BackboneScorer base class<a class="headerlink" href="#backbonescorer-base-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.BackboneScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">BackboneScorer</code><a class="headerlink" href="#promod3.scoring.BackboneScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">BackboneScorer</code><a class="headerlink" href="#promod3.scoring.BackboneScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Base class for all the backbone scorers listed below.</p>
<dl class="method">
<dt id="promod3.scoring.BackboneScorer.AttachEnvironment">
-<code class="sig-name descname">AttachEnvironment</code><span class="sig-paren">(</span><em class="sig-param">env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>env</strong> (<a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – Link scorer to this score environment.</p>
-</dd>
-</dl>
+<code class="descname">AttachEnvironment</code><span class="sig-paren">(</span><em>env</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.AttachEnvironment" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env</strong> (<a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a>) – Link scorer to this score environment.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScorer.CalculateScore">
-<code class="sig-name descname">CalculateScore</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateScore</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates score for one or several stretches given the structural
information in the attached environment. Unless otherwise noted in the
scorer, a lower “score” is better!</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Score for the given stretch(es).</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>(for most scorers) <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if scorer was
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score for the given stretch(es).</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">(for most scorers) <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if scorer was
never attached to a score environment, if scorer has never been
properly initialized or if <em>start_resnum</em> / <em>num_residues</em> /
<em>chain_idx</em> lead to invalid positions.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.BackboneScorer.CalculateScoreProfile">
-<code class="sig-name descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em class="sig-param">start_resnum</em>, <em class="sig-param">num_residues</em>, <em class="sig-param">chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates per residue scores for one or several stretches given the
structural information in the attached environment.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
-<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</p></li>
-<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Scores for the given stretch(es), one for each residue.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> or <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Scores for the given stretch(es), one for each residue.</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> or <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p>same <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> as <a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CalculateScore()</span></code></a>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">same <code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> as <a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CalculateScore()</span></code></a>.</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -266,111 +293,126 @@ of <a class="reference external" href="https://docs.python.org/3.7/library/funct
<h2>CBPackingScorer class<a class="headerlink" href="#cbpackingscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.CBPackingScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">CBPackingScorer</code><span class="sig-paren">(</span><em class="sig-param">cutoff</em>, <em class="sig-param">max_count</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">CBPackingScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>max_count</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates pseudo
energies by counting the number of other CB positions within a certain
<em>cutoff</em> radius of the CB position of the residue to be evaluated.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadCBPackingScorer" title="promod3.scoring.LoadCBPackingScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadCBPackingScorer()</span></code></a>) or by setting all energies (see
<a class="reference internal" href="#promod3.scoring.CBPackingScorer.SetEnergy" title="promod3.scoring.CBPackingScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other cbeta atoms are counted.</p></li>
-<li><p><strong>max_count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If number of other cbeta atoms exceeds <em>max_count</em>, it will
-be set to this number.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other cbeta atoms are counted.</li>
+<li><strong>max_count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – If number of other cbeta atoms exceeds <em>max_count</em>, it will
+be set to this number.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0 or <em>max_count</em> < 1.</p>
-</dd>
-</dl>
-<dl class="method">
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0 or <em>max_count</em> < 1.</p>
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.scoring.CBPackingScorer.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.CBPackingScorer.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.CBPackingScorer.Save" title="promod3.scoring.CBPackingScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.CBPackingScorer.SavePortable" title="promod3.scoring.CBPackingScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded scorer</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBPackingScorer.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.CBPackingScorer.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBPackingScorer.SetEnergy">
-<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">aa</em>, <em class="sig-param">count</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aa</em>, <em>count</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every type of amino acids and for every <em>count</em> <= <em>max_count</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</p></li>
-<li><p><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of surrounding CB positions for which to set energy.</p></li>
-<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
+<li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of surrounding CB positions for which to set energy.</li>
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBPackingScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadCBPackingScorer">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadCBPackingScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadCBPackingScorer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The default predefined CBPackingScorer (loaded from disk)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a></p>
-</dd>
-</dl>
+<code class="descclassname">promod3.scoring.</code><code class="descname">LoadCBPackingScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadCBPackingScorer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined CBPackingScorer (loaded from disk)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBPackingScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -378,7 +420,7 @@ of residues to be scored. True by default.</p>
<h2>CBetaScorer class<a class="headerlink" href="#cbetascorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.CBetaScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">CBetaScorer</code><span class="sig-paren">(</span><em class="sig-param">cutoff</em>, <em class="sig-param">bins</em>, <em class="sig-param">seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">CBetaScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>bins</em>, <em>seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates a pairwise
pseudo interaction energy between CB atoms which are located within a <em>cutoff</em>
and which are at least <em>seq_sep</em> residues apart. An energy is assigned to each
@@ -386,134 +428,155 @@ distance using equally sized bins and distinguishing all possible pairs
of amino acids.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadCBetaScorer" title="promod3.scoring.LoadCBetaScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadCBetaScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.CBetaScorer.SetEnergy" title="promod3.scoring.CBetaScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other cbeta atoms are considered.</p></li>
-<li><p><strong>bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
-of [0, <em>cutoff</em>]).</p></li>
-<li><p><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Minimal separation in sequence two cbeta atoms must have to
-be considered.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other cbeta atoms are considered.</li>
+<li><strong>bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
+of [0, <em>cutoff</em>]).</li>
+<li><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Minimal separation in sequence two cbeta atoms must have to
+be considered.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>bins</em> < 1 or
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>bins</em> < 1 or
<em>seq_sep</em> < 1.</p>
-</dd>
-</dl>
-<dl class="method">
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.scoring.CBetaScorer.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.CBetaScorer.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.CBetaScorer.Save" title="promod3.scoring.CBetaScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.CBetaScorer.SavePortable" title="promod3.scoring.CBetaScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded scorer</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBetaScorer.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.CBetaScorer.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBetaScorer.SetEnergy">
-<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">aa1</em>, <em class="sig-param">aa2</em>, <em class="sig-param">bin</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aa1</em>, <em>aa2</em>, <em>bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of amino acids and for every <em>bin</em> < <em>bins</em>.
Internal symmetry is enforced => Calling SetEnergy(aa1, aa2, bin, energy) is
equivalent to calling SetEnergy(aa1, aa2, bin, energy) AND
SetEnergy(aa2, aa1, bin, energy).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
-<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
-<li><p><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</p></li>
-<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
+<li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBetaScorer.DoInternalScores">
-<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
-the scored residues. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBetaScorer.DoExternalScores">
-<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
residues towards the surrounding environment.
-True by default.</p>
-</dd>
-</dl>
+True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.CBetaScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadCBetaScorer">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadCBetaScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadCBetaScorer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The default predefined CBetaScorer (loaded from disk)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a></p>
-</dd>
-</dl>
+<code class="descclassname">promod3.scoring.</code><code class="descname">LoadCBetaScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadCBetaScorer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined CBetaScorer (loaded from disk)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">CBetaScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -521,7 +584,7 @@ of residues to be scored. True by default.</p>
<h2>ReducedScorer class<a class="headerlink" href="#reducedscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.ReducedScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">ReducedScorer</code><span class="sig-paren">(</span><em class="sig-param">cutoff</em>, <em class="sig-param">dist_bins</em>, <em class="sig-param">angle_bins</em>, <em class="sig-param">dihedral_bins</em>, <em class="sig-param">seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ReducedScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>dist_bins</em>, <em>angle_bins</em>, <em>dihedral_bins</em>, <em>seq_sep</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates a pairwise
pseudo interaction energy between the reduced representation of residues.
Every residue gets represented by its CA position p and a directional
@@ -530,78 +593,84 @@ distance < <em>cutoff</em> and which are at least <em>seq_sep</em> residues a
considered to be interacting. For interacting residues r1 and r2, we can
define a line l between p1 and p2. The potential then considers:</p>
<ul class="simple">
-<li><p>dist => distance between p1 and p2</p></li>
-<li><p>alpha => angle between v1 and l</p></li>
-<li><p>beta => angle between v2 and l</p></li>
-<li><p>gamma => dihedral between (p1+v1,p1,p2,p2+v2)</p></li>
+<li>dist => distance between p1 and p2</li>
+<li>alpha => angle between v1 and l</li>
+<li>beta => angle between v2 and l</li>
+<li>gamma => dihedral between (p1+v1,p1,p2,p2+v2)</li>
</ul>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadReducedScorer" title="promod3.scoring.LoadReducedScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadReducedScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.ReducedScorer.SetEnergy" title="promod3.scoring.ReducedScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other CA atoms are searched.</p></li>
-<li><p><strong>dist_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
-of [0, <em>cutoff</em>]).</p></li>
-<li><p><strong>angle_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize angles (range
-of [0, pi]).</p></li>
-<li><p><strong>dihedral_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize dihedrals
-(range of [-pi, pi]).</p></li>
-<li><p><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Minimal separation in sequence two residues must have to
-be considered.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Radius in which other CA atoms are searched.</li>
+<li><strong>dist_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize distances (range
+of [0, <em>cutoff</em>]).</li>
+<li><strong>angle_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize angles (range
+of [0, pi]).</li>
+<li><strong>dihedral_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize dihedrals
+(range of [-pi, pi]).</li>
+<li><strong>seq_sep</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Minimal separation in sequence two residues must have to
+be considered.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>dist_bins</em> < 1,
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>cutoff</em> < 0, <em>dist_bins</em> < 1,
<em>angle_bins</em> < 1, <em>dihedral_bins</em> < 1 or <em>seq_sep</em> < 1.</p>
-</dd>
-</dl>
-<dl class="method">
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.scoring.ReducedScorer.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.ReducedScorer.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.ReducedScorer.Save" title="promod3.scoring.ReducedScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.ReducedScorer.SavePortable" title="promod3.scoring.ReducedScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded scorer</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ReducedScorer.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.ReducedScorer.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ReducedScorer.SetEnergy">
-<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">aa1</em>, <em class="sig-param">aa2</em>, <em class="sig-param">dist_bin</em>, <em class="sig-param">alpha_bin</em>, <em class="sig-param">beta_bin</em>, <em class="sig-param">gamma_bin</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aa1</em>, <em>aa2</em>, <em>dist_bin</em>, <em>alpha_bin</em>, <em>beta_bin</em>, <em>gamma_bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of amino acids, every <em>dist_bin</em> < <em>dist_bins</em>, every
<em>alpha_bin</em> < <em>angle_bins</em>, every <em>beta_bin</em> < <em>angle_bins</em> and every
@@ -611,71 +680,86 @@ SetEnergy(aa1, aa2, dist_bin, alpha_bin, beta_bin, energy) is
equivalent to calling
SetEnergy(aa1, aa2, dist_bin, alpha_bin, beta_bin, energy) AND
SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
-<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
-<li><p><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</p></li>
-<li><p><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the alpha angle.</p></li>
-<li><p><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the beta angle.</p></li>
-<li><p><strong>gamma_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the gamma dihedral.</p></li>
-<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
+<li><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
+<li><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the alpha angle.</li>
+<li><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the beta angle.</li>
+<li><strong>gamma_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the gamma dihedral.</li>
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ReducedScorer.DoInternalScores">
-<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
-the scored residues. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ReducedScorer.DoExternalScores">
-<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
residues towards the surrounding environment.
-True by default.</p>
-</dd>
-</dl>
+True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ReducedScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadReducedScorer">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadReducedScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadReducedScorer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The default predefined ReducedScorer (loaded from disk)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a></p>
-</dd>
-</dl>
+<code class="descclassname">promod3.scoring.</code><code class="descname">LoadReducedScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadReducedScorer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined ReducedScorer (loaded from disk)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ReducedScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -683,43 +767,52 @@ of residues to be scored. True by default.</p>
<h2>ClashScorer class<a class="headerlink" href="#clashscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.ClashScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">ClashScorer</code><a class="headerlink" href="#promod3.scoring.ClashScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ClashScorer</code><a class="headerlink" href="#promod3.scoring.ClashScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Calculates a simple
clash score of a loop itself and with the set environment. There is no need to
define any parameters here as all interaction energies are fixed (see Eq. (11)
-in <a class="reference internal" href="../references.html#canutescu2003b" id="id1"><span>[canutescu2003b]</span></a>).</p>
+in <a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>).</p>
<dl class="method">
<dt id="promod3.scoring.ClashScorer.DoInternalScores">
-<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
-the scored residues. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ClashScorer.DoExternalScores">
-<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
residues towards the surrounding environment.
-True by default.</p>
-</dd>
-</dl>
+True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.ClashScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -729,17 +822,17 @@ of residues to be scored. True by default.</p>
<h2>HBondScorer class<a class="headerlink" href="#hbondscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.HBondScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">HBondScorer</code><span class="sig-paren">(</span><em class="sig-param">min_d</em>, <em class="sig-param">max_d</em>, <em class="sig-param">min_alpha</em>, <em class="sig-param">max_alpha</em>, <em class="sig-param">min_beta</em>, <em class="sig-param">max_beta</em>, <em class="sig-param">min_gamma</em>, <em class="sig-param">max_gamma</em>, <em class="sig-param">d_bins</em>, <em class="sig-param">alpha_bins</em>, <em class="sig-param">beta_bins</em>, <em class="sig-param">gamma_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">HBondScorer</code><span class="sig-paren">(</span><em>min_d</em>, <em>max_d</em>, <em>min_alpha</em>, <em>max_alpha</em>, <em>min_beta</em>, <em>max_beta</em>, <em>min_gamma</em>, <em>max_gamma</em>, <em>d_bins</em>, <em>alpha_bins</em>, <em>beta_bins</em>, <em>gamma_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates pairwise
HBond pseudo energies similar to the one defined in the Rosetta energy
function. It considers the CA, C and O positions from backbone hbond acceptors
in interaction with the N and H positions from the backbone hbond donors. 4
Parameters describe their relative orientation.</p>
<ul class="simple">
-<li><p>dist => H-O distance</p></li>
-<li><p>alpha => O-H-N angle</p></li>
-<li><p>beta => C-N-H angle</p></li>
-<li><p>gamma => CA-C-O-H dihedral angle</p></li>
+<li>dist => H-O distance</li>
+<li>alpha => O-H-N angle</li>
+<li>beta => C-N-H angle</li>
+<li>gamma => CA-C-O-H dihedral angle</li>
</ul>
<p>A pseudo energy function for these parameters is evaluated for three different
states. State 1 for helical residues, state 2 for extended residues and state
@@ -748,147 +841,168 @@ thats the one from which the energy is extracted. In all other cases, the
energy is extracted from the 0 state.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadHBondScorer" title="promod3.scoring.LoadHBondScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadHBondScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.HBondScorer.SetEnergy" title="promod3.scoring.HBondScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>min_d</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal H-O distance to consider interaction</p></li>
-<li><p><strong>max_d</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal H-O distance to consider interaction</p></li>
-<li><p><strong>min_alpha</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal O-H-N angle to consider interaction</p></li>
-<li><p><strong>max_alpha</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal O-H-N angle to consider interaction</p></li>
-<li><p><strong>min_beta</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal C-N-H angle to consider interaction</p></li>
-<li><p><strong>max_beta</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal C-N-H angle to consider interaction</p></li>
-<li><p><strong>min_gamma</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal CA-C-O-H dihedral to consider interaction</p></li>
-<li><p><strong>max_gamma</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal CA-C-O-H dihedral to consider interaction</p></li>
-<li><p><strong>d_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize H-O distances
-(range of [<em>min_d</em>, <em>max_d</em>]).</p></li>
-<li><p><strong>alpha_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize O-H-N angles
-(range of [<em>min_alpha</em>, <em>max_alpha</em>]).</p></li>
-<li><p><strong>beta_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize C-N-H angles
-(range of [<em>min_beta</em>, <em>max_beta</em>]).</p></li>
-<li><p><strong>gamma_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize CA-C-O-H angles
-(range of [<em>min_gamma</em>, <em>max_gamma</em>]).</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>min_d</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal H-O distance to consider interaction</li>
+<li><strong>max_d</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal H-O distance to consider interaction</li>
+<li><strong>min_alpha</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal O-H-N angle to consider interaction</li>
+<li><strong>max_alpha</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal O-H-N angle to consider interaction</li>
+<li><strong>min_beta</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal C-N-H angle to consider interaction</li>
+<li><strong>max_beta</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal C-N-H angle to consider interaction</li>
+<li><strong>min_gamma</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Minimal CA-C-O-H dihedral to consider interaction</li>
+<li><strong>max_gamma</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Maximal CA-C-O-H dihedral to consider interaction</li>
+<li><strong>d_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize H-O distances
+(range of [<em>min_d</em>, <em>max_d</em>]).</li>
+<li><strong>alpha_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize O-H-N angles
+(range of [<em>min_alpha</em>, <em>max_alpha</em>]).</li>
+<li><strong>beta_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize C-N-H angles
+(range of [<em>min_beta</em>, <em>max_beta</em>]).</li>
+<li><strong>gamma_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize CA-C-O-H angles
+(range of [<em>min_gamma</em>, <em>max_gamma</em>]).</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if one of the bin parameters is
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if one of the bin parameters is
< 1 or a max parameter is smaller than its min counterpart.</p>
-</dd>
-</dl>
-<dl class="method">
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.scoring.HBondScorer.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.HBondScorer.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.HBondScorer.Save" title="promod3.scoring.HBondScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.HBondScorer.SavePortable" title="promod3.scoring.HBondScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded scorer</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.HBondScorer.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.HBondScorer.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.HBondScorer.SetEnergy">
-<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">state</em>, <em class="sig-param">d_bin</em>, <em class="sig-param">alpha_bin</em>, <em class="sig-param">beta_bin</em>, <em class="sig-param">gamma_bin</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>state</em>, <em>d_bin</em>, <em>alpha_bin</em>, <em>beta_bin</em>, <em>gamma_bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every state ([0, 1, 2]), every <em>d_bin</em> < <em>d_bins</em>, every
<em>alpha_bin</em> < <em>alpha_bins</em>, every <em>beta_bin</em> < <em>beta_bins</em> and every
<em>gamma_bin</em> < <em>gamma_bins</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>state</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – State describing the actual secondary structure
-(1: helical, 2: extended, 0: other)</p></li>
-<li><p><strong>d_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the H-O distance.</p></li>
-<li><p><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the O-H-N angle.</p></li>
-<li><p><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the C-N-H angle.</p></li>
-<li><p><strong>gamma_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the CA-C-O-H dihedral.</p></li>
-<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>state</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – State describing the actual secondary structure
+(1: helical, 2: extended, 0: other)</li>
+<li><strong>d_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the H-O distance.</li>
+<li><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the O-H-N angle.</li>
+<li><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the C-N-H angle.</li>
+<li><strong>gamma_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the CA-C-O-H dihedral.</li>
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.HBondScorer.DoInternalScores">
-<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
-the scored residues. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.HBondScorer.DoExternalScores">
-<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
residues towards the surrounding environment.
-True by default.</p>
-</dd>
-</dl>
+True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.HBondScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadHBondScorer">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadHBondScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadHBondScorer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The default predefined HBondScorer (loaded from disk)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a></p>
-</dd>
-</dl>
+<code class="descclassname">promod3.scoring.</code><code class="descname">LoadHBondScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadHBondScorer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined HBondScorer (loaded from disk)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">HBondScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -896,7 +1010,7 @@ of residues to be scored. True by default.</p>
<h2>SSAgreementScorer class<a class="headerlink" href="#ssagreementscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.SSAgreementScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">SSAgreementScorer</code><a class="headerlink" href="#promod3.scoring.SSAgreementScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">SSAgreementScorer</code><a class="headerlink" href="#promod3.scoring.SSAgreementScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates a secondary
structure agreement score. The scorer has a score for each combination of
psipred prediction, its confidence and the actually occurring secondary
@@ -912,93 +1026,104 @@ defined (see <a class="reference internal" href="backbone_score_env.html#promod3
is to be calculated.</p>
<p>Note that for this scorer a higher “score” is better! So take care when
combining this to other scores, where it is commonly the other way around.</p>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.scoring.SSAgreementScorer.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.SSAgreementScorer.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.SSAgreementScorer.Save" title="promod3.scoring.SSAgreementScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.SSAgreementScorer.SavePortable" title="promod3.scoring.SSAgreementScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded scorer</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SSAgreementScorer</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SSAgreementScorer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.SSAgreementScorer.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.SSAgreementScorer.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.SSAgreementScorer.SetScore">
-<code class="sig-name descname">SetScore</code><span class="sig-paren">(</span><em class="sig-param">psipred_state</em>, <em class="sig-param">psipred_confidence</em>, <em class="sig-param">dssp_state</em>, <em class="sig-param">score</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.SetScore" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetScore</code><span class="sig-paren">(</span><em>psipred_state</em>, <em>psipred_confidence</em>, <em>dssp_state</em>, <em>score</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.SetScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup a single score for a combination of states. Unless a predefined scorer
is loaded, this must be called for every combination of states.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>psipred_state</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – must be one of [‘H’, ‘E’, ‘C’]</p></li>
-<li><p><strong>psipred_confidence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – must be in range [0, 9]</p></li>
-<li><p><strong>dssp_state</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – must be one of [‘H’, ‘E’, ‘C’, ‘G’, ‘B’, ‘S’, ‘T’, ‘I’]</p></li>
-<li><p><strong>score</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – score to be set</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>psipred_state</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – must be one of [‘H’, ‘E’, ‘C’]</li>
+<li><strong>psipred_confidence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – must be in range [0, 9]</li>
+<li><strong>dssp_state</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – must be one of [‘H’, ‘E’, ‘C’, ‘G’, ‘B’, ‘S’, ‘T’, ‘I’]</li>
+<li><strong>score</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – score to be set</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.SSAgreementScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadSSAgreementScorer">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadSSAgreementScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadSSAgreementScorer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The default predefined structure agreement scorer (loaded from disk)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SSAgreementScorer</span></code></a></p>
-</dd>
-</dl>
+<code class="descclassname">promod3.scoring.</code><code class="descname">LoadSSAgreementScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadSSAgreementScorer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined structure agreement scorer (loaded from disk)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">SSAgreementScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -1006,7 +1131,7 @@ of residues to be scored. True by default.</p>
<h2>TorsionScorer class<a class="headerlink" href="#torsionscorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.TorsionScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">TorsionScorer</code><span class="sig-paren">(</span><em class="sig-param">group_definitions</em>, <em class="sig-param">torsion_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">TorsionScorer</code><span class="sig-paren">(</span><em>group_definitions</em>, <em>torsion_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates pseudo
energies based on the identity of three consecutive residues and the phi/psi
dihedral angles of the central residue. The first phi and last psi angle get
@@ -1014,111 +1139,126 @@ determined with the help of the environment if set.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadTorsionScorer" title="promod3.scoring.LoadTorsionScorer"><code class="xref py py-func docutils literal notranslate"><span class="pre">LoadTorsionScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.TorsionScorer.SetEnergy" title="promod3.scoring.TorsionScorer.SetEnergy"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetEnergy()</span></code></a>)
for each group definition.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>group_definitions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – List of group definitions defining amino acid
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>group_definitions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – List of group definitions defining amino acid
triplets (same style as used in the
-<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> class).</p></li>
-<li><p><strong>torsion_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize the torsion
-angles (range of [0, 2*pi]).</p></li>
+<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> class).</li>
+<li><strong>torsion_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of equally sized bins to discretize the torsion
+angles (range of [0, 2*pi]).</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>torsion_bins</em> < 1 or if there is
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>torsion_bins</em> < 1 or if there is
a possible combination of the 20 standard amino acids not matching
any entry of <em>group_definitions</em></p>
-</dd>
-</dl>
-<dl class="method">
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.scoring.TorsionScorer.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.TorsionScorer.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.scoring.TorsionScorer.Save" title="promod3.scoring.TorsionScorer.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.scoring.TorsionScorer.SavePortable" title="promod3.scoring.TorsionScorer.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The loaded scorer</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded scorer</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.TorsionScorer.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.scoring.TorsionScorer.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.TorsionScorer.SetEnergy">
-<code class="sig-name descname">SetEnergy</code><span class="sig-paren">(</span><em class="sig-param">group_idx</em>, <em class="sig-param">phi_bin</em>, <em class="sig-param">psi_bin</em>, <em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>group_idx</em>, <em>phi_bin</em>, <em>psi_bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every <em>group_idx</em> < len(<em>group_definitions</em>), every <em>phi_bin</em> <
<em>torsion_bins</em> and every <em>psi_bin</em> < <em>torsion_bins</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>group_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of group definition as set in constructor with
-numbering starting at 0.</p></li>
-<li><p><strong>phi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the phi angle.</p></li>
-<li><p><strong>psi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the psi angle.</p></li>
-<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>group_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of group definition as set in constructor with
+numbering starting at 0.</li>
+<li><strong>phi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the phi angle.</li>
+<li><strong>psi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the psi angle.</li>
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if inputs are invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.TorsionScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="promod3.scoring.LoadTorsionScorer">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">LoadTorsionScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadTorsionScorer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The default predefined TorsionScorer (loaded from disk)</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a></p>
-</dd>
-</dl>
+<code class="descclassname">promod3.scoring.</code><code class="descname">LoadTorsionScorer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.LoadTorsionScorer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The default predefined TorsionScorer (loaded from disk)</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionScorer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -1126,7 +1266,7 @@ of residues to be scored. True by default.</p>
<h2>PairwiseScorer class<a class="headerlink" href="#pairwisescorer-class" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.scoring.PairwiseScorer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">PairwiseScorer</code><a class="headerlink" href="#promod3.scoring.PairwiseScorer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">PairwiseScorer</code><a class="headerlink" href="#promod3.scoring.PairwiseScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneScorer</span></code></a>. Evaluates a list of
generic pairwise functions (see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunction</span></code></a>).
That are set in the attached scoring environment
@@ -1135,36 +1275,45 @@ That are set in the attached scoring environment
combining this to other scores, where it is commonly the other way around.</p>
<dl class="method">
<dt id="promod3.scoring.PairwiseScorer.DoInternalScores">
-<code class="sig-name descname">DoInternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
-the scored residues. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.PairwiseScorer.DoExternalScores">
-<code class="sig-name descname">DoExternalScores</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>, true by default.) – Whether to include pairwise interactions of the scored
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>, true by default.) – Whether to include pairwise interactions of the scored
residues towards the surrounding environment.
-True by default.</p>
-</dd>
-</dl>
+True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.PairwiseScorer.DoNormalize">
-<code class="sig-name descname">DoNormalize</code><span class="sig-paren">(</span><em class="sig-param">do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
-of residues to be scored. True by default.</p>
-</dd>
-</dl>
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -1174,7 +1323,6 @@ of residues to be scored. True by default.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -1195,12 +1343,12 @@ of residues to be scored. True by default.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -1217,7 +1365,7 @@ of residues to be scored. True by default.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
<li>Previous: <a href="backbone_score_env.html" title="previous chapter">Backbone Score Environment</a></li>
<li>Next: <a href="all_atom_scorers.html" title="next chapter">All Atom Scorers</a></li>
</ul></li>
@@ -1226,33 +1374,27 @@ of residues to be scored. True by default.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
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<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/scoring/backbone_scorers.rst.txt"
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index f123fcfb603869474f368d4c16c89441124db4dd..ebc4d6c9bffda1a6c3c14b758a59734dec80e3aa 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>scoring - Loop Scoring — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>scoring - Loop Scoring — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="module-promod3.scoring">
@@ -107,7 +106,6 @@ scorers to it and finally score some loops:</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -128,12 +126,12 @@ scorers to it and finally score some loops:</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -157,33 +155,27 @@ scorers to it and finally score some loops:</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
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-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/scoring/index.rst.txt"
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index c08269ec5d9a8b8d2a6543e912bb67fdb1fdde09..0de14121fe084c5aea2c6ace5fcaf4684ed7c45a 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Other Scoring Functions — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Other Scoring Functions — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="other-scoring-functions">
@@ -39,56 +38,64 @@
<h2>Scoring Functions from SCWRL3<a class="headerlink" href="#scoring-functions-from-scwrl3" title="Permalink to this headline">¶</a></h2>
<dl class="method">
<dt id="promod3.scoring.SCWRL3PairwiseScore">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">SCWRL3PairwiseScore</code><span class="sig-paren">(</span><em class="sig-param">d</em>, <em class="sig-param">Rij</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3PairwiseScore" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.scoring.</code><code class="descname">SCWRL3PairwiseScore</code><span class="sig-paren">(</span><em>d</em>, <em>Rij</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3PairwiseScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Pairwise score from the SCWRL3 sidechain construction algorithm
-<a class="reference internal" href="../references.html#canutescu2003b" id="id1"><span>[canutescu2003b]</span></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>d</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Distance between the two interacting particles</p></li>
-<li><p><strong>Rij</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <p>Summed hard-sphere radii of the interacting particles.
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>d</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Distance between the two interacting particles</li>
+<li><strong>Rij</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <p>Summed hard-sphere radii of the interacting particles.
Suggestions from the paper:</p>
<ul>
-<li><p>carbon: 1.6</p></li>
-<li><p>oxygen: 1.3</p></li>
-<li><p>nitrogen: 1.3</p></li>
-<li><p>sulfur: 1.7</p></li>
+<li>carbon: 1.6</li>
+<li>oxygen: 1.3</li>
+<li>nitrogen: 1.3</li>
+<li>sulfur: 1.7</li>
</ul>
-</p></li>
+</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The score</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The score</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.scoring.SCWRL3DisulfidScore">
-<code class="sig-prename descclassname">promod3.scoring.</code><code class="sig-name descname">SCWRL3DisulfidScore</code><span class="sig-paren">(</span><em class="sig-param">ca_pos_one</em>, <em class="sig-param">cb_pos_one</em>, <em class="sig-param">sg_pos_one ca_pos_two</em>, <em class="sig-param">cb_pos_two</em>, <em class="sig-param">sg_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3DisulfidScore" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.scoring.</code><code class="descname">SCWRL3DisulfidScore</code><span class="sig-paren">(</span><em>ca_pos_one</em>, <em>cb_pos_one</em>, <em>sg_pos_one ca_pos_two</em>, <em>cb_pos_two</em>, <em>sg_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3DisulfidScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Implements the empirically derived disulfid score from the SCWRL3 sidechain
-construction algorithm <a class="reference internal" href="../references.html#canutescu2003b" id="id2"><span>[canutescu2003b]</span></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>ca_pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CA carbon position of first amino acid</p></li>
-<li><p><strong>cb_pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CB carbon position of first amino acid</p></li>
-<li><p><strong>sg_pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – SG sulfur position of first amino acid</p></li>
-<li><p><strong>ca_pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CA carbon position of second amino acid</p></li>
-<li><p><strong>cb_pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CB carbon position of second amino acid</p></li>
-<li><p><strong>sg_pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – SG sulfur position of second amino acid</p></li>
+construction algorithm <a class="reference internal" href="../references.html#canutescu2003b" id="id2">[canutescu2003b]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>ca_pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CA carbon position of first amino acid</li>
+<li><strong>cb_pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CB carbon position of first amino acid</li>
+<li><strong>sg_pos_one</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – SG sulfur position of first amino acid</li>
+<li><strong>ca_pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CA carbon position of second amino acid</li>
+<li><strong>cb_pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – CB carbon position of second amino acid</li>
+<li><strong>sg_pos_two</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geoom.Vec3</span></code>) – SG sulfur position of second amino acid</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The score</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The score</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -96,7 +103,6 @@ construction algorithm <a class="reference internal" href="../references.html#ca
</div>
-
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@@ -117,12 +123,12 @@ construction algorithm <a class="reference internal" href="../references.html#ca
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-<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -139,42 +145,36 @@ construction algorithm <a class="reference internal" href="../references.html#ca
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
<li>Previous: <a href="all_atom_scorers.html" title="previous chapter">All Atom Scorers</a></li>
- <li>Next: <a href="../loop/index.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+ <li>Next: <a href="../loop/index.html" title="next chapter"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
</ul></li>
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- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
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+ <input type="text" name="q" />
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+ <input type="hidden" name="check_keywords" value="yes" />
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- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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diff --git a/doc/html/search.html b/doc/html/search.html
index f7798e62a96be319378692b7be00baf0e62abe9a..a60fd4630084ef95efe75cbfb5c15432c6e4eb59 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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- <meta charset="utf-8" />
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+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
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@@ -32,8 +37,6 @@
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@@ -61,7 +64,6 @@
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+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
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index 3000dc92e1c757f089c9d49457a0eb0d1ae50705..ab93b18c302e32f6f994e19d7d37073235a063ec 100644
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+++ b/doc/html/searchindex.js
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25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,biasini2013:[19,38],biasini:38,bienert:38,big:[25,37],bilinearli:51,bin:[1,8,16,18,26,27,28,39,41,51],bin_siz:[28,51],binari:[1,4,8,16,17,25,26,27,39,41,51],bind:[0,3,13,20,28],bins_per_dimens:27,bioinformat:38,biol:38,biolog:38,biologi:[19,38],biophi:38,biopolym:38,bit:[1,8,16,31,35],bitwis:26,blank:8,block:[3,30,45,47],blosum62:[13,23,26,28,40],boilerpl:20,bond:[0,3,9,22,25,26,32,33,35,36,38,41,47,49,50,51,54],bond_force_const:25,bond_length:[9,25],bool:[1,8,10,11,13,14,21,22,25,26,29,31,32,33,34,35,36,37,39,41,44,49,50,51],boost:[2,8,37],boost_librari:4,boost_root:2,bootstrap:[6,7],bore:34,both:[3,21,26,29,35,44,47,51],bound:[21,25,28,31,49,50],boundari:28,br_vinaparticl:49,bracket:20,bradlei:25,branch:[4,8,17],branchnam:16,brew:4,bridg:[24,25,32,35,36],briefli:16,bring:8,broken:1,bromin:49,broyden:35,bsd:20,bug:[3,8,16],bugfix:3,build:[1,3,4,6,7,8,16,18,19,25,28,30,34,44,45,47,48,50,54],build_disulfid:36,builder:2,buildfromrawmodel:[30,35],buildrawmodel:[0,3,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,5,25,26,40,45],bunch:[1,13,16],bundl:20,bytecod:1,c_coord:9,c_num:29,c_p_vinaparticl:[49,50],c_po:[9,22,41],c_stem:[9,23,26,29,31,32,34],c_stem_psi:34,c_str:37,c_ter:[32,50],c_vinaparticl:[49,50],ca_coord:9,ca_pairwise_funct:40,ca_po:[9,22],ca_pos_on:[43,44],ca_pos_two:[43,44],ca_posit:[28,44],ca_rmsd:[23,26],cach:[2,26,28],calcul:[8,22,26,27,28,31,32,34,39,40,41,42,44,45,46,47,49,50],calculateallatomscor:31,calculatebackbonescor:31,calculatelinearcombin:[31,34,39,41],calculatescor:[39,41,42],calculatescoreprofil:[39,41],calculatesequenceprofilescor:31,calculatestemrmsd:31,calculatestructureprofilescor:31,call:[1,2,4,8,11,13,14,15,16,21,25,26,27,29,31,34,35,36,37,39,40,41,49,50,51],callabl:[13,16],calpha:35,calul:27,came:8,can:[0,1,2,3,4,5,7,8,9,10,11,13,14,15,16,18,19,21,22,23,25,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,44,45,46,47,48,50,51,52,53],cand:35,candid:[3,30,33,34,35,54],cannot:[0,8,13,20,25,26,27,29,35,37,39,41,48,49,50,51],canutescu2003:[32,38,49],canutescu2003b:[38,39,41,43,44],canutescu:38,cap:10,capabl:[24,30,34],captur:1,carbon:[9,22,43,49,50],carbonyl:[49,50],care:[0,8,10,31,32,35,37,41],carlo:[0,3,10,28,31,34,35,46],carmsd:[22,23,26],carri:[8,11,20],cast:37,categori:4,caus:[16,20,33],caution:21,caviti:26,cb_in_sidechain:50,cb_pack:[28,35,41],cb_packing_scor:37,cb_pairwise_funct:40,cb_po:22,cb_pos_on:[43,44],cb_pos_two:[43,44],cb_posit:44,cbeta:[28,31,34,35,41,42],cbeta_scor:[37,42],cbetaenvlisten:8,cbetascor:[8,35,37,42],cbpackingscor:[8,35,37,42],ccd:[3,30,31,34],ccdcloser:34,cdef:35,center:[33,49],central:[22,27,41],centroid:31,certain:[1,2,4,8,10,16,26,27,28,29,35,37,39,40,41],certainli:1,ch1particl:49,ch2particl:49,ch3particl:49,ch_name:26,chain:[0,8,13,21,22,23,24,28,29,31,34,35,36,38,39,40,41],chain_idx:[8,21,31,34,35,36,39,40,41],chain_idx_list:36,chain_idx_on:40,chain_idx_two:40,chain_index:[26,34,39],chain_indic:40,chain_nam:[26,35],chainhandl:[21,22,29],chainid:0,chakravarti:38,chakravarty1999:[26,38],chanc:[8,10,35],chang:[1,3,4,5,7,8,10,16,20,21,27,28,29,32,34,35,36,39],change_frequ:[10,34],changelog:[8,19],chapter:[29,33],charact:[13,20,26,35],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32,34,35,37,50,51,54],check_dupl:28,check_io:37,check_xml:8,checkbasetyp:37,checker:7,checkfinalmodel:35,checkmagicnumb:37,checkout:[8,16],checktypes:37,chem:38,chemdict_tool:5,chemdicttool:7,chemic:[5,15,21,35,39],chemistri:[35,38],chemlib:[5,7],chi1:51,chi2:51,chi3:51,chi4:51,chi:51,child:13,childclass:1,chlorin:49,chmod:8,choos:[20,31,34],chose:5,chosen:[0,13,34,35],cif:[0,5,7,13],ciiipgatcpgdyan:35,circumv:50,cis:[22,49,51],cl_vinaparticl:49,claim:20,clash:[3,28,31,32,34,35,39,41,42,44,47],clash_scor:42,clash_thresh:35,clashscor:[31,33,34,35,42],classic:48,claus:20,clean:[2,8,16],cleanli:37,clear:[14,21,22,31,35,40],clearenviron:[21,40],cleargap:29,clearpo:21,clearresidu:21,clip:13,clone:[8,18],close:[16,18,22,26,28,31,32,34,35,36,44],close_at:28,closed_posit:34,closegap:35,closelargedelet:35,closer:[3,26,30,31],closerbas:34,closesmalldelet:[32,35],closest:[28,35],closur:[32,35,38],clustal:[0,13],cluster:[3,31,37,40],cluster_thresh:[28,40],clutter:[1,8,26],cmake:[3,8,14,15,17,18,20,54],cmake_support:[4,8,16,20],cmakecach:2,cmakelist:[1,2,4,8,16],coars:8,code:[0,1,2,3,4,5,6,7,8,11,13,14,15,16,17,18,19,20,21,22,26,27,33,35,47,49,53],codetest:[4,8],coil:[24,28],collect:[11,14,21,28,40],collis:49,column:[26,28,35],combin:[20,25,26,27,28,31,34,35,38,39,41,44,49,51],come:[1,3,4,8,11,13,35,36,42,46,51],command:[0,1,7,8,11,12,16,18,54],commandlin:13,comment:[16,20],commerci:[8,20],commit:[3,8,16],common:[8,13,20,28],commonli:[8,18,30,31,41],commun:20,comp_lib:50,compar:[3,8,22,23,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:20,increas:[0,10,28,31,32,35,50],increment:28,incur:20,indemn:20,indemnifi:20,independ:[0,3,25,36,48],index:[8,10,21,22,25,26,27,28,29,31,32,33,34,35,39,40,41,45,49,50,51],index_four:25,index_on:25,index_thre:25,index_two:25,indic:[8,10,11,13,20,21,22,25,26,27,28,29,31,32,35,36,40,44,47,49],indirect:20,individu:[7,20,39,41],inf:[10,32,35],infin:32,infinit:32,influenc:[13,28,40,50],info:[26,31,35,40],inform:[0,5,7,8,13,16,20,22,23,26,28,29,31,34,35,38,40,41,42,53],infring:20,inherit:[1,39,40,41,46],init:16,init_bb_list:34,init_frag:34,initi:[3,10,21,22,26,28,31,32,34,35,36,39,40,41,46,49,50,51],initial_bb:31,initial_epsilon:[10,52],initialis:1,inlin:37,inner:14,input:[0,1,3,13,16,18,25,26,27,28,32,34,35,36,39,40,41,44,48,52],insert:[21,22,29,31,34,35,52],insertinto:[21,22,31],insertloop:[29,35],insertloopcleargap:[29,31,35],insid:[1,4],insight:16,instal:[8,16,37,54],instanc:[3,8,13,24,25,37,53],instead:[0,1,2,3,4,8,11,26,28,29,31,34,35,50],institut:20,instruct:2,int16_t:37,int32_t:37,int_32_t:37,integ:[8,13,21,40],integr:[4,8,38],intend:[1,8,34,49],intent:26,intention:20,interact:[3,8,25,32,39,40,41,43,44,45,49],intercept:[39,41],interest:[1,10,25,26,34,37,49,51],interfac:[0,3,4,8,20,50],intermedi:8,intern:[0,1,3,4,5,8,16,21,24,25,26,27,28,31,32,34,35,36,37,38,39,40,41,46,49,50,52],internal_e_prefac:50,internal_e_prefactor:49,internal_energi:49,internet:8,interpl:51,interpol:[40,51],interpret:[8,11],intervent:8,intrins:2,introduc:[1,3,4,8,16,32,35],introduct:[12,17],invalid:[8,21,25,26,29,32,35,36,39,40,41,45,49,51],invalid_vinaparticl:49,invok:[2,4,8,15,16],involv:[16,30,44,49],iodin:49,ios:37,iostream:37,ipython:7,irrevoc:20,is_c_ter:[25,36],is_cter:25,is_hbond_acceptor:50,is_hbond_donor:50,is_major:35,is_n_ter:[25,36],is_nter:25,isallatomscoringsetup:[31,35],isallset:21,isanyset:21,isbackbonescoringsetup:35,isctermin:29,isempti:31,isen:14,isntermin:29,isoleucin:49,isset:21,issimilar:51,issourc:37,issu:[3,12,16,17,20,32,35,37],istermin:29,isvalid:47,item:[1,8,16,21,22,25,26,35,40],iter:[10,26,27,28,31,32,34,35,49],its:[0,1,2,4,5,8,11,16,20,25,26,30,31,33,34,35,41,48,49,50,51],itself:[3,4,8,16,26,34,36,37,39,41],januari:20,job:[8,26,34,35],johner:38,join:[8,21,23,26,31,32,34,36],jone:[38,49],jones1999:[26,38],journal:38,json:[0,13],jupyt:7,just:[1,2,8,13,15,16,23,25,26,28,29,31,35,50],kabsch1983:[26,38],kabsch:38,keep:[0,1,2,4,5,8,13,16,28,30,35,47],keep_non_converg:31,keep_sidechain:[8,36],kei:[0,13,26,28,31,34,35,39,40,41],kept:[8,16,25,31,32,36,45,49],kernel:[7,38],keyword:27,kic:[30,31,34],kicclos:34,kick:13,kill_electrostat:25,kind:[1,8,20],kinemat:32,know:[2,51],knowledg:51,known:[4,11,21,40,50],krivov2009:[10,38,47,49],krivov:38,kwarg:1,l_e:49,lab:48,label:[16,25],lack:35,languag:[4,20],larg:[5,27,32,35],larger:[10,14,22,26,28,35,50],largest:[28,31,44],last:[1,2,3,4,21,22,25,29,31,32,34,35,40,41,48],last_psi:22,later:[1,8,10,21,28,47],latest:[2,3,5,8],latter:[0,5,16,35],launcher:[4,8],law:20,lawsuit:20,layer:44,layout:[26,37],lbfg:35,lddt:7,leach1998:[10,38],leach:38,lead:[0,8,9,11,22,25,31,32,36,39,41,48],learn:28,least:[0,2,4,8,10,16,20,22,25,26,35,39,41,44],leav:1,left:[10,11,32],legal:[8,20],lemon:38,len:[22,23,25,26,28,31,35,36,41,47],length:[0,9,10,21,24,25,26,27,28,29,31,32,34,35,36,37,39,40,44],length_dep_weight:35,length_depend:31,lennard:49,less:[0,10,16,22,25,26,27,31,35,39,41,50,51],let:[1,8,22,26,28,31,47],letter:[3,5,21,22,26,27,34,49],leu:49,leu_h:21,leucin:49,level:[2,3,8,14,15,16,30,35],lexicograph:35,liabil:20,liabl:20,lib64:8,lib:[5,7,37],libexec:[4,8],libpromod3_nam:4,librari:[0,3,4,8,15,36,38,47,50,54],library1:4,library2:4,licenc:48,licens:[3,17,19],licensor:20,lies:26,life:16,ligand:[3,35,36,49,50],like:[0,1,4,8,16,35,37,48],limit:[0,3,20,26,32,35],line:[0,1,7,8,9,12,16,27,41,54],linear:[26,28,31,34,39,40,41],linear_weight:[31,34,39,41],linearcombin:31,linearli:49,linearscor:34,link:[0,2,4,8,16,20,21,25,26,28,34,36,39,40,41,42],link_cmd:4,linkcheck:[2,8,16],linker:[4,35],linker_length:35,list:[0,1,2,3,4,7,8,9,10,11,13,20,21,22,25,26,27,28,29,30,31,32,33,34,35,36,37,39,40,41,44,45,46,47,49,50,51,52],listen:8,literalinclud:8,litig:20,littl:[4,8,16,37],live:[4,8],lj_pair:25,load:[1,8,13,15,21,23,25,26,27,28,31,32,35,36,37,39,41,42,47,51,54],loadalign:[30,35],loadallatominteractionscor:39,loadallatompackingscor:39,loadamberforcefield:35,loadbb:26,loadbbdeplib:[0,36,47,48],loadcach:28,loadcbetascor:[31,34,41,42],loadcbpackingscor:41,loadcharmm:25,loadcharmmforcefield:35,loaddefaultallatomoverallscor:39,loaddefaultbackboneoverallscor:41,loadent:[0,13],loadfragdb:[23,24,31,35],loadhbondscor:41,loadlib:[0,36,48],loadpdb:[8,21,23,25,26,28,30,31,32,34,35,36,42,47],loadport:[25,26,27,37,39,41,51],loadreducedscor:41,loadsequenceprofil:[13,26,31],loadssagreementscor:41,loadstructuredb:[23,24,26,31,35],loadtorsionsampl:[22,24,27,34],loadtorsionsamplercoil:[24,31,35],loadtorsionsamplerextend:24,loadtorsionsamplerhel:24,loadtorsionscor:41,local:[2,5,7,25,26,27,39,41,51],localhost:7,locat:[2,3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Actions","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3\u2019s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"xref py py-func docutils literal notranslate\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame - The Rigid Part","Rotamer Graph","<code class=\"xref py py-mod docutils literal notranslate\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers & Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For 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v:26,below:[0,8,20,21,25,26,28,31,32,36,37,39,41,44,49],below_thre:26,benefici:20,besid:[2,4,10,13,26],best:[4,31,35,44],best_candid:31,beta:[9,22,33,41],beta_bin:41,better:[25,31,34,35,39,41],between:[1,3,10,13,22,25,26,28,29,31,32,34,35,36,37,39,40,41,42,43,44,45,49,50,51],beyond:13,biasini2013:[19,38],biasini:38,bienert:38,big:[25,37],bilinearli:51,bin:[1,8,16,18,26,27,28,39,41,51],bin_siz:[28,51],binari:[1,4,8,16,17,25,26,27,39,41,51],bind:[0,3,13,20,28],bins_per_dimens:27,bioinformat:38,biol:38,biolog:38,biologi:[19,38],biophi:38,biopolym:38,bit:[1,8,16,31,35],bitwis:26,blank:8,block:[3,30,45,47],blosum62:[13,23,26,28,40],boilerpl:20,bond:[0,3,9,22,25,26,32,33,35,36,38,41,47,49,50,51,54],bond_force_const:25,bond_length:[9,25],bool:[1,8,10,11,13,14,21,22,25,26,29,31,32,33,34,35,36,37,39,41,44,49,50,51],boost:[2,8,37],boost_librari:4,boost_root:2,bootstrap:[6,7],bore:34,both:[3,21,26,29,35,44,47,51],bound:[21,25,28,31,49,50],boundari:28,br_vinaparticl:49,bracket:20,bradlei:25,branch:[4,8,17],branchnam:16,brew:4,bridg:[24,25,32,35,36],briefli:16,bring:8,broken:1,bromin:49,broyden:35,bsd:20,bug:[3,8,16],bugfix:3,build:[1,3,4,6,7,8,16,18,19,25,28,30,34,44,45,47,48,50,54],build_disulfid:36,builder:2,buildfromrawmodel:[30,35],buildrawmodel:[0,3,30,31,35],buildsidechain:35,buildup:[47,49],built:[4,5,25,26,40,45],bunch:[1,13,16],bundl:20,bytecod:1,c_coord:9,c_num:29,c_p_vinaparticl:[49,50],c_po:[9,22,41],c_stem:[9,23,26,29,31,32,34],c_stem_psi:34,c_str:37,c_ter:[32,50],c_vinaparticl:[49,50],ca_coord:9,ca_pairwise_funct:40,ca_po:[9,22],ca_pos_on:[43,44],ca_pos_two:[43,44],ca_posit:[28,44],ca_rmsd:[23,26],cach:[2,26,28],calcul:[8,22,26,27,28,31,32,34,39,40,41,42,44,45,46,47,49,50],calculateallatomscor:31,calculatebackbonescor:31,calculatelinearcombin:[31,34,39,41],calculatescor:[39,41,42],calculatescoreprofil:[39,41],calculatesequenceprofilescor:31,calculatestemrmsd:31,calculatestructureprofilescor:31,call:[1,2,4,8,11,13,14,15,16,21,25,26,27,29,31,34,35,36,37,39,40,41,49,50,51],callabl:[13,16],calpha:35,calul:27,came:8,can:[0,1,2,3,4,5,7,8,9,10,11,13,14,15,16,18,19,21,22,23,25,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,44,45,46,47,48,50,51,52,53],cand:35,candid:[3,30,33,34,35,54],cannot:[0,8,13,20,25,26,27,29,35,37,39,41,48,49,50,51],canutescu2003:[32,38,49],canutescu2003b:[38,39,41,43,44],canutescu:38,cap:10,capabl:[24,30,34],captur:1,carbon:[9,22,43,49,50],carbonyl:[49,50],care:[0,8,10,31,32,35,37,41],carlo:[0,3,10,28,31,34,35,46],carmsd:[22,23,26],carri:[8,11,20],cast:37,categori:4,caus:[16,20,33],caution:21,caviti:26,cb_in_sidechain:50,cb_pack:[28,35,41],cb_packing_scor:37,cb_pairwise_funct:40,cb_po:22,cb_pos_on:[43,44],cb_pos_two:[43,44],cb_posit:44,cbeta:[28,31,34,35,41,42],cbeta_scor:[37,42],cbetaenvlisten:8,cbetascor:[8,35,37,42],cbpackingscor:[8,35,37,42],ccd:[3,30,31,34],ccdcloser:34,cdef:35,center:[33,49],central:[22,27,41],centroid:31,certain:[1,2,4,8,10,16,26,27,28,29,35,37,39,40,41],certainli:1,ch1particl:49,ch2particl:49,ch3particl:49,ch_name:26,chain:[0,8,13,21,22,23,24,28,29,31,34,35,36,38,39,40,41],chain_idx:[8,21,31,34,35,36,39,40,41],chain_idx_list:36,chain_idx_on:40,chain_idx_two:40,chain_index:[26,34,39],chain_indic:40,chain_nam:[26,35],chainhandl:[21,22,29],chainid:0,chakravarti:38,chakravarty1999:[26,38],chanc:[8,10,35],chang:[1,3,4,5,7,8,10,16,20,21,27,28,29,32,34,35,36,39],change_frequ:[10,34],changelog:[8,19],chapter:[29,33],charact:[13,20,26,35],charg:[8,20,21,25,32,49,50],charmm:[21,25,35],check:[0,1,2,3,5,8,11,13,14,16,22,25,26,30,32,34,35,37,50,51,54],check_dupl:28,check_io:37,check_xml:8,checkbasetyp:37,checker:7,checkfinalmodel:35,checkmagicnumb:37,checkout:[8,16],checktypes:37,chem:38,chemdict_tool:5,chemdicttool:7,chemic:[5,15,21,35,39],chemistri:[35,38],chemlib:[5,7],chi1:51,chi2:51,chi3:51,chi4:51,chi:51,child:13,childclass:1,chlorin:49,chmod:8,choos:[20,31,34],chose:5,chosen:[0,13,34,35],cif:[0,5,7,13],ciiipgatcpgdyan:35,circumv:50,cis:[22,49,51],cl_vinaparticl:49,claim:20,clash:[3,28,31,32,34,35,39,41,42,44,47],clash_scor:42,clash_thresh:35,clashscor:[31,33,34,35,42],classic:48,claus:20,clean:[2,8,16],cleanli:37,clear:[14,21,22,31,35,40],clearenviron:[21,40],cleargap:29,clearpo:21,clearresidu:21,clip:13,clone:[8,18],close:[16,18,22,26,28,31,32,34,35,36,44],close_at:28,closed_posit:34,closegap:35,closelargedelet:35,closer:[3,26,30,31],closerbas:34,closesmalldelet:[32,35],closest:[28,35],closur:[32,35,38],clustal:[0,13],cluster:[3,31,37,40],cluster_thresh:[28,40],clutter:[1,8,26],cmake:[3,8,14,15,17,18,20,54],cmake_support:[4,8,16,20],cmakecach:2,cmakelist:[1,2,4,8,16],coars:8,code:[0,1,2,3,4,5,6,7,8,11,13,14,15,16,17,18,19,20,21,22,26,27,33,35,47,49,53],codetest:[4,8],coil:[24,28],collect:[11,14,21,28,40],collis:49,column:[26,28,35],combin:[20,25,26,27,28,31,34,35,38,39,41,44,49,51],come:[1,3,4,8,11,13,35,36,42,46,51],command:[0,1,7,8,11,12,16,18,54],commandlin:13,comment:[16,20],commerci:[8,20],commit:[3,8,16],common:[8,13,20,28],commonli:[8,18,30,31,41],commun:20,comp_lib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51],fasta:[0,13,30,35],faster:[10,25,26,32,33,40],fastest:[32,35],favor:33,favourit:1,featur:[16,17,23,28,31,35,37,38,53],fed:[4,16],fedora:[3,8],fee:20,feed:[4,21,31],feel:[8,16],fellow:8,fetch:[13,16,18,28],few:[2,8,16,25,37,42],ff_aa:25,ff_aa_on:25,ff_aa_two:25,ff_ala:25,ff_arg:25,ff_asn:25,ff_asp:25,ff_cy:25,ff_cys2:25,ff_gln:25,ff_glu:25,ff_gly:25,ff_hisd:25,ff_hise:25,ff_ile:25,ff_leu:25,ff_lookup:[25,32,35],ff_lookup_charmm:37,ff_ly:25,ff_met:25,ff_phe:25,ff_pro:25,ff_ser:25,ff_thr:25,ff_trp:25,ff_tyr:25,ff_val:25,ff_xxx:25,fiddl:30,field:[20,35,37,51],fifti:20,figur:16,file:[0,1,2,3,4,5,7,8,12,13,15,16,17,18,20,25,26,27,28,33,39,41,48,51],filecheck:16,fileexist:11,fileextens:11,filegzip:11,filenam:[0,8,11,13,25,26,27,28,37,39,41,48,51],filenotfound:33,fill:[4,8,13,16,23,26,29,30,31,33,35],fillfromdatabas:[31,35],fillfrommontecarlosampl:[31,35],fillloopsbydatabas:35,fillloopsbymontecarlo:35,filo:40,filtercandid:33,filtercandidateswithsc:33,final_model:[30,35],find:[3,4,7,8,10,16,21,23,28,31,32,35,44,46,48,51,53],findatom:28,findchain:42,findeigen3:20,finder:30,findmotif:28,findpython:3,findwithin:[8,28],fine:8,finish:52,fire:[1,7],first:[0,1,3,8,10,13,16,21,22,25,26,27,28,29,31,32,34,35,36,39,40,41,43,44,47,49,50,51],fit:[16,20,22,26,30,31,34,54],fix:[3,8,11,16,25,32,35,36,37,39,41],fix_cterm:32,fix_nterm:32,fix_surrounding_hydrogen:25,flag1:4,flag2:4,flag:[0,2,3,4,8,10,11,13,22,26,28,35,36,49,50],flanking_rot_angle_on:22,flanking_rot_angle_two:22,fletch:[26,47],fletcher:35,flexibl:[0,19,36,44,47,49,50,52],flip:51,flood:26,fluorin:49,flush:[1,16],fold:38,folder:[2,4,8,16,18,37],follow:[0,1,2,4,5,7,8,10,11,16,18,20,22,23,25,26,28,29,30,31,35,36,37,39,41,47,49,50,51],fontsiz:27,forbidden:8,forc:[25,32,35],force_const:[25,32],forcefield:[23,32,35],forcefieldaminoacid:25,forcefieldbondinfo:25,forcefieldconnect:25,forcefieldharmonicangleinfo:25,forcefieldharmonicimproperinfo:25,forcefieldljpairinfo:25,forcefieldlookup:[25,32,35,37],forcefieldperiodicdihedralinfo:25,forcefieldureybradleyangleinfo:25,forg:16,forget:[1,8],form:[14,20,24,25,26,30,35,40,49,51],formal:[31,32,49,51],format:[0,5,13,20,26,48],formula:33,forward:16,found:[1,3,4,8,11,13,16,19,21,23,26,28,31,32,33,34,35,36,44,46,49,51],foundat:1,four:[9,34],frac:10,fraction:[26,28,32,34],frag_db:[23,26,31,37],frag_length:[23,26,28],frag_map:26,frag_po:[23,26,28],frag_residu:[23,26],frag_seq:[23,26],frag_siz:26,fragdb:[23,24,26,31,35,37],fragger:[13,23,26,28,34,35],fragger_handl:[13,35],fragger_map:26,fraggerhandl:[0,13,26,28,35],fraggermap:[26,28],fragment:[0,3,9,13,22,23,24,28,31,32,34,35,38,47],fragment_db:35,fragment_handl:28,fragment_info:26,fragment_length:[26,28],fragmentinfo:[26,31],fragments_per_posit:28,fragmentsampl:34,frame:[3,16,35,36,46,47,49,50,52,54],frame_energi:49,frame_residu:[45,47],frameresidu:[45,49,50],framework:[8,19,38],free:[0,8,20,35,49,51],frequenc:[26,34],frm:36,frmrotam:[44,49,50,52],frmrotamergroup:[44,46,49,50],from:[0,1,2,3,4,5,6,7,8,9,10,11,13,16,18,20,21,22,23,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,44,46,47,49,50,51],fromhhm:26,fromhoriz:26,fromresidu:51,front:[1,11,16],fstream:37,fudg:25,fulfil:[26,51],full:[0,1,3,8,10,21,25,26,28,29,30,31,34,35,36,47,49,50],full_queri:28,full_seq:[29,31],fullgapextend:[29,35],fulli:[8,16,21,22,26,29,30,36],function_typ:40,functions_specific_to_your_act:8,fundament:37,funni:[2,8],further:[10,28,29,35,36,37,50],furthermor:[37,50],futur:[3,25,26],gamma:[40,41,44],gamma_bin:41,gap:[0,3,9,18,24,25,30,31,33,35,36,54],gapextend:[29,35],gapfre:26,gapless:[0,13],gather:[4,12,16,26,28,47,49,51],gauc:51,gauch:51,gauche_minu:51,gauche_plu:51,gaussian1:49,gaussian2:49,gciiipgatcpgdyan:[31,35],gener:[0,1,2,3,5,7,8,10,13,14,16,18,19,20,23,24,26,27,28,30,31,32,33,35,36,37,39,40,41,48,49,50,51,54],generatedenovotrajectori:28,generatestructureprofil:26,geom:[21,22,25,26,28,32,35,44,49],geometr:[3,9,23,28,31,38,44],geometri:[12,23,26,31,54],geoom:43,get:[0,1,2,8,16,19,21,22,23,25,26,28,30,31,32,33,34,35,36,37,39,40,41,44,47,48,51,52,54],getaa:[21,22,25],getaaa:21,getaah:21,getactivesubrotam:49,getallatomposit:[21,32,36],getallatomscoringkei:31,getallatomweight:31,getanchoratomindex:21,getangl:47,getangularbins:26,getatomcount:8,getatomnam:21,getatomnameamb:21,getatomnamecharmm:21,getaveragescor:31,getbackbonelist:[23,26],getbackbonescoringkei:31,getbackboneweight:31,getbins:27,getbinsperdimens:27,getbound:22,getc:22,getca:22,getcb:22,getchain:29,getchainindex:29,getchainnam:29,getchains:8,getcharg:25,getclust:31,getclusteredcandid:31,getcollisiondist:49,getconfid:26,getcoordidx:26,getcoordinfo:26,getcpuplatformsupport:25,getcreationd:5,getdefault:[25,32,35],getdefaultlib:5,getdihedralangl:26,getdihedralconfigur:51,getdistbins:26,getdisulfidbridg:25,getdisulfidconnect:25,getdsspstat:26,getel:21,getenviron:21,getenvsetdata:8,getepsilon:25,getfirstindex:21,getforcefieldaminoacid:25,getfragmentinfo:[26,31],getframeenergi:49,getfudgelj:25,getfudgeqq:25,geth1index:21,geth2index:21,geth3index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Actions","<code class=\"docutils literal notranslate\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3\u2019s Share Of CMake","Docker","ProMod3 and Containers","Singularity","Contributing","Geometry functions","Graph Minimizer","<code class=\"docutils literal notranslate\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal notranslate\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal notranslate\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"docutils literal notranslate\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","ProMod3","License","Handling All Atom Positions","Representing Loops","<code class=\"docutils literal notranslate\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"docutils literal notranslate\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"docutils literal notranslate\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","References","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"docutils literal notranslate\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame - The Rigid Part","Rotamer Graph","<code class=\"docutils literal notranslate\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers & Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For 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\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 2d8800954685db9e06127789b0d5d5b5a88287f7..3d8e50950092529e4ae9bd789e0e12de31fbe8e2 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Disulfid Bond Evaluation — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Disulfid Bond Evaluation — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="disulfid-bond-evaluation">
@@ -41,7 +40,7 @@ the sulfur atoms. It is possible to improve performance in sidechain
reconstruction regarding cysteins when finding and separately handle
disulfid bonds. The scoring module implements an empirically derived disulfid
score (<a class="reference internal" href="../scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore" title="promod3.scoring.SCWRL3DisulfidScore"><code class="xref py py-func docutils literal notranslate"><span class="pre">promod3.scoring.SCWRL3DisulfidScore()</span></code></a>) as defined in
-<a class="reference internal" href="../references.html#canutescu2003b" id="id1"><span>[canutescu2003b]</span></a>. The paper proposes two rotamers to be in a disulfid
+<a class="reference internal" href="../references.html#canutescu2003b" id="id1">[canutescu2003b]</a>. The paper proposes two rotamers to be in a disulfid
bonded state, if the resulting disulfid score plus the self energies of the
involved rotamers is below 45. If there are several cysteines close together,
this problem gets another layer of complexity. One has to assure, that
@@ -50,7 +49,7 @@ of disulfid bonds is geometrically optimal. SCWRL4 proposes an approach,
that has also been implemented here.</p>
<dl class="method">
<dt id="promod3.sidechain.DisulfidScore">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">DisulfidScore</code><span class="sig-paren">(</span><em class="sig-param">rotamer_one</em>, <em class="sig-param">rotamer_two</em>, <em class="sig-param">ca_pos_one</em>, <em class="sig-param">cb_pos_one</em>, <em class="sig-param">ca_pos_two</em>, <em class="sig-param">cb_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.DisulfidScore" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">DisulfidScore</code><span class="sig-paren">(</span><em>rotamer_one</em>, <em>rotamer_two</em>, <em>ca_pos_one</em>, <em>cb_pos_one</em>, <em>ca_pos_two</em>, <em>cb_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.DisulfidScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Directly extracts the positions of the gamma sulfurs from the rotamers by
searching for particles with the name “SG”.
The found positions are then passed to
@@ -61,71 +60,78 @@ of gamma sulfurs per rotamer (at least one), it then evaluates the score
for all possible combinations of gamma sulfurs and takes the minimum score.
To get a final DisulfidScore, it finally adds the self energies of the
rotamers to the result of the geometric expression.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</p></li>
-<li><p><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</p></li>
-<li><p><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</p></li>
-<li><p><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</p></li>
-<li><p><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</p></li>
-<li><p><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</li>
+<li><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</li>
+<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
+<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
+<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
+<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if given rotamers do not contain
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if given rotamers do not contain
exactly (in case of <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a>) or at least (in case of
<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) one particle representing the gamma sulfur.</p>
-</dd>
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The result of the raw score plus the average
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The result of the raw score plus the average
self energies of the input rotamers</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.ResolveCysteins">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">ResolveCysteins</code><span class="sig-paren">(</span><em class="sig-param">rotamer_groups</em>, <em class="sig-param">ca_positions</em>, <em class="sig-param">cb_positions</em><span class="optional">[</span>, <em class="sig-param">score_threshold=45.0</em>, <em class="sig-param">optimize_subrotamers=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ResolveCysteins" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ResolveCysteins</code><span class="sig-paren">(</span><em>rotamer_groups</em>, <em>ca_positions</em>, <em>cb_positions</em><span class="optional">[</span>, <em>score_threshold=45.0</em>, <em>optimize_subrotamers=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ResolveCysteins" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to optimize disulfid bond network. In a first step, all disulfid bonds
get detected using <a class="reference internal" href="#promod3.sidechain.DisulfidScore" title="promod3.sidechain.DisulfidScore"><code class="xref py py-func docutils literal notranslate"><span class="pre">DisulfidScore()</span></code></a>. If the value between two rotamers is
below <strong>score_threshold</strong>, they’re assumed to be bonded. The function then
tries to detect the largest possible set of disulfide bonds, with no
cysteine being part of more than one bond. If several largest sets are
possible, the one with the optimal sum of scores gets estimated.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>) – Every group represents a cysteine</p></li>
-<li><p><strong>ca_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</p></li>
-<li><p><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</p></li>
-<li><p><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
-as a disulfid bond</p></li>
-<li><p><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
+<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>) – Every group represents a cysteine</li>
+<li><strong>ca_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
+<li><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
+<li><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
+as a disulfid bond</li>
+<li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
rotamer groups, the active subrotamers get
optimized. For every pair of rotamers
participating in a disulfid bond, the subrotamers
with best <a class="reference internal" href="#promod3.sidechain.DisulfidScore" title="promod3.sidechain.DisulfidScore"><code class="xref py py-func docutils literal notranslate"><span class="pre">DisulfidScore()</span></code></a> get activated in
the input <strong>rotamer_groups</strong>. This has an effect
-when the rotamers get applied on residues.</p></li>
+when the rotamers get applied on residues.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> objects with equal
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> containing two <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> objects with equal
length. Both lists contain <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> objects with two elements.
The tuples in the first list describe the indices of cysteins
participating in disulfid bonds. The tuples in the second list
describe the optimal rotamers in the according rotamer groups.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -146,12 +152,12 @@ describe the optimal rotamers in the according rotamer groups.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -168,7 +174,7 @@ describe the optimal rotamers in the according rotamer groups.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="graph.html" title="previous chapter">Rotamer Graph</a></li>
<li>Next: <a href="loading.html" title="next chapter">Loading Rotamer Libraries</a></li>
</ul></li>
@@ -177,33 +183,27 @@ describe the optimal rotamers in the according rotamer groups.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
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-
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</div>
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</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/disulfid.rst.txt"
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index 528c859ef98f26d0a2534ddadf1f3c9edab16cb8..e85a1e8ff373c6e2aaf478b1af6ed7691f9c7397 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Frame - The Rigid Part — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Frame - The Rigid Part — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="frame-the-rigid-part">
@@ -47,55 +46,66 @@ belonging to the frame residue with the same residue index are neglected.</p>
<h2>The Frame Objects<a class="headerlink" href="#the-frame-objects" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.FrameResidue">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">FrameResidue</code><span class="sig-paren">(</span><em class="sig-param">particles</em>, <em class="sig-param">residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a>) – particles building frame residue</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Interaction energies between the constructed frame
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">FrameResidue</code><span class="sig-paren">(</span><em>particles</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a>) – particles building frame residue</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Interaction energies between the constructed frame
residue and any rotamer associated to the same
-residue index are neglected</p></li>
+residue index are neglected</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.sidechain.FrameResidue.__len__">
-<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of particles in <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of particles in <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FrameResidue.__getitem__">
-<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue.__getitem__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> index</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> at position <strong>index</strong></p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</p>
-</dd>
-</dl>
+<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FrameResidue.__getitem__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> index</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> at position <strong>index</strong></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.sidechain.Frame">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">Frame</code><span class="sig-paren">(</span><em class="sig-param">frame_residues</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Frame" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">Frame</code><span class="sig-paren">(</span><em>frame_residues</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Frame" title="Permalink to this definition">¶</a></dt>
<dd><p>The <a class="reference internal" href="#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> object is used as a container for rigid particles, that
can be passed to rotamer groups for calculating frame energies.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>frame_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>) – residues building the frame.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frame_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>) – residues building the frame.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -103,7 +113,6 @@ can be passed to rotamer groups for calculating frame energies.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -124,12 +133,12 @@ can be passed to rotamer groups for calculating frame energies.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -146,7 +155,7 @@ can be passed to rotamer groups for calculating frame energies.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="rotamer.html" title="previous chapter">Representing Sidechains - Rotamers & Co.</a></li>
<li>Next: <a href="rotamer_constructor.html" title="next chapter">Rotamer Constructor</a></li>
</ul></li>
@@ -155,33 +164,27 @@ can be passed to rotamer groups for calculating frame energies.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
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-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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<a href="../_sources/sidechain/frame.rst.txt"
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index deda2927ca84a31f1c03e2212d2c1081c1193514..61732485dc5627272f1857dcc88e22d4d5619ba1 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Rotamer Graph — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Rotamer Graph — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="rotamer-graph">
@@ -43,25 +42,28 @@ overall solution has to be found. ProMod3 implements a
tree decomposition, A* and Monte Carlo algorithms.</p>
<dl class="class">
<dt id="promod3.sidechain.RotamerGraph">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerGraph</code><a class="headerlink" href="#promod3.sidechain.RotamerGraph" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerGraph</code><a class="headerlink" href="#promod3.sidechain.RotamerGraph" title="Permalink to this definition">¶</a></dt>
<dd><p>The <a class="reference internal" href="#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerGraph</span></code></a> objects inherits from
<a class="reference internal" href="../core/graph_minimizer.html#promod3.core.GraphMinimizer" title="promod3.core.GraphMinimizer"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.core.GraphMinimizer</span></code></a> and extends the minimizer by static
initialization functions.</p>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.sidechain.RotamerGraph.CreateFromRRMList">
-<em class="property">static </em><code class="sig-name descname">CreateFromRRMList</code><span class="sig-paren">(</span><em class="sig-param">rotamer_groups</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.CreateFromRRMList" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">CreateFromRRMList</code><span class="sig-paren">(</span><em>rotamer_groups</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.CreateFromRRMList" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.sidechain.RotamerGraph.CreateFromFRMList">
-<em class="property">static </em><code class="sig-name descname">CreateFromFRMList</code><span class="sig-paren">(</span><em class="sig-param">rotamer_groups</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.CreateFromFRMList" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> or <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>
+<em class="property">static </em><code class="descname">CreateFromFRMList</code><span class="sig-paren">(</span><em>rotamer_groups</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.CreateFromFRMList" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> or <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>
objects representing the possible sidechain
-conformations for every amino acid position.</p>
-</dd>
-</dl>
+conformations for every amino acid position.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -70,7 +72,6 @@ conformations for every amino acid position.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -91,12 +92,12 @@ conformations for every amino acid position.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -113,7 +114,7 @@ conformations for every amino acid position.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="rotamer_lib.html" title="previous chapter">Rotamer Library</a></li>
<li>Next: <a href="disulfid.html" title="next chapter">Disulfid Bond Evaluation</a></li>
</ul></li>
@@ -122,33 +123,27 @@ conformations for every amino acid position.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/graph.rst.txt"
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index 58f4b468a3882dbc95e82d7297ab04dd23e75820..e6e40a3b78011f7f26bea103c0f5ac16172bc58b 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>sidechain - Sidechain Modelling — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>sidechain - Sidechain Modelling — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,14 +30,12 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="module-promod3.sidechain">
<span id="sidechain-sidechain-modelling"></span><h1><a class="reference internal" href="#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code></a> - Sidechain Modelling<a class="headerlink" href="#module-promod3.sidechain" title="Permalink to this headline">¶</a></h1>
<p>Tools and algorithms to model sidechains given backbone coordinates. The full
-module is heavily based on SCWRL4 <a class="reference internal" href="../references.html#krivov2009" id="id1"><span>[krivov2009]</span></a> . The according paper describes
+module is heavily based on SCWRL4 <a class="reference internal" href="../references.html#krivov2009" id="id1">[krivov2009]</a> . The according paper describes
the modelling of sidechains using two different rotamer models. A rigid model,
as well as a flexible model. Both models are implemented in ProMod3 and can be
applied in flexible ways.</p>
@@ -169,7 +168,6 @@ pipelines available in the modelling module.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -190,12 +188,12 @@ pipelines available in the modelling module.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="current reference internal" href="#"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -219,33 +217,27 @@ pipelines available in the modelling module.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/index.rst.txt"
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index 84357123fcc616a047076060cbdc293c8c0cabd2..d54af5fd4e741da4b8dad8ae3bb522993a715f17 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Loading Rotamer Libraries — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Loading Rotamer Libraries — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,15 +30,13 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="loading-rotamer-libraries">
<h1>Loading Rotamer Libraries<a class="headerlink" href="#loading-rotamer-libraries" title="Permalink to this headline">¶</a></h1>
<p>There are several rotamer libraries that can be used in ProMod3 . ProMod3
is optimized for the use with backbone dependent rotamer libraries such
-as the 2010 library provided by the Dunbrack lab <a class="reference internal" href="../references.html#shapovalov2011" id="id1"><span>[shapovalov2011]</span></a>.
+as the 2010 library provided by the Dunbrack lab <a class="reference internal" href="../references.html#shapovalov2011" id="id1">[shapovalov2011]</a>.
You can request a licence <a class="reference external" href="http://dunbrack.fccc.edu/bbdep2010/">here</a>
and generate such a library as described in
extras/data_generation/rotamer_library/README. Alternatively, ProMod3
@@ -45,70 +44,73 @@ provides its own backbone dependent or backbone independent libraries
that can be loaded with <a class="reference internal" href="#promod3.sidechain.LoadBBDepLib" title="promod3.sidechain.LoadBBDepLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadBBDepLib()</span></code></a> / <a class="reference internal" href="#promod3.sidechain.LoadLib" title="promod3.sidechain.LoadLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">LoadLib()</span></code></a>.</p>
<dl class="method">
<dt id="promod3.sidechain.LoadBBDepLib">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">LoadBBDepLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadBBDepLib" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadBBDepLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadBBDepLib" title="Permalink to this definition">¶</a></dt>
<dd><p>A backbone dependent rotamer library shipped with ProMod3. You can find
details on how it is created in extras/data_generation/rotamer_library/README.
All scripts to build it are in the same directory as the README file and
build the basis for custom versions.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The requested Library</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The requested Library</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.LoadLib">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">LoadLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadLib" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">LoadLib</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.LoadLib" title="Permalink to this definition">¶</a></dt>
<dd><p>A backbone independent rotamer library shipped with ProMod3. You can find
details on how it is created in extras/data_generation/rotamer_library/README.
All scripts to build it are in the same directory as the README file and
build the basis for custom versions.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The requested library</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The requested library</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.ReadDunbrackFile">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">ReadDunbrackFile</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ReadDunbrackFile" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ReadDunbrackFile</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ReadDunbrackFile" title="Permalink to this definition">¶</a></dt>
<dd><p>Reads a file as it is provided when you get a licence for the 2010 library of
the Dunbrack lab. It can only read the classic version, where all rotamers
are in a single file. Specific distributions of non-rotameric sidechains
cannot be read. You can find an example described in
extras/data_generation/rotamer_library/README</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> – Name of the file</p>
-</dd>
-<dt class="field-even">Throws</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file does not exist, the format
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> – Name of the file</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Throws:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file does not exist, the format
is not valid or when the library is incomplete leading to problems
to make the library static. Most likely your input file is
-incomplete if the last problem gets triggered.</p>
-</dd>
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The read library</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a></p>
-</dd>
-</dl>
+incomplete if the last problem gets triggered.</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The read library</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -129,12 +131,12 @@ incomplete if the last problem gets triggered.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -151,7 +153,7 @@ incomplete if the last problem gets triggered.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="disulfid.html" title="previous chapter">Disulfid Bond Evaluation</a></li>
<li>Next: <a href="subrotamer_optimizer.html" title="next chapter">Subrotamer Optimization</a></li>
</ul></li>
@@ -160,33 +162,27 @@ incomplete if the last problem gets triggered.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
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<script type="text/javascript">$('#searchbox').show(0);</script>
-
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</div>
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- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/loading.rst.txt"
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index 4201fcc72369bf35b5c80dda56cd9c426d1e87e1..e33eb6e988202302ca3ad1bef062b3fb14235bb4 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Representing Sidechains - Rotamers & Co. — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Representing Sidechains - Rotamers & Co. — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="representing-sidechains-rotamers-co">
@@ -50,38 +49,38 @@ As an example there are histidine in two possible protonation states,
that affect the hbond term or different versions of proline/cysteine.</p>
<dl class="class">
<dt id="promod3.sidechain.RotamerID">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerID</code><a class="headerlink" href="#promod3.sidechain.RotamerID" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerID</code><a class="headerlink" href="#promod3.sidechain.RotamerID" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the amino acids. Possible values:</p>
<table class="hlist"><tr><td><ul class="simple">
-<li><p>ARG - Arginine</p></li>
-<li><p>ASN - Asparagine</p></li>
-<li><p>ASP - Aspartate</p></li>
-<li><p>GLN - Glutamine</p></li>
-<li><p>GLU - Glutamate</p></li>
-<li><p>LYS - Lysine</p></li>
-<li><p>SER - Serine</p></li>
-<li><p>CYS - Cystein</p></li>
-<li><p>CYH - “free” Cystein</p></li>
-<li><p>CYD - disulfid bonded Cystein</p></li>
-<li><p>MET - Methionine</p></li>
-<li><p>TRP - Tryptophane</p></li>
-<li><p>TYR - Tyrosine</p></li>
-<li><p>THR - Threonine</p></li>
+<li>ARG - Arginine</li>
+<li>ASN - Asparagine</li>
+<li>ASP - Aspartate</li>
+<li>GLN - Glutamine</li>
+<li>GLU - Glutamate</li>
+<li>LYS - Lysine</li>
+<li>SER - Serine</li>
+<li>CYS - Cystein</li>
+<li>CYH - “free” Cystein</li>
+<li>CYD - disulfid bonded Cystein</li>
+<li>MET - Methionine</li>
+<li>TRP - Tryptophane</li>
+<li>TYR - Tyrosine</li>
+<li>THR - Threonine</li>
</ul>
</td><td><ul class="simple">
-<li><p>VAL - Valine</p></li>
-<li><p>ILE - Isoleucine</p></li>
-<li><p>LEU - Leucine</p></li>
-<li><p>PRO - Proline</p></li>
-<li><p>CPR - cis-Proline</p></li>
-<li><p>TPR - trans-Proline</p></li>
-<li><p>HIS - Histidine</p></li>
-<li><p>HSD - d-protonated Histidine</p></li>
-<li><p>HSE - e-protonated Histidine</p></li>
-<li><p>PHE - Phenylalanine</p></li>
-<li><p>GLY - Glycine</p></li>
-<li><p>ALA - Alanine</p></li>
-<li><p>XXX - Invalid</p></li>
+<li>VAL - Valine</li>
+<li>ILE - Isoleucine</li>
+<li>LEU - Leucine</li>
+<li>PRO - Proline</li>
+<li>CPR - cis-Proline</li>
+<li>TPR - trans-Proline</li>
+<li>HIS - Histidine</li>
+<li>HSD - d-protonated Histidine</li>
+<li>HSE - e-protonated Histidine</li>
+<li>PHE - Phenylalanine</li>
+<li>GLY - Glycine</li>
+<li>ALA - Alanine</li>
+<li>XXX - Invalid</li>
</ul>
</td></tr></table>
<p>The RotamerID enum can be accessed either directly as <code class="docutils literal notranslate"><span class="pre">promod3.sidechain.ARG</span></code>
@@ -95,34 +94,38 @@ functions exist to get RotamerIDs from the <a class="reference external" href="h
or from amino acid three letter codes.</p>
<dl class="method">
<dt id="promod3.sidechain.TLCToRotID">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">TLCToRotID</code><span class="sig-paren">(</span><em class="sig-param">tlc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.TLCToRotID" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">TLCToRotID</code><span class="sig-paren">(</span><em>tlc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.TLCToRotID" title="Permalink to this definition">¶</a></dt>
<dd><p>Directly translates the three letter code into a RotamerID. Following
exactly the naming convention defined above.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>tlc</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Three letter code of amino acid</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>tlc</strong> cannot be recoginzed.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>tlc</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Three letter code of amino acid</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>tlc</strong> cannot be recoginzed.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.AAToRotID">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">AAToRotID</code><span class="sig-paren">(</span><em class="sig-param">aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.AAToRotID" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">AAToRotID</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.AAToRotID" title="Permalink to this definition">¶</a></dt>
<dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
to generate special IDs this way
(e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not
defined in <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -135,97 +138,105 @@ For every energy function available in ProMod3, there’s a particle creation
function.</p>
<dl class="class">
<dt id="promod3.sidechain.PScoringFunction">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">PScoringFunction</code><a class="headerlink" href="#promod3.sidechain.PScoringFunction" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">PScoringFunction</code><a class="headerlink" href="#promod3.sidechain.PScoringFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>The available scoring functions between <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> objects</p>
<ul class="simple">
-<li><p>SCWRL4 - <a class="reference internal" href="#scwrl4-scoring-function"><span class="std std-ref">The SCWRL4 scoring function</span></a></p></li>
-<li><p>SCWRL3 - <a class="reference internal" href="#scwrl3-scoring-function"><span class="std std-ref">The SCWRL3 scoring function</span></a></p></li>
-<li><p>VINA - <a class="reference internal" href="#vina-scoring-function"><span class="std std-ref">The VINA scoring function</span></a></p></li>
+<li>SCWRL4 - <a class="reference internal" href="#scwrl4-scoring-function"><span class="std std-ref">The SCWRL4 scoring function</span></a></li>
+<li>SCWRL3 - <a class="reference internal" href="#scwrl3-scoring-function"><span class="std std-ref">The SCWRL3 scoring function</span></a></li>
+<li>VINA - <a class="reference internal" href="#vina-scoring-function"><span class="std std-ref">The VINA scoring function</span></a></li>
</ul>
</dd></dl>
<dl class="class">
<dt id="promod3.sidechain.Particle">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">Particle</code><a class="headerlink" href="#promod3.sidechain.Particle" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">Particle</code><a class="headerlink" href="#promod3.sidechain.Particle" title="Permalink to this definition">¶</a></dt>
<dd><p>The particle class. There’s no constructor. You can either use the
<a class="reference internal" href="rotamer_constructor.html#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a> to create full <code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerGroup</span></code> objects
with all underlying particles or the energy function specific creation
functions.</p>
<dl class="method">
<dt id="promod3.sidechain.Particle.PairwiseScore">
-<code class="sig-name descname">PairwiseScore</code><span class="sig-paren">(</span><em class="sig-param">other_particle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.PairwiseScore" title="Permalink to this definition">¶</a></dt>
+<code class="descname">PairwiseScore</code><span class="sig-paren">(</span><em>other_particle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.PairwiseScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates score between the two particles</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>other_particle</strong> (<a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a>) – The interacting particle</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The score</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the scoring function
-parametrization of the two particles is inconsistent</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other_particle</strong> (<a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a>) – The interacting particle</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The score</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the scoring function
+parametrization of the two particles is inconsistent</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.Particle.GetName">
-<code class="sig-name descname">GetName</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetName" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The name of the particle, which corresponds to the
-atom name</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetName</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetName" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The name of the particle, which corresponds to the
+atom name</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.Particle.GetCollisionDistance">
-<code class="sig-name descname">GetCollisionDistance</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetCollisionDistance" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The “collision distance” all pairs of particles with
+<code class="descname">GetCollisionDistance</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetCollisionDistance" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The “collision distance” all pairs of particles with
their distance below the sum of their collision
distances are considered as interacting and thus
-evaluated by the underlying scoring function.</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
-</dd>
-</dl>
+evaluated by the underlying scoring function.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.Particle.GetPos">
-<code class="sig-name descname">GetPos</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetPos" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The position of the particle</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetPos</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetPos" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The position of the particle</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.Particle.GetScoringFunction">
-<code class="sig-name descname">GetScoringFunction</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetScoringFunction" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The underlying scoring function</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.PScoringFunction" title="promod3.sidechain.PScoringFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PScoringFunction</span></code></a></p>
-</dd>
-</dl>
+<code class="descname">GetScoringFunction</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetScoringFunction" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The underlying scoring function</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.PScoringFunction" title="promod3.sidechain.PScoringFunction"><code class="xref py py-class docutils literal notranslate"><span class="pre">PScoringFunction</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -234,53 +245,57 @@ evaluated by the underlying scoring function.</p>
<span id="scwrl4-scoring-function"></span><h3>The SCWRL4 scoring function<a class="headerlink" href="#the-scwrl4-scoring-function" title="Permalink to this headline">¶</a></h3>
<p>The SCWRL4 scoring function combines a Lennard-Jones style term with
a hydrogen bond term. Details can be found in the relevant publication
-<a class="reference internal" href="../references.html#krivov2009" id="id1"><span>[krivov2009]</span></a>.</p>
+<a class="reference internal" href="../references.html#krivov2009" id="id1">[krivov2009]</a>.</p>
<dl class="class">
<dt id="promod3.sidechain.SCWRL4ParticleType">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SCWRL4ParticleType</code><a class="headerlink" href="#promod3.sidechain.SCWRL4ParticleType" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL4ParticleType</code><a class="headerlink" href="#promod3.sidechain.SCWRL4ParticleType" title="Permalink to this definition">¶</a></dt>
<dd><p>The SCWRL4 energy function differentiates between following particle types
that define the behaviour of the Lennard-Jones style term:</p>
<ul class="simple">
-<li><p>HParticle - represents hydrogen</p></li>
-<li><p>CParticle - default representation of a carbon</p></li>
-<li><p>CH1Particle - represents carbon bound to 1 hydrogen</p></li>
-<li><p>CH2Particle - represents carbon bound to 2 hydrogen</p></li>
-<li><p>CH3Particle - represents carbon bound to 3 hydrogen</p></li>
-<li><p>NParticle - represents nitrogen</p></li>
-<li><p>OParticle - default representation of oxygen</p></li>
-<li><p>OCParticle - represents carbonyl-oxygen for ASP/GLU</p></li>
-<li><p>SParticle - represents sulfur</p></li>
+<li>HParticle - represents hydrogen</li>
+<li>CParticle - default representation of a carbon</li>
+<li>CH1Particle - represents carbon bound to 1 hydrogen</li>
+<li>CH2Particle - represents carbon bound to 2 hydrogen</li>
+<li>CH3Particle - represents carbon bound to 3 hydrogen</li>
+<li>NParticle - represents nitrogen</li>
+<li>OParticle - default representation of oxygen</li>
+<li>OCParticle - represents carbonyl-oxygen for ASP/GLU</li>
+<li>SParticle - represents sulfur</li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.CreateSCWRL4Particle">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">CreateSCWRL4Particle</code><span class="sig-paren">(</span><em class="sig-param">name</em>, <em class="sig-param">particle_type</em>, <em class="sig-param">pos</em><span class="optional">[</span>, <em class="sig-param">charge</em>, <em class="sig-param">lone_pairs=None</em>, <em class="sig-param">polar_direction=None</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateSCWRL4Particle" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">CreateSCWRL4Particle</code><span class="sig-paren">(</span><em>name</em>, <em>particle_type</em>, <em>pos</em><span class="optional">[</span>, <em>charge</em>, <em>lone_pairs=None</em>, <em>polar_direction=None</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateSCWRL4Particle" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> that can evaluate the SCWRL4 scoring
function</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
-<li><p><strong>particle_type</strong> (<a class="reference internal" href="#promod3.sidechain.SCWRL4ParticleType" title="promod3.sidechain.SCWRL4ParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">SCWRL4ParticleType</span></code></a>) – The type of the particle</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
-<li><p><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The charge of the particle, relevant for the hydrogen
-bond term</p></li>
-<li><p><strong>lone_pairs</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</li>
+<li><strong>particle_type</strong> (<a class="reference internal" href="#promod3.sidechain.SCWRL4ParticleType" title="promod3.sidechain.SCWRL4ParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">SCWRL4ParticleType</span></code></a>) – The type of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+<li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The charge of the particle, relevant for the hydrogen
+bond term</li>
+<li><strong>lone_pairs</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
relevant for the hydrogen bond term. If set, the
particle is a potential hydrogen bond acceptor.
An example would be the Serine OG atom, where you can
represent the two lone pairs with vectors pointing
-from the OG position towards the lone pair centers.</p></li>
-<li><p><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
+from the OG position towards the lone pair centers.</li>
+<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
relevant for the hydrogen bond term. If set, the
particle is a potential hydrogen bond donor. An
example would be the Serine HG hydrogen. The
<em>polar_direction</em> would be a vector
-estimated as follows: hg_pos-og_pos.</p></li>
+estimated as follows: hg_pos-og_pos.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -288,22 +303,26 @@ estimated as follows: hg_pos-og_pos.</p></li>
<span id="scwrl3-scoring-function"></span><h3>The SCWRL3 scoring function<a class="headerlink" href="#the-scwrl3-scoring-function" title="Permalink to this headline">¶</a></h3>
<p>The SCWRL3 scoring function implements a simple repulsion term that depends on
the hard-sphere radius of the involved particles.
-Details can be found in the relevant publication <a class="reference internal" href="../references.html#canutescu2003" id="id2"><span>[canutescu2003]</span></a>.</p>
+Details can be found in the relevant publication <a class="reference internal" href="../references.html#canutescu2003" id="id2">[canutescu2003]</a>.</p>
<dl class="method">
<dt id="promod3.sidechain.CreateSCWRL3Particle">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">CreateSCWRL3Particle</code><span class="sig-paren">(</span><em class="sig-param">name</em>, <em class="sig-param">radius</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateSCWRL3Particle" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">CreateSCWRL3Particle</code><span class="sig-paren">(</span><em>name</em>, <em>radius</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateSCWRL3Particle" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> that can evaluate the SCWRL3 scoring
function</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
-<li><p><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The hard-sphere radius of the particle, relevant for the
-repulsion term.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</li>
+<li><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The hard-sphere radius of the particle, relevant for the
+repulsion term.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -311,7 +330,7 @@ repulsion term.</p></li>
<span id="vina-scoring-function"></span><h3>The VINA scoring function<a class="headerlink" href="#the-vina-scoring-function" title="Permalink to this headline">¶</a></h3>
<p>The VINA scoring function is a combination of functional forms that are named
gaussian1, gaussian2, repulsion, hydrophobic and hbond in the Autodock Vina
-software <a class="reference internal" href="../references.html#trott2010" id="id3"><span>[trott2010]</span></a>. VINA only evaluates heavy atoms. Gaussian1, gaussian2
+software <a class="reference internal" href="../references.html#trott2010" id="id3">[trott2010]</a>. VINA only evaluates heavy atoms. Gaussian1, gaussian2
and repulsion are evaluated for all pairs of particles. Hydrophobic is only
evaluated between C_VINAParticle <a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a> and hbond is
evaluated between hydrogen bond donor/acceptor pairs. While SCWRL3 and SCWRL4
@@ -322,96 +341,100 @@ the Autodock Vina Software. They’re set as global variables and can be
extracted with:</p>
<dl class="method">
<dt id="promod3.sidechain.GetVINAWeightGaussian1">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetVINAWeightGaussian1</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightGaussian1" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetVINAWeightGaussian1</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightGaussian1" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="promod3.sidechain.GetVINAWeightGaussian2">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetVINAWeightGaussian2</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightGaussian2" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetVINAWeightGaussian2</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightGaussian2" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="promod3.sidechain.GetVINAWeightRepulsion">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetVINAWeightRepulsion</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightRepulsion" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetVINAWeightRepulsion</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightRepulsion" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="promod3.sidechain.GetVINAWeightHydrophobic">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetVINAWeightHydrophobic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightHydrophobic" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetVINAWeightHydrophobic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightHydrophobic" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="promod3.sidechain.GetVINAWeightHBond">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetVINAWeightHBond</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightHBond" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetVINAWeightHBond</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetVINAWeightHBond" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<p>You can set custom weights. A call to the following functions overwrites
according weights globally which affects any subsequent score evaluation:</p>
<dl class="method">
<dt id="promod3.sidechain.SetVINAWeightGaussian1">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SetVINAWeightGaussian1</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightGaussian1" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">SetVINAWeightGaussian1</code><span class="sig-paren">(</span><em>w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightGaussian1" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="promod3.sidechain.SetVINAWeightGaussian2">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SetVINAWeightGaussian2</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightGaussian2" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">SetVINAWeightGaussian2</code><span class="sig-paren">(</span><em>w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightGaussian2" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="promod3.sidechain.SetVINAWeightRepulsion">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SetVINAWeightRepulsion</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightRepulsion" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">SetVINAWeightRepulsion</code><span class="sig-paren">(</span><em>w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightRepulsion" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="promod3.sidechain.SetVINAWeightHydrophobic">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SetVINAWeightHydrophobic</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightHydrophobic" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">SetVINAWeightHydrophobic</code><span class="sig-paren">(</span><em>w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightHydrophobic" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="promod3.sidechain.SetVINAWeightHBond">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SetVINAWeightHBond</code><span class="sig-paren">(</span><em class="sig-param">w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightHBond" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">SetVINAWeightHBond</code><span class="sig-paren">(</span><em>w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SetVINAWeightHBond" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<p>The VINA scoring function differentiates between the following particle types:</p>
<dl class="class">
<dt id="promod3.sidechain.VINAParticleType">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">VINAParticleType</code><a class="headerlink" href="#promod3.sidechain.VINAParticleType" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">VINAParticleType</code><a class="headerlink" href="#promod3.sidechain.VINAParticleType" title="Permalink to this definition">¶</a></dt>
<dd><ul class="simple">
-<li><p>O_D_VINAParticle - Oxygen that can be a hydrogen bond donor</p></li>
-<li><p>N_D_VINAParticle - Nitrogen that can be a hydrogen bond donor</p></li>
-<li><p>O_A_VINAParticle - Oxygen that can be a hydrogen bond acceptor</p></li>
-<li><p>N_A_VINAParticle - Nitrogen that can be a hydrogen bond acceptor</p></li>
-<li><p>O_AD_VINAParticle - Oxygen that can be a hydrogen bond donor and acceptor</p></li>
-<li><p>N_AD_VINAParticle - Nitrogen that can be a hydrogen bond donor and acceptor</p></li>
-<li><p>O_VINAParticle - Oxygen</p></li>
-<li><p>N_VINAParticle - Nitrogen</p></li>
-<li><p>S_VINAParticle - Sulfur</p></li>
-<li><p>P_VINAParticle - Phosphorus</p></li>
-<li><p>C_P_VINAParticle - Polar carbon that is covalently bound to a charged atom</p></li>
-<li><p>C_VINAParticle - Hydrophobic carbon that is only bound to other carbons or hydrogens</p></li>
-<li><p>F_VINAParticle - Fluorine</p></li>
-<li><p>Cl_VINAParticle - Chlorine</p></li>
-<li><p>Br_VINAParticle - Bromine</p></li>
-<li><p>I_VINAParticle - Iodine</p></li>
-<li><p>M_VINAParticle - Metals</p></li>
-<li><p>INVALID_VINAParticle - Invalid particle…</p></li>
+<li>O_D_VINAParticle - Oxygen that can be a hydrogen bond donor</li>
+<li>N_D_VINAParticle - Nitrogen that can be a hydrogen bond donor</li>
+<li>O_A_VINAParticle - Oxygen that can be a hydrogen bond acceptor</li>
+<li>N_A_VINAParticle - Nitrogen that can be a hydrogen bond acceptor</li>
+<li>O_AD_VINAParticle - Oxygen that can be a hydrogen bond donor and acceptor</li>
+<li>N_AD_VINAParticle - Nitrogen that can be a hydrogen bond donor and acceptor</li>
+<li>O_VINAParticle - Oxygen</li>
+<li>N_VINAParticle - Nitrogen</li>
+<li>S_VINAParticle - Sulfur</li>
+<li>P_VINAParticle - Phosphorus</li>
+<li>C_P_VINAParticle - Polar carbon that is covalently bound to a charged atom</li>
+<li>C_VINAParticle - Hydrophobic carbon that is only bound to other carbons or hydrogens</li>
+<li>F_VINAParticle - Fluorine</li>
+<li>Cl_VINAParticle - Chlorine</li>
+<li>Br_VINAParticle - Bromine</li>
+<li>I_VINAParticle - Iodine</li>
+<li>M_VINAParticle - Metals</li>
+<li>INVALID_VINAParticle - Invalid particle…</li>
</ul>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.CreateVINAParticle">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">CreateVINAParticle</code><span class="sig-paren">(</span><em class="sig-param">name</em>, <em class="sig-param">particle_type</em>, <em class="sig-param">pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateVINAParticle" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">CreateVINAParticle</code><span class="sig-paren">(</span><em>name</em>, <em>particle_type</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateVINAParticle" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> that can evaluate the VINA scoring
function</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
-<li><p><strong>radius</strong> (<a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>) – The type of the particle</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</li>
+<li><strong>radius</strong> (<a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>) – The type of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -420,335 +443,404 @@ function</p>
<h2>Rotamers<a class="headerlink" href="#rotamers" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RRMRotamer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RRMRotamer</code><span class="sig-paren">(</span><em class="sig-param">particles</em>, <em class="sig-param">probability</em>, <em class="sig-param">internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RRMRotamer</code><span class="sig-paren">(</span><em>particles</em>, <em>probability</em>, <em>internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer" title="Permalink to this definition">¶</a></dt>
<dd><p>The RRMRotamer represents a rotamer of the so called rigid rotamer model.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> objects</p></li>
-<li><p><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Probability of rotamers. In case of the SCWRL4
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> objects</li>
+<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Probability of rotamers. In case of the SCWRL4
energy calculation, this directly controls the
-internal energy of that rotamer.</p></li>
-<li><p><strong>internal_e_prefactor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor applied to the internal energy calculated
+internal energy of that rotamer.</li>
+<li><strong>internal_e_prefactor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor applied to the internal energy calculated
as -log(<strong>probability</strong>/max_probability),
where max_probability is the maximum
rotamer probability of any rotamer in a
-particular <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>.</p></li>
+particular <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.__getitem__">
-<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.__getitem__" title="Permalink to this definition">¶</a></dt>
<dd><p>Access particle at specified index</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of particle of interest</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> at specified index</p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of particle of interest</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> at specified index</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.__len__">
-<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of particles the rotamer contains</p>
-</dd>
-</dl>
+<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of particles the rotamer contains</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.ApplyOnResidue">
-<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">consider_hydrogens=False</em>, <em class="sig-param">new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>res</em>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Iterates over every particle and searches for the according atom in
<strong>res</strong>. If it’s present, the position gets reset to the particle position.
If not, a new atom gets added to <strong>res</strong>. No atoms are removed from <strong>res</strong>
in this process.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
-<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
-<strong>res</strong></p></li>
-<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
-default value (“”)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+<strong>res</strong></li>
+<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
+default value (“”)</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
are present in <em>res</em></p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">all_atom</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span></dt>
+<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>all_atom</em>, <em>res_idx</em><span class="sig-paren">)</span></dt>
<dd><p>Set all sidechain atom positions for given residue to the positions of the
particles in the rotamer.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</p></li>
-<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</li>
+<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_idx</em> is invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_idx</em> is invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.ToFrameResidue">
-<code class="sig-name descname">ToFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.ToFrameResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ToFrameResidue</code><span class="sig-paren">(</span><em>res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.ToFrameResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates and returns a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> based on the internal
particles.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx passed over to <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> constructor</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The constructed <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx passed over to <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> constructor</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The constructed <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.GetInternalEnergyPrefactor">
-<code class="sig-name descname">GetInternalEnergyPrefactor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Prefactor used in internal energy calculation</p>
-</dd>
-</dl>
+<code class="descname">GetInternalEnergyPrefactor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Prefactor used in internal energy calculation</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.GetInternalEnergy">
-<code class="sig-name descname">GetInternalEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetInternalEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Internal Energy if calculated, 0.0 otherwise</p>
-</dd>
-</dl>
+<code class="descname">GetInternalEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetInternalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Internal Energy if calculated, 0.0 otherwise</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.GetFrameEnergy">
-<code class="sig-name descname">GetFrameEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetFrameEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns frame energy. This energy can either be manually set or calculated
using a <a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> and the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> this rotamer
belongs to.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Frame energy if calculated, 0.0 otherwise</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Frame energy if calculated, 0.0 otherwise</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.GetSelfEnergy">
-<code class="sig-name descname">GetSelfEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetSelfEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Self energy consisting of internal plus frame energy</p>
-</dd>
-</dl>
+<code class="descname">GetSelfEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetSelfEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Self energy consisting of internal plus frame energy</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.GetProbability">
-<code class="sig-name descname">GetProbability</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetProbability" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>probability of this rotamer</p>
-</dd>
-</dl>
+<code class="descname">GetProbability</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.GetProbability" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">probability of this rotamer</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.SetInternalEnergyPrefactor">
-<code class="sig-name descname">SetInternalEnergyPrefactor</code><span class="sig-paren">(</span><em class="sig-param">prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy prefactor to be set</p>
-</dd>
-</dl>
+<code class="descname">SetInternalEnergyPrefactor</code><span class="sig-paren">(</span><em>prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy prefactor to be set</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.SetInternalEnergy">
-<code class="sig-name descname">SetInternalEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetInternalEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy to be set</p>
-</dd>
-</dl>
+<code class="descname">SetInternalEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetInternalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy to be set</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.SetFrameEnergy">
-<code class="sig-name descname">SetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy to be set</p>
-</dd>
-</dl>
+<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy to be set</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.AddFrameEnergy">
-<code class="sig-name descname">AddFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy to be added</p>
-</dd>
-</dl>
+<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy to be added</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamer.SetProbability">
-<code class="sig-name descname">SetProbability</code><span class="sig-paren">(</span><em class="sig-param">probability</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetProbability" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal probability to be set</p>
-</dd>
-</dl>
+<code class="descname">SetProbability</code><span class="sig-paren">(</span><em>probability</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.SetProbability" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal probability to be set</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.sidechain.FRMRotamer">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">FRMRotamer</code><span class="sig-paren">(</span><em class="sig-param">particles</em>, <em class="sig-param">T</em>, <em class="sig-param">probability</em>, <em class="sig-param">internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">FRMRotamer</code><span class="sig-paren">(</span><em>particles</em>, <em>T</em>, <em>probability</em>, <em>internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer" title="Permalink to this definition">¶</a></dt>
<dd><p>The FRMRotamer represents a rotamer of the so called flexible rotamer model,
where one rotamer gets represented by several subrotamers.
The idea is that all particles of all subrotamers are given at
initialization. Subrotamers are then defined by providing lists of indices.
One particle can be part of several subrotamers.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> objects</p></li>
-<li><p><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Probability of rotamers. In case of the SCWRL4
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> objects</li>
+<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Probability of rotamers. In case of the SCWRL4
energy calculation, this directly controls the
-internal energy of that rotamer.</p></li>
-<li><p><strong>T</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Temperature factor, that is used to generate a final
+internal energy of that rotamer.</li>
+<li><strong>T</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Temperature factor, that is used to generate a final
energy given the subrotamers according to the formalism
-described in the SCWRL4 paper.</p></li>
-<li><p><strong>internal_e_prefactor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor applied to the internal energy calculated
+described in the SCWRL4 paper.</li>
+<li><strong>internal_e_prefactor</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Factor applied to the internal energy calculated
as -log(<strong>probability</strong>/max_probability),
where max_probability is the maximum
rotamer probability of any rotamer in a
-particular <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>.</p></li>
+particular <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>.</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.__getitem__">
-<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.__getitem__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.__getitem__" title="Permalink to this definition">¶</a></dt>
<dd><p>Access particle at specified index</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of particle of interest</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> at specified index</p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of particle of interest</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal notranslate"><span class="pre">Particle</span></code></a> at specified index</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.__len__">
-<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of particles the rotamer contains</p>
-</dd>
-</dl>
+<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of particles the rotamer contains</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetNumSubrotamers">
-<code class="sig-name descname">GetNumSubrotamers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetNumSubrotamers" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of subrotamers</p>
-</dd>
-</dl>
+<code class="descname">GetNumSubrotamers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetNumSubrotamers" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of subrotamers</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.ApplyOnResidue">
-<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">consider_hydrogens=False</em>, <em class="sig-param">new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>res</em>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Iterates over every particle of the active subrotamer and searches for the
according atom in <strong>res</strong>. If it’s present, the position gets reset to the
particle position. If not, a new atom gets added to <strong>res</strong>.
No atoms are removed from <strong>res</strong> in this process.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
-<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
-the sidechain</p></li>
-<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
-default value (“”)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+the sidechain</li>
+<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
+default value (“”)</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
are present in <em>res</em></p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">all_atom</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span></dt>
+<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>all_atom</em>, <em>res_idx</em><span class="sig-paren">)</span></dt>
<dd><p>Set all sidechain atom positions for given residue to the positions of the
particles in the active surotamer.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</p></li>
-<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</li>
+<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_idx</em> is invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res_idx</em> is invalid</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.ToFrameResidue">
-<code class="sig-name descname">ToFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ToFrameResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ToFrameResidue</code><span class="sig-paren">(</span><em>res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ToFrameResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates and returns a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> based on the internal
particles of the active subrotamer.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx passed over to <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> constructor</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The constructed <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx passed over to <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> constructor</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The constructed <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.ToRRMRotamer">
-<code class="sig-name descname">ToRRMRotamer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ToRRMRotamer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ToRRMRotamer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ToRRMRotamer" title="Permalink to this definition">¶</a></dt>
<dd><p>Generates and returns a <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> based on the internal
particles of the active subrotamer. Following parameters of the
returned rotamer get set: probability (probability of the whole FRMRotamer),
@@ -759,216 +851,268 @@ calculated), internal_energy (the internal energy of the whole FRMRotamer)</p>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetSubrotamerDefinition">
-<code class="sig-name descname">GetSubrotamerDefinition</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetSubrotamerDefinition" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of subrotamer</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of particle indices belonging to this
-particular subrotamer</p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</p>
-</dd>
-</dl>
+<code class="descname">GetSubrotamerDefinition</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetSubrotamerDefinition" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of subrotamer</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of particle indices belonging to this
+particular subrotamer</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetInternalEnergyPrefactor">
-<code class="sig-name descname">GetInternalEnergyPrefactor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Prefactor used in internal energy calculation</p>
-</dd>
-</dl>
+<code class="descname">GetInternalEnergyPrefactor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Prefactor used in internal energy calculation</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetInternalEnergy">
-<code class="sig-name descname">GetInternalEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetInternalEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Internal Energy if calculated, 0.0 otherwise</p>
-</dd>
-</dl>
+<code class="descname">GetInternalEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetInternalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Internal Energy if calculated, 0.0 otherwise</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetFrameEnergy">
-<code class="sig-name descname">GetFrameEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetFrameEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns frame energy. This energy can either be manually set or calculated
using a <a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> and the <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a> this rotamer
belongs to.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Frame energy if calculated, 0.0 otherwise</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Frame energy if calculated, 0.0 otherwise</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">GetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetFrameEnergy</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span></dt>
<dd><p>Returns frame energy of specified <strong>index</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of subrotamer you want the frame energy from</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Frame energy if calculated, 0.0 otherwise</p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of subrotamer you want the frame energy from</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Frame energy if calculated, 0.0 otherwise</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if index is invalid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetSelfEnergy">
-<code class="sig-name descname">GetSelfEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetSelfEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Self energy consisting of internal plus frame energy</p>
-</dd>
-</dl>
+<code class="descname">GetSelfEnergy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetSelfEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Self energy consisting of internal plus frame energy</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetTemperature">
-<code class="sig-name descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetTemperature" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>The temperature factor for this rotamer</p>
-</dd>
-</dl>
+<code class="descname">GetTemperature</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetTemperature" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The temperature factor for this rotamer</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetProbability">
-<code class="sig-name descname">GetProbability</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetProbability" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Probability of this rotamer</p>
-</dd>
-</dl>
+<code class="descname">GetProbability</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetProbability" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Probability of this rotamer</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetInternalEnergyPrefactor">
-<code class="sig-name descname">SetInternalEnergyPrefactor</code><span class="sig-paren">(</span><em class="sig-param">prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy prefactor to be set</p>
-</dd>
-</dl>
+<code class="descname">SetInternalEnergyPrefactor</code><span class="sig-paren">(</span><em>prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetInternalEnergyPrefactor" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy prefactor to be set</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetInternalEnergy">
-<code class="sig-name descname">SetInternalEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetInternalEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy to be set</p>
-</dd>
-</dl>
+<code class="descname">SetInternalEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetInternalEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy to be set</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetFrameEnergy">
-<code class="sig-name descname">SetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for full rotamer to be set</p>
-</dd>
-</dl>
+<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for full rotamer to be set</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">SetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em>, <em class="sig-param">index</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for single subrotamer to be set</p></li>
-<li><p><strong>index</strong> – Index of subrotamer</p></li>
+<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>energy</em>, <em>index</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for single subrotamer to be set</li>
+<li><strong>index</strong> – Index of subrotamer</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.AddFrameEnergy">
-<code class="sig-name descname">AddFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for full rotamer to be added</p>
-</dd>
-</dl>
+<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for full rotamer to be added</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">AddFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">energy</em>, <em class="sig-param">index</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for single subrotamer to be added</p></li>
-<li><p><strong>index</strong> – Index of subrotamer</p></li>
+<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>energy</em>, <em>index</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Frame energy for single subrotamer to be added</li>
+<li><strong>index</strong> – Index of subrotamer</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.AddSubrotamerDefinition">
-<code class="sig-name descname">AddSubrotamerDefinition</code><span class="sig-paren">(</span><em class="sig-param">indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.AddSubrotamerDefinition" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of indices defining a subrotamer</p>
-</dd>
-</dl>
+<code class="descname">AddSubrotamerDefinition</code><span class="sig-paren">(</span><em>indices</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.AddSubrotamerDefinition" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of indices defining a subrotamer</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetActiveSubrotamer">
-<code class="sig-name descname">SetActiveSubrotamer</code><span class="sig-paren">(</span><em class="sig-param">idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetActiveSubrotamer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetActiveSubrotamer</code><span class="sig-paren">(</span><em>idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetActiveSubrotamer" title="Permalink to this definition">¶</a></dt>
<dd><p>The provided <strong>idx</strong> relates to the subrotamer definitions added at the
rotamer buildup. This idx controls which subrotamer is used when
<a class="reference internal" href="#promod3.sidechain.FRMRotamer.ApplyOnResidue" title="promod3.sidechain.FRMRotamer.ApplyOnResidue"><code class="xref py py-func docutils literal notranslate"><span class="pre">ApplyOnResidue()</span></code></a>, <a class="reference internal" href="#promod3.sidechain.FRMRotamer.ToFrameResidue" title="promod3.sidechain.FRMRotamer.ToFrameResidue"><code class="xref py py-func docutils literal notranslate"><span class="pre">ToFrameResidue()</span></code></a> or <a class="reference internal" href="#promod3.sidechain.FRMRotamer.ToRRMRotamer" title="promod3.sidechain.FRMRotamer.ToRRMRotamer"><code class="xref py py-func docutils literal notranslate"><span class="pre">ToRRMRotamer()</span></code></a>
gets called. By default, the value is 0 => first added subrotamer
definition gets used.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of subrotamer definition applied on residues</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of subrotamer definition applied on residues</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.GetActiveSubrotamer">
-<code class="sig-name descname">GetActiveSubrotamer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetActiveSubrotamer" title="Permalink to this definition">¶</a></dt>
+<code class="descname">GetActiveSubrotamer</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.GetActiveSubrotamer" title="Permalink to this definition">¶</a></dt>
<dd><p>Get the index of the active subrotamer</p>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetTemperature">
-<code class="sig-name descname">SetTemperature</code><span class="sig-paren">(</span><em class="sig-param">temperature</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetTemperature" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>temperature</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Temperature factor for this rotamer</p>
-</dd>
-</dl>
+<code class="descname">SetTemperature</code><span class="sig-paren">(</span><em>temperature</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetTemperature" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>temperature</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Temperature factor for this rotamer</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamer.SetProbability">
-<code class="sig-name descname">SetProbability</code><span class="sig-paren">(</span><em class="sig-param">probability</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetProbability" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal probability to be set</p>
-</dd>
-</dl>
+<code class="descname">SetProbability</code><span class="sig-paren">(</span><em>probability</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.SetProbability" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal probability to be set</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -978,110 +1122,132 @@ definition gets used.</p>
<h2>Rotamer Groups<a class="headerlink" href="#rotamer-groups" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RRMRotamerGroup">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">rotamers</em>, <em class="sig-param">residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RRMRotamerGroup</code><span class="sig-paren">(</span><em>rotamers</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
<dd><p>The RRMRotamerGroup groups several <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> objects for the same
residue position.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> objects</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Location of residue this <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> objects</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Location of residue this <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>
represents. This index is important when calculating
frame energies to neglect the interactions to frame
-particles of the same residue.</p></li>
+particles of the same residue.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if provided <em>rotamers</em> is empty</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if provided <em>rotamers</em> is empty</p>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.__len__">
-<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of rotamers in group</p>
-</dd>
-</dl>
+<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of rotamers in group</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.__getitem__">
-<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.__getitem__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> at given <em>index</em></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> is invalid</p>
-</dd>
-</dl>
+<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.__getitem__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> at given <em>index</em></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> is invalid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.ApplyOnResidue">
-<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">res</em>, <em class="sig-param">consider_hydrogens=False</em>, <em class="sig-param">new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>index</em>, <em>res</em>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">all_atom</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span></dt>
+<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>index</em>, <em>all_atom</em>, <em>res_idx</em><span class="sig-paren">)</span></dt>
<dd><p>Calls ApplyOnResidue function on rotamer at position <em>index</em></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
-<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
-the sidechain</p></li>
-<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
-default value (“”)</p></li>
-<li><p><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</p></li>
-<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+the sidechain</li>
+<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
+default value (“”)</li>
+<li><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</li>
+<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
are present in <em>res</em> or when <em>index</em> or <em>res_idx</em> are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.Merge">
-<code class="sig-name descname">Merge</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.Merge" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Merge</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.Merge" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds all rotamers in <em>other</em> to current <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.SetFrameEnergy">
-<code class="sig-name descname">SetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates sets the energy of all rotamers in the group towards the
given <strong>frame</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.AddFrameEnergy">
-<code class="sig-name descname">AddFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates adds the energy of all rotamers in the group towards the
given <strong>frame</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThresh">
-<code class="sig-name descname">ApplySelfEnergyThresh</code><span class="sig-paren">(</span><em class="sig-param">thresh=30</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThresh" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplySelfEnergyThresh</code><span class="sig-paren">(</span><em>thresh=30</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThresh" title="Permalink to this definition">¶</a></dt>
<dd><p>Searches rotamer with lowest self energy <em>l_e</em> and deletes all
rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
</dd></dl>
@@ -1090,110 +1256,132 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<dl class="class">
<dt id="promod3.sidechain.FRMRotamerGroup">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">FRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">rotamers</em>, <em class="sig-param">residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">FRMRotamerGroup</code><span class="sig-paren">(</span><em>rotamers</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
<dd><p>The FRMRotamerGroup groups several <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> objects for the same
residue position.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> objects</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Location of residue this <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – A list of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> objects</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Location of residue this <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>
represents. This index is important when calculating
frame energies to neglect the interactions to frame
-particles of the same residue.</p></li>
+particles of the same residue.</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if provided <em>rotamers</em> is empty</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if provided <em>rotamers</em> is empty</p>
+</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.__len__">
-<code class="sig-name descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.__len__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Number of rotamers in group</p>
-</dd>
-</dl>
+<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.__len__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of rotamers in group</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.__getitem__">
-<code class="sig-name descname">__getitem__</code><span class="sig-paren">(</span><em class="sig-param">index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.__getitem__" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> at given <em>index</em></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> is invalid</p>
-</dd>
-</dl>
+<code class="descname">__getitem__</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.__getitem__" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> at given <em>index</em></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>index</em> is invalid</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.ApplyOnResidue">
-<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">res</em>, <em class="sig-param">consider_hydrogens=False</em>, <em class="sig-param">new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>index</em>, <em>res</em>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
<dt>
-<code class="sig-name descname">ApplyOnResidue</code><span class="sig-paren">(</span><em class="sig-param">index</em>, <em class="sig-param">all_atom</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span></dt>
+<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>index</em>, <em>all_atom</em>, <em>res_idx</em><span class="sig-paren">)</span></dt>
<dd><p>Calls ApplyOnResidue function on rotamer at position <em>index</em></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
-<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
-the sidechain</p></li>
-<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
-default value (“”)</p></li>
-<li><p><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</p></li>
-<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
+the sidechain</li>
+<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
+default value (“”)</li>
+<li><strong>all_atom</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Container to which to apply rotamer</li>
+<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index into <em>all_atom</em></li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
are present in <em>res</em> or when <em>index</em> or <em>res_idx</em> are invalid</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.Merge">
-<code class="sig-name descname">Merge</code><span class="sig-paren">(</span><em class="sig-param">other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.Merge" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Merge</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.Merge" title="Permalink to this definition">¶</a></dt>
<dd><p>Adds all rotamers in <em>other</em> to current <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a></p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.SetFrameEnergy">
-<code class="sig-name descname">SetFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates sets the energy of all rotamers in the group towards the
given <strong>frame</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.AddFrameEnergy">
-<code class="sig-name descname">AddFrameEnergy</code><span class="sig-paren">(</span><em class="sig-param">frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>frame</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates adds the energy of all rotamers in the group towards the
given <strong>frame</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>frame</strong> (<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a>) – Frame containing rigid particles</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThresh">
-<code class="sig-name descname">ApplySelfEnergyThresh</code><span class="sig-paren">(</span><em class="sig-param">thresh=30</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThresh" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ApplySelfEnergyThresh</code><span class="sig-paren">(</span><em>thresh=30</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThresh" title="Permalink to this definition">¶</a></dt>
<dd><p>Searches rotamer with lowest self energy <em>l_e</em> and deletes all
rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
</dd></dl>
@@ -1205,7 +1393,6 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -1226,12 +1413,12 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -1248,8 +1435,8 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
<li>Next: <a href="frame.html" title="next chapter">Frame - The Rigid Part</a></li>
</ul></li>
</ul></li>
@@ -1257,33 +1444,27 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
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- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/rotamer.rst.txt"
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 188163de022b7e2fd1ec974874720da82ef954a3..3e5431c2715fae4618854aff7f6ecaed7223de42 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Rotamer Constructor — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Rotamer Constructor — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="rotamer-constructor">
@@ -41,171 +40,187 @@ convenient functionality provided by ProMod3.</p>
<h2>The RotamerConstructor Baseclass<a class="headerlink" href="#the-rotamerconstructor-baseclass" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RotamerConstructor">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerConstructor</code><a class="headerlink" href="#promod3.sidechain.RotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerConstructor</code><a class="headerlink" href="#promod3.sidechain.RotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class that cannot be initialized from Python. It builds
an interface implemented by scoring function specific constructors
(e.g. <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="promod3.sidechain.SCWRL4RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SCWRL4RotamerConstructor</span></code></a>).</p>
<dl class="method">
<dt id="promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">
-<code class="sig-name descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">rot_lib</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em>, <em class="sig-param">probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">all_atom_pos</em>, <em class="sig-param">aa_res_idx</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">rot_lib</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em>, <em class="sig-param">probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd></dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">rot_lib_entries</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em>, <em class="sig-param">probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib_entries</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd></dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em class="sig-param">all_atom_pos</em>, <em class="sig-param">aa_res_idx</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">rot_lib_entries</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em>, <em class="sig-param">probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib_entries</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>All functions are also avaible for their flexible rotamer model counterpart.
=>ConstructFRMRotamerGroup(…) with the same parameters.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</p></li>
-<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</p></li>
-<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
-extract the required backbone atoms</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain.</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li>
+<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</li>
+<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
+extract the required backbone atoms</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain.</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
energy of the sidechain particles towards particles
-representing the own backbone…</p></li>
-<li><p><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a> / <a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a>) – To search for rotamers</p></li>
-<li><p><strong>rot_lib_entries</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – <a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> objects to circumvent the
-direct use of a rotamer library</p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi dihedral angle</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi dihedral angle</p></li>
-<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
-<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
-<li><p><strong>probability_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – For some rotamers, there might be many low
+representing the own backbone…</li>
+<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a> / <a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a>) – To search for rotamers</li>
+<li><strong>rot_lib_entries</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – <a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> objects to circumvent the
+direct use of a rotamer library</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi dihedral angle</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi dihedral angle</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
+<li><strong>probability_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – For some rotamers, there might be many low
probability entries in the library.
The function adds single rotamers to the group until
the cumulative probability of the added rotamers is
-larger or equal <strong>probability_cutoff</strong>.</p></li>
+larger or equal <strong>probability_cutoff</strong>.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>The rotamer group containing all constructed rotamers
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The rotamer group containing all constructed rotamers
with internal energies assigned.</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when not all required backbone
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when not all required backbone
atoms are present in <strong>residue</strong> or not all required atom
positions are set in <strong>all_atom_pos</strong></p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerConstructor.ConstructBackboneFrameResidue">
-<code class="sig-name descname">ConstructBackboneFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructBackboneFrameResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ConstructBackboneFrameResidue</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructBackboneFrameResidue" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">ConstructBackboneFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">all_atom_pos</em>, <em class="sig-param">aa_res_idx</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854 n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="descname">ConstructBackboneFrameResidue</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854 n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>Constructs frame residues only containing backbone atoms (the ones that
don’t show up in a rotamer).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
-<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</p></li>
-<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
-extract the backbone positions</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
+<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
+<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
+extract the backbone positions</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
energy of the sidechain particles towards particles
-representing the own backbone…</p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
-<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
+representing the own backbone…</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
</ul>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when not all required backbone
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when not all required backbone
atoms are present in <strong>residue</strong> or not all required atom
positions are set in <strong>all_atom_pos</strong>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue">
-<code class="sig-name descname">ConstructSidechainFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ConstructSidechainFrameResidue</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">ConstructSidechainFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">all_atom_pos</em>, <em class="sig-param">aa_res_idx</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854 n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<code class="descname">ConstructSidechainFrameResidue</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854 n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>Constructs frame residues only containing sidechain atoms (the ones that
you observe in a rotamer).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
-<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</p></li>
-<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
-extract the backbone positions</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
+<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
+<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
+extract the backbone positions</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal notranslate"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
energy of the sidechain particles towards particles
-representing the own backbone…</p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
-<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
+representing the own backbone…</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
</ul>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when not all required sidechain
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> when not all required sidechain
atoms are present in <strong>residue</strong> or not all required sidechain
atom positions are set in <strong>all_atom_pos</strong>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerConstructor.AssignInternalEnergies">
-<code class="sig-name descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em class="sig-param">rot_group</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
<dd><p>Assigns an internal energy to every rotamer in <em>rot_group</em>, i.e. an energy
value before looking at any structural component of the energy function.
The default implementation simply assigns 0.0 to every rotamer, it’s up
to the energy function specific constructors to override that behaviour.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
-to be assigned</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
-<em>rot_group</em></p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
-<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
+to be assigned</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+<em>rot_group</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -215,14 +230,16 @@ to be assigned</p></li>
<h2>Scoring Function Specific RotamerConstructors<a class="headerlink" href="#scoring-function-specific-rotamerconstructors" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SCWRL4RotamerConstructor</code><span class="sig-paren">(</span><em class="sig-param">cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL4RotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>This object implements the full interface defined in
<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
are parametrized according to the SCWRL4 method. They contain all heavy atoms,
but also the polar hydrogens.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
the cb atom. This flag also affects the construction
of frame residues and controls whether the cb atom
shows up in the backbone frame residues or sidechain
@@ -231,34 +248,39 @@ This is useful when you want to represent ALA or
GLY with actual rotamers, but be aware of increased
runtime. This flag can be set to False for most
modeling applications and you just don’t generate
-any rotamers for ALA and GLY.</p>
-</dd>
-</dl>
+any rotamers for ALA and GLY.</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue">
-<code class="sig-name descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">residue</em>, <em class="sig-param">residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
This can be useful to mark a region occupied by a ligand. Note, that
there won’t be any parametrization of hbonds in this function. All heavy
atoms of the residue will be represented as carbons and hydrogens are
skipped.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
-construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">
-<code class="sig-name descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em class="sig-param">residue</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em>, <em>comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms based on the passed compounds library.
This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal notranslate"><span class="pre">ConstructFrameResidue()</span></code></a>,
@@ -268,28 +290,32 @@ Only non-hydrogen atoms are considered and by default added as uncharged
carbons. Special treatment is used for atoms known by the compounds library
in the following cases:</p>
<ul class="simple">
-<li><p>carbons, nitrogens, oxygens and sulfur particles use an appropriate type
-as in the <code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainParticle</span></code> enumeration</p></li>
-<li><p>carbonyls are added as charged oxygen particles as hbond acceptors</p></li>
+<li>carbons, nitrogens, oxygens and sulfur particles use an appropriate type
+as in the <code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainParticle</span></code> enumeration</li>
+<li>carbonyls are added as charged oxygen particles as hbond acceptors</li>
</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
-construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</p></li>
-<li><p><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
+<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.AssignInternalEnergies">
-<code class="sig-name descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em class="sig-param">rot_group</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a>.
Takes the rotamer group and assigns every single rotamer its internal
energy based on the probabilistic approach used by SCWRL4.
@@ -298,34 +324,40 @@ rotamer specific and max_p is the maximum probablity of any of the rotamers
in <strong>rot_group</strong>. If you construct a rotamer group by the
ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
is already called at construction and the energies are properly assigned.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
-to be assigned</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
-<em>rot_group</em></p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
-<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
+to be assigned</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+<em>rot_group</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.sidechain.SCWRL3RotamerConstructor">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SCWRL3RotamerConstructor</code><span class="sig-paren">(</span><em class="sig-param">cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL3RotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>This object implements the full interface defined in
<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
are parametrized according to the SCWRL3 method. They contain only heavy atoms.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
the cb atom. This flag also affects the construction
of frame residues and controls whether the cb atom
shows up in the backbone frame residues or sidechain
@@ -334,12 +366,13 @@ This is useful when you want to represent ALA or
GLY with actual rotamers, but be aware of increased
runtime. This flag can be set to False for most
modeling applications and you just don’t generate
-any rotamers for ALA and GLY.</p>
-</dd>
-</dl>
+any rotamers for ALA and GLY.</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies">
-<code class="sig-name descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em class="sig-param">rot_group</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a>.
Takes the rotamer group and assigns every single rotamer its internal
energy based on the probabilistic approach used by SCWRL3.
@@ -348,34 +381,40 @@ rotamer specific and max_p is the maximum probablity of any of the rotamers
in <strong>rot_group</strong>. If you construct a rotamer group by the
ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
is already called at construction and the energies are properly assigned.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
-to be assigned</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
-<em>rot_group</em></p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
-<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
+to be assigned</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+<em>rot_group</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="promod3.sidechain.VINARotamerConstructor">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">VINARotamerConstructor</code><span class="sig-paren">(</span><em class="sig-param">cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">VINARotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>This object implements the full interface defined in
<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
are parametrized according to the VINA method. They contain only heavy atoms.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
the cb atom. This flag also affects the construction
of frame residues and controls whether the cb atom
shows up in the backbone frame residues or sidechain
@@ -384,12 +423,13 @@ This is useful when you want to represent ALA or
GLY with actual rotamers, but be aware of increased
runtime. This flag can be set to False for most
modeling applications and you just don’t generate
-any rotamers for ALA and GLY.</p>
-</dd>
-</dl>
+any rotamers for ALA and GLY.</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies">
-<code class="sig-name descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em class="sig-param">rot_group</em>, <em class="sig-param">id</em>, <em class="sig-param">residue_index</em><span class="optional">[</span>, <em class="sig-param">phi = -1.0472</em>, <em class="sig-param">psi = -0.7854</em>, <em class="sig-param">n_ter = False</em>, <em class="sig-param">c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerConstructor</span></code></a>.
Takes the rotamer group and assigns every single rotamer its internal
energy based on the probabilistic approach used by SCWRL3/SCWRL4.
@@ -398,26 +438,30 @@ rotamer specific and max_p is the maximum probablity of any of the rotamers
in <strong>rot_group</strong>. If you construct a rotamer group by the
ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
is already called at construction and the energies are properly assigned.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
-to be assigned</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</p></li>
-<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
-<em>rot_group</em></p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</p></li>
-<li><p><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</p></li>
-<li><p><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>rot_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a> / <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>) – containing all rotamers for which internal energies have
+to be assigned</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The index of the residue which is represented by
+<em>rot_group</em></li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The dihedral angle of the current residue</li>
+<li><strong>n_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is n-terminal</li>
+<li><strong>c_ter</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Whether the residue is c-terminal</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">
-<code class="sig-name descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>res</em>, <em>res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms. It is important that the residue has
proper bonds assigned, as they influence the atom typing procedure.
@@ -427,10 +471,10 @@ Alternatively you can assign generic properties to oxygens and nitrogens
to circumvent the requirement of hydrogens. This is further described for
the case of oxygen.</p>
<ul class="simple">
-<li><p>Carbon is assigned C_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a> if its only
+<li>Carbon is assigned C_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a> if its only
bound to other carbons or hydrogens (and deuterium). All other carbons are
-assigned C_P_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</p></li>
-<li><p>In case of oxygen, the heuristic first checks for set generic properties.
+assigned C_P_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>In case of oxygen, the heuristic first checks for set generic properties.
If the atom has the bool properties “is_hbond_acceptor” AND
“is_hbond_donor” set, it decides between the according oxygen types
in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>. If the generic properties are not set,
@@ -439,68 +483,76 @@ if its bound to a hydrogen (or deuterium). You can set the generic
properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
at.SetBoolProp(“is_hbond_donor”, False) and
at.SetBoolProp(“is_hbond_acceptor”, True). An oxygen with those
-generic properties is assigned O_A_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</p></li>
-<li><p>In case of nitrogen, the heuristic again first checks for set generic
+generic properties is assigned O_A_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>In case of nitrogen, the heuristic again first checks for set generic
properties.
If the atom has the bool properties “is_hbond_acceptor” AND
“is_hbond_donor” set, it decides between the according nitrogen types
in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>. If not, nitrogen is expected to be an
hbond donor if it is bound to a hydrogen (or deuterium) and
an hbond acceptor if it is bound to less than 3 other atoms (sounds
-horrible but works surprisingly well).</p></li>
-<li><p>Atoms of elements [“MG”, “MN”, “ZN”, “CA”, “FE”] are assigned
-M_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</p></li>
-<li><p>Atoms of elements [“S”, “P”, “F”, “CL”, “BR”, “I”] are assigned their
-corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</p></li>
-<li><p>All other atoms are neglected and not added to the returned
-<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</p></li>
+horrible but works surprisingly well).</li>
+<li>Atoms of elements [“MG”, “MN”, “ZN”, “CA”, “FE”] are assigned
+M_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>Atoms of elements [“S”, “P”, “F”, “CL”, “BR”, “I”] are assigned their
+corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>All other atoms are neglected and not added to the returned
+<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</li>
</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
-<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p></li>
-<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index that is set in <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></li>
+<li><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index that is set in <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></li>
</ul>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic">
-<code class="sig-name descname">ConstructRRMRotamerHeuristic</code><span class="sig-paren">(</span><em class="sig-param">res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ConstructRRMRotamerHeuristic</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
<dd><p>Construct a <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> with the atom typing heuristic
as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
-<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic">
-<code class="sig-name descname">ConstructFRMRotamerHeuristic</code><span class="sig-paren">(</span><em class="sig-param">res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
+<code class="descname">ConstructFRMRotamerHeuristic</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
<dd><p>Construct a <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> with the atom typing heuristic
as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method. The
constructed <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a> only contains one subrotamer that
contains the atoms from <em>residue</em>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
-<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -510,7 +562,6 @@ contains the atoms from <em>residue</em>.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -531,12 +582,12 @@ contains the atoms from <em>residue</em>.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
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-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -553,7 +604,7 @@ contains the atoms from <em>residue</em>.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="frame.html" title="previous chapter">Frame - The Rigid Part</a></li>
<li>Next: <a href="rotamer_lib.html" title="next chapter">Rotamer Library</a></li>
</ul></li>
@@ -562,33 +613,27 @@ contains the atoms from <em>residue</em>.</p>
</ul>
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- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
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+ <input type="text" name="q" />
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+ <input type="hidden" name="check_keywords" value="yes" />
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+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
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<a href="../_sources/sidechain/rotamer_constructor.rst.txt"
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 382c4eb5bbba3e9620b278c6b47bd2ce09aebba7..6dd76800bccb8370dbcd92c5bda8d59d0b3edeb4 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Rotamer Library — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Rotamer Library — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="rotamer-library">
@@ -53,95 +52,103 @@ mode you can get the rotamers out of it or dump it to disk.</p>
<h2>The Non Backbone Dependent Rotamer Library<a class="headerlink" href="#the-non-backbone-dependent-rotamer-library" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RotamerLib">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerLib</code><a class="headerlink" href="#promod3.sidechain.RotamerLib" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerLib</code><a class="headerlink" href="#promod3.sidechain.RotamerLib" title="Permalink to this definition">¶</a></dt>
<dd><p>Non backbone dependent rotamer library</p>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.sidechain.RotamerLib.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.sidechain.RotamerLib.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.sidechain.RotamerLib.Save" title="promod3.sidechain.RotamerLib.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.sidechain.RotamerLib.SavePortable" title="promod3.sidechain.RotamerLib.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A rotamer library</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A rotamer library</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLib</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLib.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.sidechain.RotamerLib.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLib.AddRotamer">
-<code class="sig-name descname">AddRotamer</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">rotamer</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.AddRotamer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</p></li>
-<li><p><strong>rotamer</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</p></li>
+<code class="descname">AddRotamer</code><span class="sig-paren">(</span><em>id</em>, <em>rotamer</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.AddRotamer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</li>
+<li><strong>rotamer</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the library is already static</p>
-</dd>
-</dl>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if the library is already static</p>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLib.QueryLib">
-<code class="sig-name descname">QueryLib</code><span class="sig-paren">(</span><em class="sig-param">id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.QueryLib" title="Permalink to this definition">¶</a></dt>
+<code class="descname">QueryLib</code><span class="sig-paren">(</span><em>id</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.QueryLib" title="Permalink to this definition">¶</a></dt>
<dd><p>The query function follows following strategies in case of
special <em>id</em> requests.</p>
<ul class="simple">
-<li><p>if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure</p></li>
-<li><p>if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure</p></li>
-<li><p>if id = CYH (“free” CYS) try to find CYH, fallback to CYS in case of failure</p></li>
-<li><p>if id = CYD (“disulfid” CYS) try to find CYD, fallback to CYS in case of failure</p></li>
-<li><p>if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure</p></li>
-<li><p>if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure</p></li>
+<li>if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure</li>
+<li>if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure</li>
+<li>if id = CYH (“free” CYS) try to find CYH, fallback to CYS in case of failure</li>
+<li>if id = CYD (“disulfid” CYS) try to find CYD, fallback to CYS in case of failure</li>
+<li>if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure</li>
+<li>if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure</li>
</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> of nonzero
-probability sorted by their probability</p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no entries for <em>id</em> can be
-found</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> of nonzero
+probability sorted by their probability</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no entries for <em>id</em> can be
+found</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLib.MakeStatic">
-<code class="sig-name descname">MakeStatic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.MakeStatic" title="Permalink to this definition">¶</a></dt>
+<code class="descname">MakeStatic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.MakeStatic" title="Permalink to this definition">¶</a></dt>
<dd><p>Once all rotamers are added, the library can be made static to become readable
and ready for io.</p>
</dd></dl>
@@ -153,85 +160,95 @@ and ready for io.</p>
<h2>The Backbone Dependent Rotamer Library<a class="headerlink" href="#the-backbone-dependent-rotamer-library" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.BBDepRotamerLib">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">BBDepRotamerLib</code><span class="sig-paren">(</span><em class="sig-param">phi_bins</em>, <em class="sig-param">psi_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">BBDepRotamerLib</code><span class="sig-paren">(</span><em>phi_bins</em>, <em>psi_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib" title="Permalink to this definition">¶</a></dt>
<dd><p>Backbone dependent rotamer library</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>phi_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – number of bins for phi backbone dihedral</p></li>
-<li><p><strong>psi_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – number of bins for psi backbone dihedral</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>phi_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – number of bins for phi backbone dihedral</li>
+<li><strong>psi_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – number of bins for psi backbone dihedral</li>
</ul>
-</dd>
-</dl>
-<dl class="method">
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.sidechain.BBDepRotamerLib.Load">
-<em class="property">static </em><code class="sig-name descname">Load</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.sidechain.BBDepRotamerLib.LoadPortable">
-<em class="property">static </em><code class="sig-name descname">LoadPortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.LoadPortable" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.Save" title="promod3.sidechain.BBDepRotamerLib.Save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Save()</span></code></a> (optimized for fast
reading) / portable file generated with <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.SavePortable" title="promod3.sidechain.BBDepRotamerLib.SavePortable"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SavePortable()</span></code></a> (slower but
less machine-dependent).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>A rotamer library</p>
-</dd>
-<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a></p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file from which to load.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A rotamer library</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal notranslate"><span class="pre">BBDepRotamerLib</span></code></a></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.Save">
-<code class="sig-name descname">Save</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.Save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.Save" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.sidechain.BBDepRotamerLib.SavePortable">
-<code class="sig-name descname">SavePortable</code><span class="sig-paren">(</span><em class="sig-param">filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</p>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Path to the file where it will be saved.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if file cannot be opened.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.AddRotamer">
-<code class="sig-name descname">AddRotamer</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">r1</em>, <em class="sig-param">r2</em>, <em class="sig-param">r3</em>, <em class="sig-param">r4</em>, <em class="sig-param">phi_bin</em>, <em class="sig-param">psi_bin</em>, <em class="sig-param">rotamer</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.AddRotamer" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</p></li>
-<li><p><strong>r1</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi1</p></li>
-<li><p><strong>r2</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi2</p></li>
-<li><p><strong>r3</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi3</p></li>
-<li><p><strong>r4</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi4</p></li>
-<li><p><strong>phi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Phi backbone dihedral description</p></li>
-<li><p><strong>psi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Psi backbone dihedral description</p></li>
-<li><p><strong>rotamer</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</p></li>
+<code class="descname">AddRotamer</code><span class="sig-paren">(</span><em>id</em>, <em>r1</em>, <em>r2</em>, <em>r3</em>, <em>r4</em>, <em>phi_bin</em>, <em>psi_bin</em>, <em>rotamer</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.AddRotamer" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</li>
+<li><strong>r1</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi1</li>
+<li><strong>r2</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi2</li>
+<li><strong>r3</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi3</li>
+<li><strong>r4</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Configuration of chi4</li>
+<li><strong>phi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Phi backbone dihedral description</li>
+<li><strong>psi_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Psi backbone dihedral description</li>
+<li><strong>rotamer</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</li>
</ul>
-</dd>
-<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if an invalid backbone angle bin
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if an invalid backbone angle bin
is given or when the library is already static.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.QueryLib">
-<code class="sig-name descname">QueryLib</code><span class="sig-paren">(</span><em class="sig-param">id</em>, <em class="sig-param">phi</em>, <em class="sig-param">psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.QueryLib" title="Permalink to this definition">¶</a></dt>
+<code class="descname">QueryLib</code><span class="sig-paren">(</span><em>id</em>, <em>phi</em>, <em>psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.QueryLib" title="Permalink to this definition">¶</a></dt>
<dd><p>The returned rotamers are either directly returned in the form as they are
added to the library or can be interpolated.
In the first option, <em>phi</em> and <em>psi</em> simply get transformed to the
@@ -245,62 +262,72 @@ This behaviour can be controlled with <a class="reference internal" href="#promo
The query function follows following strategies in case of
special <em>id</em> requests.</p>
<ul class="simple">
-<li><p>if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure</p></li>
-<li><p>if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure</p></li>
-<li><p>if id = CYH (“free” CYS) try to find CYH, fallback to CYS in case of failure</p></li>
-<li><p>if id = CYD (“disulfid” CYS) try to find CYD, fallback to CYS in case of failure</p></li>
-<li><p>if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure</p></li>
-<li><p>if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure</p></li>
+<li>if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure</li>
+<li>if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure</li>
+<li>if id = CYH (“free” CYS) try to find CYH, fallback to CYS in case of failure</li>
+<li>if id = CYD (“disulfid” CYS) try to find CYD, fallback to CYS in case of failure</li>
+<li>if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure</li>
+<li>if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure</li>
</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</p></li>
-<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle in range [-pi,pi[</p></li>
-<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle in range [-pi,pi[</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle in range [-pi,pi[</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle in range [-pi,pi[</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> of nonzero
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> of nonzero
probability for given phi/psi pair sorted by their probability</p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no entries for <em>id</em> can be
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no entries for <em>id</em> can be
found</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.MakeStatic">
-<code class="sig-name descname">MakeStatic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.MakeStatic" title="Permalink to this definition">¶</a></dt>
+<code class="descname">MakeStatic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.MakeStatic" title="Permalink to this definition">¶</a></dt>
<dd><p>Once all rotamers are added, the library can be made static to become readable
and ready for io. Several things get checked during this process</p>
<ul class="simple">
-<li><p>For every phi/psi bin combination of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>,
-the same number of rotamers must have been added</p></li>
-<li><p>All configuration combinations of the added rotamers in one phi/psi bin
-of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a> must be unique</p></li>
-<li><p>The configuration combinations of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a> must
-be consistent across all phi/psi bins</p></li>
+<li>For every phi/psi bin combination of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>,
+the same number of rotamers must have been added</li>
+<li>All configuration combinations of the added rotamers in one phi/psi bin
+of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a> must be unique</li>
+<li>The configuration combinations of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a> must
+be consistent across all phi/psi bins</li>
</ul>
-<dl class="field-list simple">
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if one of the points above is
-not fulfilled</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if one of the points above is
+not fulfilled</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.BBDepRotamerLib.SetInterpolate">
-<code class="sig-name descname">SetInterpolate</code><span class="sig-paren">(</span><em class="sig-param">interpolate</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.SetInterpolate" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>interpolate</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Controls behaviour when <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.QueryLib" title="promod3.sidechain.BBDepRotamerLib.QueryLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">QueryLib()</span></code></a>
-gets called</p>
-</dd>
-</dl>
+<code class="descname">SetInterpolate</code><span class="sig-paren">(</span><em>interpolate</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.SetInterpolate" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>interpolate</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Controls behaviour when <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib.QueryLib" title="promod3.sidechain.BBDepRotamerLib.QueryLib"><code class="xref py py-meth docutils literal notranslate"><span class="pre">QueryLib()</span></code></a>
+gets called</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -315,225 +342,250 @@ convenience functions. For analytical purposes they provide some comparison
functionalities.</p>
<dl class="class">
<dt id="promod3.sidechain.RotamerLibEntry">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerLibEntry</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerLibEntry</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="class">
<dt>
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">RotamerLibEntry</code><span class="sig-paren">(</span><em class="sig-param">p</em>, <em class="sig-param">chi1</em>, <em class="sig-param">chi2</em>, <em class="sig-param">chi3</em>, <em class="sig-param">chi4</em>, <em class="sig-param">sig1</em>, <em class="sig-param">sig2</em>, <em class="sig-param">sig3</em>, <em class="sig-param">sig4</em><span class="sig-paren">)</span></dt>
-<dd><dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>p</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Probability of rotamer</p></li>
-<li><p><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi1 dihedral in range [-pi,pi[</p></li>
-<li><p><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi2 dihedral in range [-pi,pi[</p></li>
-<li><p><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi3 dihedral in range [-pi,pi[</p></li>
-<li><p><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi4 dihedral in range [-pi,pi[</p></li>
-<li><p><strong>sig1</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi1 dihedral</p></li>
-<li><p><strong>sig2</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi2 dihedral</p></li>
-<li><p><strong>sig3</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi3 dihedral</p></li>
-<li><p><strong>sig4</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi4 dihedral</p></li>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerLibEntry</code><span class="sig-paren">(</span><em>p</em>, <em>chi1</em>, <em>chi2</em>, <em>chi3</em>, <em>chi4</em>, <em>sig1</em>, <em>sig2</em>, <em>sig3</em>, <em>sig4</em><span class="sig-paren">)</span></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>p</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Probability of rotamer</li>
+<li><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi1 dihedral in range [-pi,pi[</li>
+<li><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi2 dihedral in range [-pi,pi[</li>
+<li><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi3 dihedral in range [-pi,pi[</li>
+<li><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Chi4 dihedral in range [-pi,pi[</li>
+<li><strong>sig1</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi1 dihedral</li>
+<li><strong>sig2</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi2 dihedral</li>
+<li><strong>sig3</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi3 dihedral</li>
+<li><strong>sig4</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Standard deviation for Chi4 dihedral</li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
<p><strong>Attributes:</strong></p>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.probability">
-<code class="sig-name descname">probability</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.probability" title="Permalink to this definition">¶</a></dt>
+<code class="descname">probability</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.probability" title="Permalink to this definition">¶</a></dt>
<dd><p>probability of rotamer</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.chi1">
-<code class="sig-name descname">chi1</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi1" title="Permalink to this definition">¶</a></dt>
+<code class="descname">chi1</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi1" title="Permalink to this definition">¶</a></dt>
<dd><p>Chi1 dihedral in range [-pi,pi[, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.chi2">
-<code class="sig-name descname">chi2</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi2" title="Permalink to this definition">¶</a></dt>
+<code class="descname">chi2</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi2" title="Permalink to this definition">¶</a></dt>
<dd><p>Chi2 dihedral in range [-pi,pi[, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.chi3">
-<code class="sig-name descname">chi3</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi3" title="Permalink to this definition">¶</a></dt>
+<code class="descname">chi3</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi3" title="Permalink to this definition">¶</a></dt>
<dd><p>Chi3 dihedral in range [-pi,pi[, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.chi4">
-<code class="sig-name descname">chi4</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi4" title="Permalink to this definition">¶</a></dt>
+<code class="descname">chi4</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.chi4" title="Permalink to this definition">¶</a></dt>
<dd><p>Chi4 dihedral in range [-pi,pi[, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.sig1">
-<code class="sig-name descname">sig1</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig1" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sig1</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig1" title="Permalink to this definition">¶</a></dt>
<dd><p>Standard deviation of Chi1 Dihedral, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.sig2">
-<code class="sig-name descname">sig2</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig2" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sig2</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig2" title="Permalink to this definition">¶</a></dt>
<dd><p>Standard deviation of Chi2 Dihedral, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.sig3">
-<code class="sig-name descname">sig3</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig3" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sig3</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig3" title="Permalink to this definition">¶</a></dt>
<dd><p>Standard deviation of Chi3 Dihedral, NaN if not defined</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.sidechain.RotamerLibEntry.sig4">
-<code class="sig-name descname">sig4</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig4" title="Permalink to this definition">¶</a></dt>
+<code class="descname">sig4</code><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.sig4" title="Permalink to this definition">¶</a></dt>
<dd><p>Standard deviation of Chi4 Dihedral, NaN if not defined</p>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.sidechain.RotamerLibEntry.FromResidue">
-<em class="property">static </em><code class="sig-name descname">FromResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.FromResidue" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">FromResidue</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.FromResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> from the given <em>res</em>.
The function tries to automatically identify the <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a> based
on the residue name. The probability and standard deviations are set to 0.0,
all not required chi angles with their corresponding standard deviations to
NaN.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if residue name cannot be
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if residue name cannot be
translated to <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a> or when not all required atoms
-are present in <em>res</em>.</p>
-</dd>
-</dl>
+are present in <em>res</em>.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt>
-<em class="property">static </em><code class="sig-name descname">FromResidue</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">id</em><span class="sig-paren">)</span></dt>
+<em class="property">static </em><code class="descname">FromResidue</code><span class="sig-paren">(</span><em>res</em>, <em>id</em><span class="sig-paren">)</span></dt>
<dd><p>Creates a <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> from the given <em>res</em>.
The probability gets set to zero and the standard deviations to 0.
All not required chi angles with their corresponding standard deviations
are NaN.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p>
-</dd>
-<dt class="field-odd">Raises</dt>
-<dd class="field-odd"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required atoms are
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if not all required atoms are
present in <em>res</em>.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLibEntry.IsSimilar">
-<code class="sig-name descname">IsSimilar</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">thresh</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.IsSimilar" title="Permalink to this definition">¶</a></dt>
+<code class="descname">IsSimilar</code><span class="sig-paren">(</span><em>other</em>, <em>thresh</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.IsSimilar" title="Permalink to this definition">¶</a></dt>
<dd><p>Compares two RotamerLibEntries for their similarity in dihedral angles.
The function goes from chi1 to chi4 and checks one after the other
for similarity. The function doesn’t know the identity of the entries
and can therefore not specifically treat symmetric rotamers
(TYR,PHE,ASP,GLU) or rotamers with ambiguous naming in general.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</p></li>
-<li><p><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
-considered similar</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</li>
+<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
+considered similar</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether the two entries have the same
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether the two entries have the same
amount of defined chi angles (not NaN) and whether
they are within the specified threshold.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">IsSimilar</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">thresh</em>, <em class="sig-param">id</em><span class="sig-paren">)</span></dt>
+<code class="descname">IsSimilar</code><span class="sig-paren">(</span><em>other</em>, <em>thresh</em>, <em>id</em><span class="sig-paren">)</span></dt>
<dd><p>Compares two RotamerLibEntries for their similarity in dihedral angles.
The function goes from chi1 to chi4 and checks one after the other
for similarity. Sidechains with ambigous naming that are symmetric
(TYR,PHE,ASP,GLU) get treated specifically. E.g. in case of aspartate,
the chi2 is checked for its actual value, but also for its flipped state.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</p></li>
-<li><p><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
-considered similar</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</li>
+<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
+considered similar</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether the two entries have the same
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether the two entries have the same
amount of defined chi angles (not NaN) and whether
they are within the specified threshold.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.RotamerLibEntry.SimilarDihedral">
-<code class="sig-name descname">SimilarDihedral</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">dihedral_idx</em>, <em class="sig-param">thresh</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.SimilarDihedral" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SimilarDihedral</code><span class="sig-paren">(</span><em>other</em>, <em>dihedral_idx</em>, <em>thresh</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.SimilarDihedral" title="Permalink to this definition">¶</a></dt>
<dd><p>Compares a specific dihedral angle.
The function doesn’t know the identity of the entries and can therefore
not specifically treat symmetric rotamers
(TYR,PHE,ASP,GLU) or rotamers with ambiguous naming in general.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</p></li>
-<li><p><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the dihedral to be checked
-(0 for chi1, 3 for chi4)</p></li>
-<li><p><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
-considered similar</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</li>
+<li><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the dihedral to be checked
+(0 for chi1, 3 for chi4)</li>
+<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
+considered similar</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether both dihedrals are defined
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether both dihedrals are defined
(not NaN) and within the specified threshold</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt>
-<code class="sig-name descname">SimilarDihedral</code><span class="sig-paren">(</span><em class="sig-param">other</em>, <em class="sig-param">dihedral_idx</em>, <em class="sig-param">thresh</em>, <em class="sig-param">id</em><span class="sig-paren">)</span></dt>
+<code class="descname">SimilarDihedral</code><span class="sig-paren">(</span><em>other</em>, <em>dihedral_idx</em>, <em>thresh</em>, <em>id</em><span class="sig-paren">)</span></dt>
<dd><p>Compares a specific dihedral angle.
Symmetric sidechains with ambigous naming (TYR,PHE,ASP,GLU)
get treated specifically. E.g. in case of aspartate, the chi2 is checked
for its actual value, but also for its flipped state.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</p></li>
-<li><p><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the dihedral to be checked
-(0 for chi1, 3 for chi4)</p></li>
-<li><p><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
-considered similar</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – The Entry you want to compare with</li>
+<li><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of the dihedral to be checked
+(0 for chi1, 3 for chi4)</li>
+<li><strong>thresh</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The max difference between two dihedrals to be
+considered similar</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether both dihedrals are defined
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a> Whether both dihedrals are defined
(not NaN) and within the specified threshold</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -548,54 +600,60 @@ The non-rotameric ones behave differently. ProMod3 offers some functionality
to estimate those configurations.</p>
<dl class="class">
<dt id="promod3.sidechain.DihedralConfiguration">
-<em class="property">class </em><code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">DihedralConfiguration</code><a class="headerlink" href="#promod3.sidechain.DihedralConfiguration" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">DihedralConfiguration</code><a class="headerlink" href="#promod3.sidechain.DihedralConfiguration" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the possible sidechain dihedral configurations</p>
<table class="hlist"><tr><td><ul class="simple">
-<li><p>TRANS - Trans configuration (120 < angle < -120)</p></li>
-<li><p>GAUCHE_PLUS - Gauche+ configuration (0 < angle < 120)</p></li>
-<li><p>GAUCHE_MINUS - Gauce- configuration (-120 < angle < 0)</p></li>
-<li><p>NON_ROTAMERIC - Dihedral without SP3-SP3 bond</p></li>
-<li><p>INVALID - Invalid configuration, e.g. chi3 of ALA (doesnt exist…)</p></li>
+<li>TRANS - Trans configuration (120 < angle < -120)</li>
+<li>GAUCHE_PLUS - Gauche+ configuration (0 < angle < 120)</li>
+<li>GAUCHE_MINUS - Gauce- configuration (-120 < angle < 0)</li>
+<li>NON_ROTAMERIC - Dihedral without SP3-SP3 bond</li>
+<li>INVALID - Invalid configuration, e.g. chi3 of ALA (doesnt exist…)</li>
</ul>
</td></tr></table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.GetRotamericConfiguration">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetRotamericConfiguration</code><span class="sig-paren">(</span><em class="sig-param">angle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetRotamericConfiguration" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetRotamericConfiguration</code><span class="sig-paren">(</span><em>angle</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetRotamericConfiguration" title="Permalink to this definition">¶</a></dt>
<dd><p>Evaluates the <em>angle</em> according to the ranges specified for
<a class="reference internal" href="#promod3.sidechain.DihedralConfiguration" title="promod3.sidechain.DihedralConfiguration"><code class="xref py py-class docutils literal notranslate"><span class="pre">DihedralConfiguration</span></code></a>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle to be evaluated</p>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>TRANS, GAUCHE_PLUS or GAUCHE_MINUS.
-INVALID if <em>angle</em> is NaN.</p>
-</dd>
-</dl>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle to be evaluated</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">TRANS, GAUCHE_PLUS or GAUCHE_MINUS.
+INVALID if <em>angle</em> is NaN.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.GetDihedralConfiguration">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">GetDihedralConfiguration</code><span class="sig-paren">(</span><em class="sig-param">entry</em>, <em class="sig-param">id</em>, <em class="sig-param">dihedral_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetDihedralConfiguration" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">GetDihedralConfiguration</code><span class="sig-paren">(</span><em>entry</em>, <em>id</em>, <em>dihedral_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.GetDihedralConfiguration" title="Permalink to this definition">¶</a></dt>
<dd><p>Estimates configuration of a sidechain dihedral angle in a specific
<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a> with the knowledge of its identity. This allows
to also return NON_ROTAMERIC (e.g. chi2 for ASN).</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>entry</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – Sidechain dihedral angle comes from here</p></li>
-<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer</p></li>
-<li><p><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Specifies angle (0 => chi1, …, 3 => chi4)</p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>entry</strong> (<a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a>) – Sidechain dihedral angle comes from here</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer</li>
+<li><strong>dihedral_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Specifies angle (0 => chi1, …, 3 => chi4)</li>
</ul>
-</dd>
-<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>Result of <a class="reference internal" href="#promod3.sidechain.GetRotamericConfiguration" title="promod3.sidechain.GetRotamericConfiguration"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetRotamericConfiguration()</span></code></a> if specified
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Result of <a class="reference internal" href="#promod3.sidechain.GetRotamericConfiguration" title="promod3.sidechain.GetRotamericConfiguration"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetRotamericConfiguration()</span></code></a> if specified
angle is Rotameric, NON_ROTAMERIC if specified angle is
valid and non rotameric, INVALID otherwise.</p>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
@@ -603,7 +661,6 @@ valid and non rotameric, INVALID otherwise.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -624,12 +681,12 @@ valid and non rotameric, INVALID otherwise.</p>
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -646,7 +703,7 @@ valid and non rotameric, INVALID otherwise.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="rotamer_constructor.html" title="previous chapter">Rotamer Constructor</a></li>
<li>Next: <a href="graph.html" title="next chapter">Rotamer Graph</a></li>
</ul></li>
@@ -655,33 +712,27 @@ valid and non rotameric, INVALID otherwise.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
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+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/rotamer_lib.rst.txt"
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index beaa0201cd26c3269fe78e36e5acbb20da232c9b..241f685e465a346f918d7686995e4e0c4d5b4194 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Subrotamer Optimization — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Subrotamer Optimization — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="subrotamer-optimization">
@@ -51,31 +50,34 @@ that you might want to prefer the currently active subrotamers if no
pairwise energies to other rotamers are observed.</p>
<dl class="method">
<dt id="promod3.sidechain.SubrotamerOptimizer">
-<code class="sig-prename descclassname">promod3.sidechain.</code><code class="sig-name descname">SubrotamerOptimizer</code><span class="sig-paren">(</span><em class="sig-param">rotamers, [active_internal_energy=-2.0, inactive_internal_energy=0.0, max_complexity=100000000, initial_epsilon=0.02</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SubrotamerOptimizer" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">SubrotamerOptimizer</code><span class="sig-paren">(</span><em>rotamers, [active_internal_energy=-2.0, inactive_internal_energy=0.0, max_complexity=100000000, initial_epsilon=0.02</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SubrotamerOptimizer" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes the <strong>rotamers</strong> of type <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>, converts all their
subrotamers into rigid rotamers, solves the sidechain reconstruction problem
and assigns the ideal subrotamers as active in the input <strong>rotamers</strong>.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – The rotamers to be optimized</p></li>
-<li><p><strong>active_internal_energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy that gets assigned to all
-currently active subrotamers</p></li>
-<li><p><strong>inactive_internal_energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy that gets assigned to all
-currently inactive subrotamers</p></li>
-<li><p><strong>max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max complexity of the internal <a class="reference internal" href="graph.html#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerGraph</span></code></a></p></li>
-<li><p><strong>initial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Epsilon value controlling the pruning of
-internal <a class="reference internal" href="graph.html#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerGraph</span></code></a></p></li>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – The rotamers to be optimized</li>
+<li><strong>active_internal_energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy that gets assigned to all
+currently active subrotamers</li>
+<li><strong>inactive_internal_energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Internal energy that gets assigned to all
+currently inactive subrotamers</li>
+<li><strong>max_complexity</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max complexity of the internal <a class="reference internal" href="graph.html#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerGraph</span></code></a></li>
+<li><strong>initial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Epsilon value controlling the pruning of
+internal <a class="reference internal" href="graph.html#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerGraph</span></code></a></li>
</ul>
-</dd>
-</dl>
+</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</div>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -96,12 +98,12 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
<li class="toctree-l2"><a class="reference internal" href="../actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="../container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="../modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2 current"><a class="reference internal" href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="../core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="../user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -118,42 +120,36 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li><a href="index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li><a href="index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li>Previous: <a href="loading.html" title="previous chapter">Loading Rotamer Libraries</a></li>
- <li>Next: <a href="../scoring/index.html" title="next chapter"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+ <li>Next: <a href="../scoring/index.html" title="next chapter"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
</ul></li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
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<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/subrotamer_optimizer.rst.txt"
diff --git a/doc/html/user_contributions.html b/doc/html/user_contributions.html
index 3bd565408368560b2ee4457d62ac1f4ea9a628a2..44fd3f6c307cb7180f9da374afbe04099aeb5b42 100644
--- a/doc/html/user_contributions.html
+++ b/doc/html/user_contributions.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Contributing — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Contributing — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="contributing">
@@ -47,7 +46,6 @@ information on that matter in the developer section of the documentation
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -68,12 +66,12 @@ information on that matter in the developer section of the documentation
<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2 current"><a class="current reference internal" href="#">Contributing</a></li>
</ul>
</li>
@@ -90,40 +88,34 @@ information on that matter in the developer section of the documentation
<ul>
<li><a href="index.html">Documentation overview</a><ul>
<li><a href="users.html">Documentation For Users</a><ul>
- <li>Previous: <a href="core/setcompoundschemlib.html" title="previous chapter"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+ <li>Previous: <a href="core/setcompoundschemlib.html" title="previous chapter"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li>Next: <a href="developers.html" title="next chapter">Documentation For Developers</a></li>
</ul></li>
</ul></li>
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- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
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- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
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<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/user_contributions.rst.txt"
diff --git a/doc/html/users.html b/doc/html/users.html
index d7adae8e715467dedc94de90210651b332effc39..81a37ae06ac1e75b57de228030d9f22fde448332 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -1,10 +1,12 @@
-<!DOCTYPE html>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
- <meta charset="utf-8" />
- <title>Documentation For Users — ProMod3 3.2.0 documentation</title>
+ <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+ <title>Documentation For Users — ProMod3 3.2.1 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -20,7 +22,6 @@
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head><body>
@@ -29,8 +30,6 @@
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
-
-
<div class="body" role="main">
<div class="section" id="documentation-for-users">
@@ -62,7 +61,7 @@ scripts using the functionality of this library.</p>
<li class="toctree-l2"><a class="reference internal" href="container/singularity.html">Singularity</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="modelling/pipeline.html">Modelling Pipeline</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/model_checking.html">Model Checking</a></li>
<li class="toctree-l2"><a class="reference internal" href="modelling/gap_handling.html">Handling Gaps</a></li>
@@ -73,7 +72,7 @@ scripts using the functionality of this library.</p>
<li class="toctree-l2"><a class="reference internal" href="modelling/algorithms.html">Modelling Algorithms</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer.html">Representing Sidechains - Rotamers & Co.</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/frame.html">Frame - The Rigid Part</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_constructor.html">Rotamer Constructor</a></li>
@@ -84,31 +83,31 @@ scripts using the functionality of this library.</p>
<li class="toctree-l2"><a class="reference internal" href="sidechain/subrotamer_optimizer.html">Subrotamer Optimization</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
<li class="toctree-l2"><a class="reference internal" href="scoring/backbone_score_env.html">Backbone Score Environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/backbone_scorers.html">Backbone Scorers</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/all_atom_scorers.html">All Atom Scorers</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/other_scoring_functions.html">Other Scoring Functions</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a><ul>
<li class="toctree-l2"><a class="reference internal" href="loop/backbone.html">Representing Loops</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/torsion_sampler.html">Sampling Dihedral Angles</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/structure_db.html">Structural Data</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/all_atom.html">Handling All Atom Positions</a></li>
-<li class="toctree-l2"><a class="reference internal" href="loop/mm_system_creation.html">Generate <code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/mm_system_creation.html">Generate <code class="docutils literal notranslate"><span class="pre">ost.mol.mm</span></code> systems</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/load_loop_objects.html">Loading Precomputed Objects</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="core/pm3argparse.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/helper.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
+<li class="toctree-l1"><a class="reference internal" href="core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="core/pm3argparse.html"><code class="docutils literal notranslate"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/helper.html"><code class="docutils literal notranslate"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/geometry.html">Geometry functions</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/runtime_profiling.html">Runtime profiling</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/graph_minimizer.html">Graph Minimizer</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l1"><a class="reference internal" href="user_contributions.html">Contributing</a></li>
</ul>
</div>
@@ -116,7 +115,6 @@ scripts using the functionality of this library.</p>
</div>
-
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
@@ -137,12 +135,12 @@ scripts using the functionality of this library.</p>
<li class="toctree-l2"><a class="reference internal" href="actions/index.html">ProMod3 Actions</a></li>
<li class="toctree-l2"><a class="reference internal" href="buildsystem.html">Building ProMod3</a></li>
<li class="toctree-l2"><a class="reference internal" href="container/index.html">ProMod3 and Containers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
-<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="xref py py-mod docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+<li class="toctree-l2"><a class="reference internal" href="modelling/index.html"><code class="docutils literal notranslate"><span class="pre">modelling</span></code> - Protein Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal notranslate"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/index.html"><code class="docutils literal notranslate"><span class="pre">scoring</span></code> - Loop Scoring</a></li>
+<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="docutils literal notranslate"><span class="pre">loop</span></code> - Loop Handling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="docutils literal notranslate"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal notranslate"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="user_contributions.html">Contributing</a></li>
</ul>
</li>
@@ -164,33 +162,27 @@ scripts using the functionality of this library.</p>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
- <h3 id="searchlabel">Quick search</h3>
+ <h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="search.html" method="get">
- <input type="text" name="q" aria-labelledby="searchlabel" />
+ <input type="text" name="q" />
<input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
-
-
-
-
-
-
-
-
</div>
</div>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2021, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 2.1.2</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.4</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/users.rst.txt"
diff --git a/extras/data_generation/structure_db/get_data_from_smtl.py b/extras/data_generation/structure_db/get_data_from_smtl.py
index 59140bbdc6e599492166a8256afc0c7961dd72c9..83785b78c2c5f00e53353bf260be99aec4efdae7 100644
--- a/extras/data_generation/structure_db/get_data_from_smtl.py
+++ b/extras/data_generation/structure_db/get_data_from_smtl.py
@@ -32,7 +32,7 @@ from sm import smtl
# the hh-suite available at: https://github.com/soedinglab/hh-suite.
pisces_path = "cullpdb_pc20_res2.0_R0.25_d180524_chains6670"
-smtl_path = "/scicore/data/databases/SMTL/"
+smtl_path = "PATH_TO_SMTL" # TO BE SET
profile_out_dir = "hmms"
structure_out_dir = "structures"
diff --git a/loop/src/CMakeLists.txt b/loop/src/CMakeLists.txt
index 6c874f584b1f8b29cba7803c056a816c5a0ce365..39da6810da8562bc25b2c39f57ae153bdcc86908 100644
--- a/loop/src/CMakeLists.txt
+++ b/loop/src/CMakeLists.txt
@@ -17,7 +17,6 @@ set(LOOP_HEADERS
idx_handler.hh
loop_object_loader.hh
mm_system_creator.hh
- paged_array.hh
psipred_prediction.hh
stem_geom.hh
structure_db.hh
diff --git a/loop/src/backbone.cc b/loop/src/backbone.cc
index 2445c55fc2b7a1554cf9bb3e35d87f70ba5f5f35..d59aac79df4296b95003efb21e4112b4055547f0 100644
--- a/loop/src/backbone.cc
+++ b/loop/src/backbone.cc
@@ -274,10 +274,8 @@ void BackboneList::InsertInto(ost::mol::ChainHandle& chain,
ost::mol::ResNum n_num = start_resnum;
ost::mol::ResNum c_num = start_resnum + this->size() -1;
- ost::mol::ResidueHandle before = chain.FindResidue(n_num);
- ost::mol::ResidueHandle after = chain.FindResidue(c_num);
-
// handle n_stem
+ ost::mol::ResidueHandle before = chain.FindResidue(n_num);
if (before.IsValid()) {
ost::mol::AtomHandle n = before.FindAtom("N");
@@ -348,8 +346,9 @@ void BackboneList::InsertInto(ost::mol::ChainHandle& chain,
}
// handle c_stem
+ ost::mol::ResidueHandle after = chain.FindResidue(c_num);
const uint last_idx = size() - 1;
- if (after.IsValid()) {
+ if (n_num != c_num && after.IsValid()) {
ost::mol::AtomHandle n = after.FindAtom("N");
ost::mol::AtomHandle ca = after.FindAtom("CA");
@@ -390,7 +389,7 @@ void BackboneList::InsertInto(ost::mol::ChainHandle& chain,
edi.RenameResidue(after, ost::conop::OneLetterCodeToResidueName(GetOLC(last_idx)));
after.SetOneLetterCode(GetOLC(last_idx));
- } else { // !after.IsValid()
+ } else if(n_num != c_num) { // !after.IsValid()
after = edi.AppendResidue(chain, ost::conop::OneLetterCodeToResidueName(GetOLC(last_idx)), c_num);
SetResidueProps(after, GetOLC(last_idx));
diff --git a/loop/src/frag_db.cc b/loop/src/frag_db.cc
index 4e0bfdd76a46e1099d77689a5170f79062a93454..8467f5cc2b83a30df17b012ca25edc1c9cbf10d8 100644
--- a/loop/src/frag_db.cc
+++ b/loop/src/frag_db.cc
@@ -258,7 +258,7 @@ void FragDB::AddFragments(uint fragment_length,
//extract all stem information of this chain to create the
//stem geoms later on
- const PagedArray<PeptideCoords, 65536>& db_coords = structure_db->GetCoords();
+ const ost::PagedArray<PeptideCoords, 65536>& db_coords = structure_db->GetCoords();
stem_coords.clear();
for(uint j = 0; j < size; ++j){
const PeptideCoords& coords = db_coords[offset + j];
diff --git a/loop/src/frag_db.hh b/loop/src/frag_db.hh
index 8deb7b197455b51be093913a5714b429fb541845..75195312aa4409f136909d23ef19aa9f9845515c 100644
--- a/loop/src/frag_db.hh
+++ b/loop/src/frag_db.hh
@@ -28,7 +28,6 @@
#include <ost/mol/entity_view.hh>
#include <ost/mol/mol.hh>
-#include <promod3/loop/paged_array.hh>
#include <promod3/loop/data_bag.hh>
#include <promod3/loop/ushort_vec.hh>
#include <promod3/loop/structure_db.hh>
diff --git a/loop/src/fragger.cc b/loop/src/fragger.cc
index 7f5ed5d1220efa2f87810d7606220e3efcd2e6f0..fa1054ed248dd7efca2caf9164bd0dc77792d040 100644
--- a/loop/src/fragger.cc
+++ b/loop/src/fragger.cc
@@ -500,14 +500,14 @@ void Fragger::FillProfiles(StructureDBPtr db,
break;
}
case SequenceProfile:{
- const PagedArray<AAFreq, 65536>& frequencies =
+ const ost::PagedArray<AAFreq, 65536>& frequencies =
db->GetAAFrequencies();
this->GenerateProfileProfile(db, profiles[i], chain_idx, frequencies,
profiles_[i]);
break;
}
case StructureProfile:{
- const PagedArray<AAFreq, 65536>& frequencies =
+ const ost::PagedArray<AAFreq, 65536>& frequencies =
db->GetAAStructFrequencies();
this->GenerateProfileProfile(db, profiles[i], chain_idx, frequencies,
profiles_[i]);
@@ -553,7 +553,7 @@ void Fragger::GenerateSeqSimProfile(StructureDBPtr db,
const ost::seq::alg::SubstWeightMatrix& subst) const{
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<char, 65536>& full_db_seq = db->GetSeq();
+ const ost::PagedArray<char, 65536>& full_db_seq = db->GetSeq();
profile.clear();
@@ -591,7 +591,7 @@ void Fragger::GenerateSeqIDProfile(StructureDBPtr db,
uint index) const{
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<char, 65536>& full_db_seq = db->GetSeq();
+ const ost::PagedArray<char, 65536>& full_db_seq = db->GetSeq();
profile.clear();
@@ -622,7 +622,7 @@ void Fragger::GenerateSSAgreementProfile(StructureDBPtr db,
const std::vector<int>& confidence) const {
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<char, 65536>& full_db_dssp = db->GetDSSP();
+ const ost::PagedArray<char, 65536>& full_db_dssp = db->GetDSSP();
profile.clear();
@@ -658,7 +658,7 @@ void Fragger::GenerateTorsionProbabilityProfile(StructureDBPtr db,
const std::vector<int>& t_sampler_indices) const {
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<DihedralInfo, 65536>& full_db_dihedrals = db->GetDihedrals();
+ const ost::PagedArray<DihedralInfo, 65536>& full_db_dihedrals = db->GetDihedrals();
profile.clear();
@@ -693,7 +693,7 @@ void Fragger::GenerateTorsionProbabilityProfile(StructureDBPtr db,
void Fragger::GenerateProfileProfile(StructureDBPtr db,
std::vector<Real>& profile,
uint index,
- const PagedArray<AAFreq,65536>& frequencies,
+ const ost::PagedArray<AAFreq,65536>& frequencies,
short** prof) const {
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
diff --git a/loop/src/fragger.hh b/loop/src/fragger.hh
index dfe545f4c434898749e4a344a5607d2b34d2d444..205f10dc692ef953ccfefa09813c49663dde3692 100644
--- a/loop/src/fragger.hh
+++ b/loop/src/fragger.hh
@@ -134,7 +134,7 @@ private:
void GenerateProfileProfile(StructureDBPtr db, std::vector<Real>& profile,
uint index,
- const PagedArray<AAFreq, 65536>& frequencies,
+ const ost::PagedArray<AAFreq, 65536>& frequencies,
short** prof) const;
diff --git a/loop/src/structure_db.hh b/loop/src/structure_db.hh
index 89395b364f9039b6205529e9712a1a8e8d8b820c..075d0a3f35b1317f73e7d6730fb4b32f1c628f3a 100644
--- a/loop/src/structure_db.hh
+++ b/loop/src/structure_db.hh
@@ -24,6 +24,7 @@
#include <list>
#include <ost/base.hh>
+#include <ost/paged_array.hh>
#include <ost/fixed_string.hh>
#include <ost/mol/entity_view.hh>
#include <ost/mol/mol.hh>
@@ -34,7 +35,6 @@
#include <ost/seq/profile_handle.hh>
#include <ost/mol/surface_handle.hh>
-#include <promod3/loop/paged_array.hh>
#include <promod3/loop/backbone.hh>
#include <promod3/core/message.hh>
#include <promod3/core/superpose.hh>
@@ -249,15 +249,15 @@ public:
const std::vector<CoordInfo>& GetCoordToc() const { return coord_toc_; }
- const PagedArray<char, 65536>& GetSeq() const {
+ const ost::PagedArray<char, 65536>& GetSeq() const {
return seq_;
}
- const PagedArray<PeptideCoords, 65536>& GetCoords() const {
+ const ost::PagedArray<PeptideCoords, 65536>& GetCoords() const {
return coords_;
}
- const PagedArray<DihedralInfo, 65536>& GetDihedrals() const {
+ const ost::PagedArray<DihedralInfo, 65536>& GetDihedrals() const {
if(!this->HasData(Dihedrals)) {
throw promod3::Error("StructureDB does not contain dihedrals!");
@@ -266,7 +266,7 @@ public:
return dihedrals_;
}
- const PagedArray<unsigned short, 65536>& GetSolvAcc() const {
+ const ost::PagedArray<unsigned short, 65536>& GetSolvAcc() const {
if(!this->HasData(SolventAccessibilities)) {
throw promod3::Error("StructureDB does not contain "
@@ -276,7 +276,7 @@ public:
return solv_acc_;
}
- const PagedArray<unsigned short, 65536>& GetResDepth() const {
+ const ost::PagedArray<unsigned short, 65536>& GetResDepth() const {
if(!this->HasData(ResidueDepths)) {
throw promod3::Error("StructureDB does not contain residue depths!");
@@ -285,7 +285,7 @@ public:
return res_depths_;
}
- const PagedArray<char, 65536>& GetDSSP() const {
+ const ost::PagedArray<char, 65536>& GetDSSP() const {
if(!this->HasData(DSSP)) {
throw promod3::Error("StructureDB does not contain dssp assignments!");
@@ -294,7 +294,7 @@ public:
return dssp_;
}
- const PagedArray<AAFreq, 65536>& GetAAFrequencies() const {
+ const ost::PagedArray<AAFreq, 65536>& GetAAFrequencies() const {
if(!this->HasData(AAFrequencies)) {
throw promod3::Error("StructureDB does not contain amino acid "
@@ -304,7 +304,7 @@ public:
return aa_frequencies_;
}
- const PagedArray<AAFreq, 65536>& GetAAStructFrequencies() const {
+ const ost::PagedArray<AAFreq, 65536>& GetAAStructFrequencies() const {
if(!this->HasData(AAFrequenciesStruct)) {
throw promod3::Error("StructureDB does not contain amino acid "
@@ -336,30 +336,30 @@ private:
std::vector<CoordInfo> coord_toc_;
// one letter codes
- PagedArray<char, 65536> seq_;
+ ost::PagedArray<char, 65536> seq_;
// backbone coordinates
- PagedArray<PeptideCoords, 65536> coords_;
+ ost::PagedArray<PeptideCoords, 65536> coords_;
// phi and psi dihedrals
- PagedArray<DihedralInfo, 65536> dihedrals_;
+ ost::PagedArray<DihedralInfo, 65536> dihedrals_;
// solvent accessibility in A^2 as calculated by Lee & Richards implementation
// in ost
- PagedArray<uint16_t, 65536> solv_acc_;
+ ost::PagedArray<uint16_t, 65536> solv_acc_;
// distance towards closest surface residue in A multiplied by 10 to allow
// accuracy of 0.1
- PagedArray<uint16_t, 65536> res_depths_;
+ ost::PagedArray<uint16_t, 65536> res_depths_;
// dssp state, which is a member of {H,B,E,G,I,T,S}
- PagedArray<char, 65536> dssp_;
+ ost::PagedArray<char, 65536> dssp_;
// Amino acid frequencies as given as input profile
- PagedArray<AAFreq, 65536> aa_frequencies_;
+ ost::PagedArray<AAFreq, 65536> aa_frequencies_;
// Amino acid frequencies as derived from structural information
- PagedArray<AAFreq, 65536> aa_frequencies_struct_;
+ ost::PagedArray<AAFreq, 65536> aa_frequencies_struct_;
};
}}
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index 5fdf7a4467a900f029adbc57eb54185b6e44c52f..337c281b22c3fee1b9a14cd941fd12e6009b3a55 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -1275,8 +1275,6 @@ def ModelTermini(mhandle, torsion_sampler, fragger_handles=None,
*fragger_handles* is given) :class:`~promod3.loop.Fragger` lists. The latter
is only used if the gap length is >= the length of fragments stored.
- Terminal gaps of length 1 are ignored by this function!
-
.. literalinclude:: ../../../tests/doc/scripts/modelling_model_termini.py
:param mhandle: Modelling handle on which to apply change.
@@ -1302,7 +1300,7 @@ def ModelTermini(mhandle, torsion_sampler, fragger_handles=None,
prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
# get terminal gaps (copies as we'll clear them as we go)
- terminal_gaps = [g.Copy() for g in mhandle.gaps if g.IsTerminal() and g.length > 1]
+ terminal_gaps = [g.Copy() for g in mhandle.gaps if g.IsTerminal()]
if len(terminal_gaps) > 0:
ost.LogInfo("Trying to model %d terminal gap(s)." % len(terminal_gaps))
else:
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index 44b2ef01f873930e79d97ebf9e66ac10e8cc26d8..a4b5e8709578a0a1b79831442c2d8c93e22dc0e9 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -531,7 +531,7 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list(),
full target sequence(s). The terminal parts will be
modelled with a crude Monte Carlo approach. Be aware
that the accuracy of those termini is likely to be
- limited. Termini of length 1 won't be modelled.
+ limited.
:type model_termini: :class:`bool`
@@ -571,7 +571,7 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list(),
if model_termini:
ModelTermini(mhandle, torsion_sampler, fragger_handles=fragger_handles)
- RemoveTerminalGaps(mhandle) # length=1 ignored above
+ RemoveTerminalGaps(mhandle)
# build sidechains
BuildSidechains(mhandle, merge_distance, fragment_db,