From e1774254a0a1f73c35203e4374ec8ee311d18cfe Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 18 Sep 2014 16:30:39 +0200
Subject: [PATCH] Updated documentation
---
doc/html/_modules/index.html | 4 +-
doc/html/_modules/promod3/core/argcheck.html | 4 +-
doc/html/_sources/contributing.txt | 224 +++++-----
doc/html/_static/basic.css | 7 +-
doc/html/_static/default.css | 2 +-
doc/html/_static/doctools.js | 5 +-
doc/html/_static/jquery.js | 6 +-
doc/html/_static/searchtools.js | 8 +-
doc/html/_static/sidebar.js | 4 +-
doc/html/_static/websupport.js | 2 +-
doc/html/buildsystem.html | 4 +-
doc/html/changelog.html | 4 +-
doc/html/contributing.html | 423 +++++++++++--------
doc/html/core/argcheck.html | 4 +-
doc/html/core/index.html | 4 +-
doc/html/developers.html | 4 +-
doc/html/genindex.html | 4 +-
doc/html/index.html | 8 +-
doc/html/meld/index.html | 4 +-
doc/html/meld/loop.html | 8 +-
doc/html/meld/rawmodel.html | 10 +-
doc/html/objects.inv | Bin 521 -> 504 bytes
doc/html/py-modindex.html | 4 +-
doc/html/search.html | 4 +-
doc/html/searchindex.js | 2 +-
doc/html/users.html | 4 +-
26 files changed, 412 insertions(+), 345 deletions(-)
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 786dbfa9..a6fe610d 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -85,8 +85,8 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 14 13:38, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:30, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
index e301ec0b..fb384b8d 100644
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ b/doc/html/_modules/promod3/core/argcheck.html
@@ -193,8 +193,8 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 14 13:38, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:30, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index 16777995..b9bd37f8 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -189,7 +189,7 @@ the Internet. Nevertheless, here is a short list of most important advices:
:file:`tests/data`
* If 'exotic' |python| modules are used, consider making the test aware of the
possibility that the module is not available
-* Test do not fail on purpose
+* Tests do not fail on purpose
* No failing tests, that are considered 'this does not affect anything'
To run the whole test suite, ``make check`` is enough. This will also trigger
@@ -359,108 +359,130 @@ top level :file:`CMakeLists.txt`:
.. code-block:: cmake
:linenos:
- :emphasize-lines: 83
-
- #-------------------------------------------------------------------------------
- # Author: Bienchen
- #-------------------------------------------------------------------------------
- # Options to CMake:
- # DISABLE_DOCUMENTATION: Don't build documentation, don't search for Sphinx
- # DISABLE_DOCTEST: Don't run example code from documentation on 'make check'
- # DISABLE_LINKCHECK: Don't test links from documentation on 'make check'
- # (if documentation is disabled, there is no doctest, linkcheck at all)
- cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
- set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
-
- project(PROMOD3 CXX C)
-
- include(PROMOD3)
-
- set(PROMOD3_VERSION_MAJOR 0)
- set(PROMOD3_VERSION_MINOR 1)
- set(PROMOD3_VERSION_PATCH 0)
- set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR}.${PROMOD3_VERSION_PATCH})
-
- if (CMAKE_COMPILER_IS_GNUCXX)
- exec_program(gcc ARGS --version OUTPUT_VARIABLE CMAKE_C_COMPILER_VERSION)
- if(CMAKE_C_COMPILER_VERSION MATCHES ".*4\\.[5-9].*")
- set(PROMOD_GCC_45 true)
- else()
- set(PROMOD_GCC_45 false)
- endif()
- endif()
-
- if (OPTIMIZE)
- set(CMAKE_BUILD_TYPE Release)
- set(_OPT ON)
- else()
- set(CMAKE_BUILD_TYPE Debug)
- set(_OPT OFF)
- endif()
-
- setup_stage()
- file(MAKE_DIRECTORY ${STAGE_DIR}
- ${EXECUTABLE_OUTPUT_PATH}
- ${HEADER_STAGE_PATH}
- ${LIB_STAGE_PATH}
- ${LIBEXEC_STAGE_PATH})
-
- setup_compiler_flags()
- setup_boost()
-
- find_package(Python 2.7 REQUIRED)
- if(NOT DISABLE_DOCUMENTATION)
- find_package(Sphinx ${PYTHON_VERSION} REQUIRED)
- set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}")
- # set this to the URL corresponding to the version of OST you are using
- set(OST_DOC_URL "http://www.openstructure.org/docs/1.3")
- endif()
- find_package(OPENSTRUCTURE 1.4 REQUIRED
- COMPONENTS io mol seq seq_alg mol_alg conop)
- find_package(QMEAN 1.0 REQUIRED)
-
- if (CMAKE_COMPILER_IS_GNUCXX)
- # do not write back into cache, otherwise the compile command line gets
- # expanded with multiple -fno-strict-aliasing flags, triggering a complete
- # rebuild whenever cmake is run
- set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing")
- if("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-attributes")
- endif("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
- endif()
-
- # basic environment
- include_directories(${Boost_INCLUDE_DIRS}
- ${OST_INCLUDE_DIR}
- ${QMEAN_INCLUDE_DIR})
-
- set(FILES_TO_BE_REMOVED ${PROJECT_BINARY_DIR}/stage)
- set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
- "${FILES_TO_BE_REMOVED}")
-
- ## sub dirs to be recognised by CMake
- ## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
- add_subdirectory(config)
- add_subdirectory(core)
- add_subdirectory(meld)
- add_subdirectory(sidechains)
- add_subdirectory(scripts)
- add_subdirectory(actions)
- add_subdirectory(extras)
- if(NOT DISABLE_DOCUMENTATION)
- add_changelog_to_doc(FILE "${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG")
- add_subdirectory(doc)
- endif()
-
- ## report setup
- message(STATUS "PROMOD3 will be built with the following options:\n"
- " OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"
- " QMEAN (-DQMEAN_ROOT) : ${QMEAN_ROOT}\n"
- " Optimized (-DOPTIMIZE) : ${_OPT}\n"
- " Python : ${PYTHON_BINARY}\n")
+ :emphasize-lines: 103
+
+ #-------------------------------------------------------------------------------
+ # Author: Bienchen
+ #-------------------------------------------------------------------------------
+ # Options to CMake:
+ # DISABLE_DOCUMENTATION: Don't build documentation, don't search for Sphinx
+ # DISABLE_DOCTEST: Don't run example code from documentation on 'make check'
+ # DISABLE_LINKCHECK: Don't test links from documentation on 'make check'
+ # (if documentation is disabled, there is no doctest, linkcheck at all)
+ cmake_minimum_required(VERSION 2.6.4 FATAL_ERROR)
+ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_SOURCE_DIR}/cmake_support)
+
+ project(ProMod3 CXX C)
+
+ include(PROMOD3)
+
+ set(PROMOD3_VERSION_MAJOR 0)
+ set(PROMOD3_VERSION_MINOR 1)
+ set(PROMOD3_VERSION_PATCH 0)
+ set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR}.${PROMOD3_VERSION_PATCH})
+
+ option(DISABLE_DOCUMENTATION "Do not build documentation" OFF)
+ option(DISABLE_DISABLE_DOCTEST "Do not check examples in documentation" OFF)
+ option(DISABLE_DISABLE_LINKCHECK "Do not check links in the documentation" OFF)
+
+ if (CMAKE_COMPILER_IS_GNUCXX)
+ exec_program(gcc ARGS --version OUTPUT_VARIABLE CMAKE_C_COMPILER_VERSION)
+ if(CMAKE_C_COMPILER_VERSION MATCHES ".*4\\.[5-9].*")
+ set(PROMOD_GCC_45 true)
+ else()
+ set(PROMOD_GCC_45 false)
+ endif()
+ endif()
+
+ if (OPTIMIZE)
+ set(CMAKE_BUILD_TYPE Release)
+ set(_OPT ON)
+ else()
+ set(CMAKE_BUILD_TYPE Debug)
+ set(_OPT OFF)
+ endif()
+
+ setup_stage()
+ file(MAKE_DIRECTORY ${STAGE_DIR}
+ ${EXECUTABLE_OUTPUT_PATH}
+ ${HEADER_STAGE_PATH}
+ ${LIB_STAGE_PATH}
+ ${LIBEXEC_STAGE_PATH})
+
+ setup_compiler_flags()
+ setup_boost()
+
+ find_package(Python 2.7 REQUIRED)
+ if(NOT DISABLE_DOCUMENTATION)
+ find_package(Sphinx ${PYTHON_VERSION} REQUIRED)
+ set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}")
+ # set this to the URL corresponding to the version of OST you are using
+ set(OST_DOC_URL "http://www.openstructure.org/docs/1.3")
+ endif()
+ find_package(OPENSTRUCTURE 1.4 REQUIRED
+ COMPONENTS io mol seq seq_alg mol_alg conop)
+ find_package(QMEAN 1.0 REQUIRED)
+
+ #The KIC loop closing algorithm requires a solver for a generalized eigen
+ #problem. Eigen3 would provide such a solver, but only allows to extract
+ #the resulting eigenvalues and not the eigenvectors.
+ #As soon as there is an Eigen3 release with the required functionality,
+ #The Lapack dependency can be dropped.
+ find_package(LAPACK)
+
+ if (CMAKE_COMPILER_IS_GNUCXX)
+ # do not write back into cache, otherwise the compile command line gets
+ # expanded with multiple -fno-strict-aliasing flags, triggering a complete
+ # rebuild whenever cmake is run
+ set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing")
+ if("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-attributes")
+ endif("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "4.6")
+ endif()
+
+ # additional packages/ headers/ etc.
+ # Eigen3 is mandatory right now but may vanish once OST switches to the same
+ # version.
+ find_package(Eigen3 3.2.1 REQUIRED)
+ if(NOT EIGEN3_FOUND)
+ message(FATAL_ERROR "Eigen3 is essential for building ${PROJECT_NAME}.")
+ endif()
+
+ # basic environment
+ include_directories(${Boost_INCLUDE_DIRS}
+ ${OST_INCLUDE_DIR}
+ ${QMEAN_INCLUDE_DIR}
+ ${EIGEN3_INCLUDE_DIR})
+
+ set(FILES_TO_BE_REMOVED ${PROJECT_BINARY_DIR}/stage)
+ set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
+ "${FILES_TO_BE_REMOVED}")
+
+ ## sub dirs to be recognised by CMake
+ ## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt
+ add_subdirectory(config)
+ add_subdirectory(core)
+ add_subdirectory(meld)
+ add_subdirectory(sidechains)
+ add_subdirectory(loop)
+ add_subdirectory(scripts)
+ add_subdirectory(actions)
+ add_subdirectory(extras)
+ if(NOT DISABLE_DOCUMENTATION)
+ add_changelog_to_doc(FILE "${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG")
+ add_subdirectory(doc)
+ endif()
+
+ ## report setup
+ message(STATUS "${PROJECT_NAME} will be built with the following options:\n"
+ " OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"
+ " QMEAN (-DQMEAN_ROOT) : ${QMEAN_ROOT}\n"
+ " Optimized (-DOPTIMIZE) : ${_OPT}\n"
+ " Python : ${PYTHON_BINARY}\n"
+ " Eigen3 : ${EIGEN3_INCLUDE_DIR}\n")
All that needs to be done for |cmake| to recognise your module is adding its
-directory as shown in line 83.
+directory as shown in line 103.
This was the final step to set up the build system. Running |cmake| at this
point would create the build environment in place. But building software in
diff --git a/doc/html/_static/basic.css b/doc/html/_static/basic.css
index a04c8e13..967e36ce 100644
--- a/doc/html/_static/basic.css
+++ b/doc/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -89,6 +89,7 @@ div.sphinxsidebar #searchbox input[type="submit"] {
img {
border: 0;
+ max-width: 100%;
}
/* -- search page ----------------------------------------------------------- */
@@ -401,10 +402,6 @@ dl.glossary dt {
margin: 0;
}
-.refcount {
- color: #060;
-}
-
.optional {
font-size: 1.3em;
}
diff --git a/doc/html/_static/default.css b/doc/html/_static/default.css
index e534a078..5f1399ab 100644
--- a/doc/html/_static/default.css
+++ b/doc/html/_static/default.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- default theme.
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/doc/html/_static/doctools.js b/doc/html/_static/doctools.js
index 8614442e..c5455c90 100644
--- a/doc/html/_static/doctools.js
+++ b/doc/html/_static/doctools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for all documentation.
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -168,6 +168,9 @@ var Documentation = {
var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : [];
if (terms.length) {
var body = $('div.body');
+ if (!body.length) {
+ body = $('body');
+ }
window.setTimeout(function() {
$.each(terms, function() {
body.highlightText(this.toLowerCase(), 'highlighted');
diff --git a/doc/html/_static/jquery.js b/doc/html/_static/jquery.js
index 198b3ff0..83589daa 100644
--- a/doc/html/_static/jquery.js
+++ b/doc/html/_static/jquery.js
@@ -1,4 +1,2 @@
-/*! jQuery v1.7.1 jquery.com | jquery.org/license */
-(function(a,b){function cy(a){return f.isWindow(a)?a:a.nodeType===9?a.defaultView||a.parentWindow:!1}function cv(a){if(!ck[a]){var b=c.body,d=f("<"+a+">").appendTo(b),e=d.css("display");d.remove();if(e==="none"||e===""){cl||(cl=c.createElement("iframe"),cl.frameBorder=cl.width=cl.height=0),b.appendChild(cl);if(!cm||!cl.createElement)cm=(cl.contentWindow||cl.contentDocument).document,cm.write((c.compatMode==="CSS1Compat"?"<!doctype html>":"")+"<html><body>"),cm.close();d=cm.createElement(a),cm.body.appendChild(d),e=f.css(d,"display"),b.removeChild(cl)}ck[a]=e}return ck[a]}function cu(a,b){var c={};f.each(cq.concat.apply([],cq.slice(0,b)),function(){c[this]=a});return c}function ct(){cr=b}function cs(){setTimeout(ct,0);return cr=f.now()}function cj(){try{return new a.ActiveXObject("Microsoft.XMLHTTP")}catch(b){}}function ci(){try{return new a.XMLHttpRequest}catch(b){}}function cc(a,c){a.dataFilter&&(c=a.dataFilter(c,a.dataType));var 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\ No newline at end of file
diff --git a/doc/html/_static/searchtools.js b/doc/html/_static/searchtools.js
index 56676b25..6e1f06bd 100644
--- a/doc/html/_static/searchtools.js
+++ b/doc/html/_static/searchtools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilties for the full-text search.
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -330,13 +330,13 @@ var Search = {
objectterms.push(tmp[i].toLowerCase());
}
- if ($u.indexOf(stopwords, tmp[i]) != -1 || tmp[i].match(/^\d+$/) ||
+ if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
tmp[i] === "") {
// skip this "word"
continue;
}
// stem the word
- var word = stemmer.stemWord(tmp[i]).toLowerCase();
+ var word = stemmer.stemWord(tmp[i].toLowerCase());
var toAppend;
// select the correct list
if (word[0] == '-') {
@@ -550,7 +550,7 @@ var Search = {
for (i = 0; i < searchterms.length; i++) {
var word = searchterms[i];
// no match but word was a required one
- if (!(files = terms[word]))
+ if ((files = terms[word]) === undefined)
break;
if (files.length === undefined) {
files = [files];
diff --git a/doc/html/_static/sidebar.js b/doc/html/_static/sidebar.js
index 5adf8952..4f09a0df 100644
--- a/doc/html/_static/sidebar.js
+++ b/doc/html/_static/sidebar.js
@@ -16,7 +16,7 @@
* Once the browser is closed the cookie is deleted and the position
* reset to the default (expanded).
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -142,7 +142,7 @@ $(function() {
var items = document.cookie.split(';');
for(var k=0; k<items.length; k++) {
var key_val = items[k].split('=');
- var key = key_val[0];
+ var key = key_val[0].replace(/ /, ""); // strip leading spaces
if (key == 'sidebar') {
var value = key_val[1];
if ((value == 'collapsed') && (!sidebar_is_collapsed()))
diff --git a/doc/html/_static/websupport.js b/doc/html/_static/websupport.js
index 19fcda56..71c0a136 100644
--- a/doc/html/_static/websupport.js
+++ b/doc/html/_static/websupport.js
@@ -4,7 +4,7 @@
*
* sphinx.websupport utilties for all documentation.
*
- * :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 9255a447..ba044996 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -212,8 +212,8 @@ builder</li>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 11:59, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 15:50, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 57c85fd1..15117151 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -127,8 +127,8 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 08:42, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 15:50, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 8536f400..53a71301 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -218,7 +218,7 @@ the Internet. Nevertheless, here is a short list of most important advices:</p>
<tt class="file docutils literal"><span class="pre">tests/data</span></tt></li>
<li>If ‘exotic’ Python modules are used, consider making the test aware of the
possibility that the module is not available</li>
-<li>Test do not fail on purpose</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, <tt class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></tt> is enough. This will also trigger
@@ -362,203 +362,247 @@ your project would be added as a module <tt class="docutils literal"><span class
Python package tree.</p>
<p>The final step towards CMake is to register your module’s directory in the
top level <tt class="file docutils literal"><span class="pre">CMakeLists.txt</span></tt>:</p>
-<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 9
-10
-11
-12
-13
-14
-15
-16
-17
-18
-19
-20
-21
-22
-23
-24
-25
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-27
-28
-29
-30
-31
-32
-33
-34
-35
-36
-37
-38
-39
-40
-41
-42
-43
-44
-45
-46
-47
-48
-49
-50
-51
-52
-53
-54
-55
-56
-57
-58
-59
-60
-61
-62
-63
-64
-65
-66
-67
-68
-69
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-71
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-73
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-75
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-78
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-80
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-84
-85
-86
-87
-88
-89
-90
-91
-92
-93
-94
-95
-96
-97</pre></div></td><td class="code"><div class="highlight"><pre> <span class="c">#-------------------------------------------------------------------------------</span>
- <span class="c"># Author: Bienchen</span>
- <span class="c">#-------------------------------------------------------------------------------</span>
- <span class="c"># Options to CMake:</span>
- <span class="c"># DISABLE_DOCUMENTATION: Don't build documentation, don't search for Sphinx</span>
- <span class="c"># DISABLE_DOCTEST: Don't run example code from documentation on 'make check'</span>
- <span class="c"># DISABLE_LINKCHECK: Don't test links from documentation on 'make check'</span>
- <span class="c"># (if documentation is disabled, there is no doctest, linkcheck at all)</span>
- <span class="nb">cmake_minimum_required</span><span class="p">(</span><span class="s">VERSION</span> <span class="s">2.6.4</span> <span class="s">FATAL_ERROR</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_MODULE_PATH</span> <span class="o">${</span><span class="nv">CMAKE_MODULE_PATH</span><span class="o">}</span> <span class="o">${</span><span class="nv">CMAKE_SOURCE_DIR</span><span class="o">}</span><span class="s">/cmake_support</span><span class="p">)</span>
+<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
+ 2
+ 3
+ 4
+ 5
+ 6
+ 7
+ 8
+ 9
+ 10
+ 11
+ 12
+ 13
+ 14
+ 15
+ 16
+ 17
+ 18
+ 19
+ 20
+ 21
+ 22
+ 23
+ 24
+ 25
+ 26
+ 27
+ 28
+ 29
+ 30
+ 31
+ 32
+ 33
+ 34
+ 35
+ 36
+ 37
+ 38
+ 39
+ 40
+ 41
+ 42
+ 43
+ 44
+ 45
+ 46
+ 47
+ 48
+ 49
+ 50
+ 51
+ 52
+ 53
+ 54
+ 55
+ 56
+ 57
+ 58
+ 59
+ 60
+ 61
+ 62
+ 63
+ 64
+ 65
+ 66
+ 67
+ 68
+ 69
+ 70
+ 71
+ 72
+ 73
+ 74
+ 75
+ 76
+ 77
+ 78
+ 79
+ 80
+ 81
+ 82
+ 83
+ 84
+ 85
+ 86
+ 87
+ 88
+ 89
+ 90
+ 91
+ 92
+ 93
+ 94
+ 95
+ 96
+ 97
+ 98
+ 99
+100
+101
+102
+103
+104
+105
+106
+107
+108
+109
+110
+111
+112
+113
+114
+115
+116
+117
+118
+119</pre></div></td><td class="code"><div class="highlight"><pre><span class="c">#-------------------------------------------------------------------------------</span>
+<span class="c"># Author: Bienchen</span>
+<span class="c">#-------------------------------------------------------------------------------</span>
+<span class="c"># Options to CMake:</span>
+<span class="c"># DISABLE_DOCUMENTATION: Don't build documentation, don't search for Sphinx</span>
+<span class="c"># DISABLE_DOCTEST: Don't run example code from documentation on 'make check'</span>
+<span class="c"># DISABLE_LINKCHECK: Don't test links from documentation on 'make check'</span>
+<span class="c"># (if documentation is disabled, there is no doctest, linkcheck at all)</span>
+<span class="nb">cmake_minimum_required</span><span class="p">(</span><span class="s">VERSION</span> <span class="s">2.6.4</span> <span class="s">FATAL_ERROR</span><span class="p">)</span>
+<span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_MODULE_PATH</span> <span class="o">${</span><span class="nv">CMAKE_MODULE_PATH</span><span class="o">}</span> <span class="o">${</span><span class="nv">CMAKE_SOURCE_DIR</span><span class="o">}</span><span class="s">/cmake_support</span><span class="p">)</span>
+
+<span class="nb">project</span><span class="p">(</span><span class="s">ProMod3</span> <span class="s">CXX</span> <span class="s">C</span><span class="p">)</span>
- <span class="nb">project</span><span class="p">(</span><span class="s">PROMOD3</span> <span class="s">CXX</span> <span class="s">C</span><span class="p">)</span>
+<span class="nb">include</span><span class="p">(</span><span class="s">PROMOD3</span><span class="p">)</span>
- <span class="nb">include</span><span class="p">(</span><span class="s">PROMOD3</span><span class="p">)</span>
+<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_MAJOR</span> <span class="s">0</span><span class="p">)</span>
+<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_MINOR</span> <span class="s">1</span><span class="p">)</span>
+<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_PATCH</span> <span class="s">0</span><span class="p">)</span>
+<span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_STRING</span> <span class="o">${</span><span class="nv">PROMOD3_VERSION_MAJOR</span><span class="o">}</span><span class="s">.</span><span class="o">${</span><span class="nv">PROMOD3_VERSION_MINOR</span><span class="o">}</span><span class="s">.</span><span class="o">${</span><span class="nv">PROMOD3_VERSION_PATCH</span><span class="o">}</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_MAJOR</span> <span class="s">0</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_MINOR</span> <span class="s">1</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_PATCH</span> <span class="s">0</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD3_VERSION_STRING</span> <span class="o">${</span><span class="nv">PROMOD3_VERSION_MAJOR</span><span class="o">}</span><span class="s">.</span><span class="o">${</span><span class="nv">PROMOD3_VERSION_MINOR</span><span class="o">}</span><span class="s">.</span><span class="o">${</span><span class="nv">PROMOD3_VERSION_PATCH</span><span class="o">}</span><span class="p">)</span>
+<span class="nb">option</span><span class="p">(</span><span class="s">DISABLE_DOCUMENTATION</span> <span class="s2">"Do not build documentation"</span> <span class="s">OFF</span><span class="p">)</span>
+<span class="nb">option</span><span class="p">(</span><span class="s">DISABLE_DISABLE_DOCTEST</span> <span class="s2">"Do not check examples in documentation"</span> <span class="s">OFF</span><span class="p">)</span>
+<span class="nb">option</span><span class="p">(</span><span class="s">DISABLE_DISABLE_LINKCHECK</span> <span class="s2">"Do not check links in the documentation"</span> <span class="s">OFF</span><span class="p">)</span>
- <span class="nb">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
- <span class="nb">exec_program</span><span class="p">(</span><span class="s">gcc</span> <span class="s">ARGS</span> <span class="s">--version</span> <span class="s">OUTPUT_VARIABLE</span> <span class="s">CMAKE_C_COMPILER_VERSION</span><span class="p">)</span>
- <span class="nb">if</span><span class="p">(</span><span class="s">CMAKE_C_COMPILER_VERSION</span> <span class="s">MATCHES</span> <span class="s2">".*4\\.[5-9].*"</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD_GCC_45</span> <span class="s">true</span><span class="p">)</span>
- <span class="nb">else</span><span class="p">()</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD_GCC_45</span> <span class="s">false</span><span class="p">)</span>
- <span class="nb">endif</span><span class="p">()</span>
- <span class="nb">endif</span><span class="p">()</span>
+<span class="nb">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
+ <span class="nb">exec_program</span><span class="p">(</span><span class="s">gcc</span> <span class="s">ARGS</span> <span class="s">--version</span> <span class="s">OUTPUT_VARIABLE</span> <span class="s">CMAKE_C_COMPILER_VERSION</span><span class="p">)</span>
+ <span class="nb">if</span><span class="p">(</span><span class="s">CMAKE_C_COMPILER_VERSION</span> <span class="s">MATCHES</span> <span class="s2">".*4\\.[5-9].*"</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD_GCC_45</span> <span class="s">true</span><span class="p">)</span>
+ <span class="nb">else</span><span class="p">()</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">PROMOD_GCC_45</span> <span class="s">false</span><span class="p">)</span>
+ <span class="nb">endif</span><span class="p">()</span>
+<span class="nb">endif</span><span class="p">()</span>
- <span class="nb">if</span> <span class="p">(</span><span class="s">OPTIMIZE</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_BUILD_TYPE</span> <span class="s">Release</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">_OPT</span> <span class="s">ON</span><span class="p">)</span>
- <span class="nb">else</span><span class="p">()</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_BUILD_TYPE</span> <span class="s">Debug</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">_OPT</span> <span class="s">OFF</span><span class="p">)</span>
- <span class="nb">endif</span><span class="p">()</span>
+<span class="nb">if</span> <span class="p">(</span><span class="s">OPTIMIZE</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_BUILD_TYPE</span> <span class="s">Release</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">_OPT</span> <span class="s">ON</span><span class="p">)</span>
+<span class="nb">else</span><span class="p">()</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_BUILD_TYPE</span> <span class="s">Debug</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">_OPT</span> <span class="s">OFF</span><span class="p">)</span>
+<span class="nb">endif</span><span class="p">()</span>
- <span class="nb">setup_stage</span><span class="p">()</span>
- <span class="nb">file</span><span class="p">(</span><span class="s">MAKE_DIRECTORY</span> <span class="o">${</span><span class="nv">STAGE_DIR</span><span class="o">}</span>
- <span class="o">${</span><span class="nv">EXECUTABLE_OUTPUT_PATH</span><span class="o">}</span>
- <span class="o">${</span><span class="nv">HEADER_STAGE_PATH</span><span class="o">}</span>
- <span class="o">${</span><span class="nv">LIB_STAGE_PATH</span><span class="o">}</span>
- <span class="o">${</span><span class="nv">LIBEXEC_STAGE_PATH</span><span class="o">}</span><span class="p">)</span>
+<span class="nb">setup_stage</span><span class="p">()</span>
+<span class="nb">file</span><span class="p">(</span><span class="s">MAKE_DIRECTORY</span> <span class="o">${</span><span class="nv">STAGE_DIR</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">EXECUTABLE_OUTPUT_PATH</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">HEADER_STAGE_PATH</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">LIB_STAGE_PATH</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">LIBEXEC_STAGE_PATH</span><span class="o">}</span><span class="p">)</span>
- <span class="nb">setup_compiler_flags</span><span class="p">()</span>
- <span class="nb">setup_boost</span><span class="p">()</span>
+<span class="nb">setup_compiler_flags</span><span class="p">()</span>
+<span class="nb">setup_boost</span><span class="p">()</span>
- <span class="nb">find_package</span><span class="p">(</span><span class="s">Python</span> <span class="s">2.7</span> <span class="s">REQUIRED</span><span class="p">)</span>
- <span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
- <span class="nb">find_package</span><span class="p">(</span><span class="s">Sphinx</span> <span class="o">${</span><span class="nv">PYTHON_VERSION</span><span class="o">}</span> <span class="s">REQUIRED</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">PYTHON_DOC_URL</span> <span class="s2">"https://docs.python.org/${PYTHON_VERSION}"</span><span class="p">)</span>
- <span class="c"># set this to the URL corresponding to the version of OST you are using</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">OST_DOC_URL</span> <span class="s2">"http://www.openstructure.org/docs/1.3"</span><span class="p">)</span>
- <span class="nb">endif</span><span class="p">()</span>
- <span class="nb">find_package</span><span class="p">(</span><span class="s">OPENSTRUCTURE</span> <span class="s">1.4</span> <span class="s">REQUIRED</span>
- <span class="s">COMPONENTS</span> <span class="s">io</span> <span class="s">mol</span> <span class="s">seq</span> <span class="s">seq_alg</span> <span class="s">mol_alg</span> <span class="s">conop</span><span class="p">)</span>
- <span class="nb">find_package</span><span class="p">(</span><span class="s">QMEAN</span> <span class="s">1.0</span> <span class="s">REQUIRED</span><span class="p">)</span>
+<span class="nb">find_package</span><span class="p">(</span><span class="s">Python</span> <span class="s">2.7</span> <span class="s">REQUIRED</span><span class="p">)</span>
+<span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
+ <span class="nb">find_package</span><span class="p">(</span><span class="s">Sphinx</span> <span class="o">${</span><span class="nv">PYTHON_VERSION</span><span class="o">}</span> <span class="s">REQUIRED</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">PYTHON_DOC_URL</span> <span class="s2">"https://docs.python.org/${PYTHON_VERSION}"</span><span class="p">)</span>
+ <span class="c"># set this to the URL corresponding to the version of OST you are using</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">OST_DOC_URL</span> <span class="s2">"http://www.openstructure.org/docs/1.3"</span><span class="p">)</span>
+<span class="nb">endif</span><span class="p">()</span>
+<span class="nb">find_package</span><span class="p">(</span><span class="s">OPENSTRUCTURE</span> <span class="s">1.4</span> <span class="s">REQUIRED</span>
+ <span class="s">COMPONENTS</span> <span class="s">io</span> <span class="s">mol</span> <span class="s">seq</span> <span class="s">seq_alg</span> <span class="s">mol_alg</span> <span class="s">conop</span><span class="p">)</span>
+<span class="nb">find_package</span><span class="p">(</span><span class="s">QMEAN</span> <span class="s">1.0</span> <span class="s">REQUIRED</span><span class="p">)</span>
- <span class="nb">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
- <span class="c"># do not write back into cache, otherwise the compile command line gets</span>
- <span class="c"># expanded with multiple -fno-strict-aliasing flags, triggering a complete</span>
- <span class="c"># rebuild whenever cmake is run</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_CXX_FLAGS_RELEASE</span> <span class="s2">"${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing"</span><span class="p">)</span>
- <span class="nb">if</span><span class="p">(</span><span class="s2">"${CMAKE_CXX_COMPILER_VERSION}"</span> <span class="s">VERSION_GREATER</span> <span class="s2">"4.6"</span><span class="p">)</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_CXX_FLAGS</span> <span class="s2">"${CMAKE_CXX_FLAGS} -Wno-attributes"</span><span class="p">)</span>
- <span class="nb">endif</span><span class="p">(</span><span class="s2">"${CMAKE_CXX_COMPILER_VERSION}"</span> <span class="s">VERSION_GREATER</span> <span class="s2">"4.6"</span><span class="p">)</span>
- <span class="nb">endif</span><span class="p">()</span>
+<span class="c">#The KIC loop closing algorithm requires a solver for a generalized eigen</span>
+<span class="c">#problem. Eigen3 would provide such a solver, but only allows to extract</span>
+<span class="c">#the resulting eigenvalues and not the eigenvectors.</span>
+<span class="c">#As soon as there is an Eigen3 release with the required functionality,</span>
+<span class="c">#The Lapack dependency can be dropped.</span>
+<span class="nb">find_package</span><span class="p">(</span><span class="s">LAPACK</span><span class="p">)</span>
- <span class="c"># basic environment</span>
- <span class="nb">include_directories</span><span class="p">(</span><span class="o">${</span><span class="nv">Boost_INCLUDE_DIRS</span><span class="o">}</span>
- <span class="o">${</span><span class="nv">OST_INCLUDE_DIR</span><span class="o">}</span>
- <span class="o">${</span><span class="nv">QMEAN_INCLUDE_DIR</span><span class="o">}</span><span class="p">)</span>
+<span class="nb">if</span> <span class="p">(</span><span class="s">CMAKE_COMPILER_IS_GNUCXX</span><span class="p">)</span>
+ <span class="c"># do not write back into cache, otherwise the compile command line gets</span>
+ <span class="c"># expanded with multiple -fno-strict-aliasing flags, triggering a complete</span>
+ <span class="c"># rebuild whenever cmake is run</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_CXX_FLAGS_RELEASE</span> <span class="s2">"${CMAKE_CXX_FLAGS_RELEASE} -fno-strict-aliasing"</span><span class="p">)</span>
+ <span class="nb">if</span><span class="p">(</span><span class="s2">"${CMAKE_CXX_COMPILER_VERSION}"</span> <span class="s">VERSION_GREATER</span> <span class="s2">"4.6"</span><span class="p">)</span>
+ <span class="nb">set</span><span class="p">(</span><span class="s">CMAKE_CXX_FLAGS</span> <span class="s2">"${CMAKE_CXX_FLAGS} -Wno-attributes"</span><span class="p">)</span>
+ <span class="nb">endif</span><span class="p">(</span><span class="s2">"${CMAKE_CXX_COMPILER_VERSION}"</span> <span class="s">VERSION_GREATER</span> <span class="s2">"4.6"</span><span class="p">)</span>
+<span class="nb">endif</span><span class="p">()</span>
- <span class="nb">set</span><span class="p">(</span><span class="s">FILES_TO_BE_REMOVED</span> <span class="o">${</span><span class="nv">PROJECT_BINARY_DIR</span><span class="o">}</span><span class="s">/stage</span><span class="p">)</span>
- <span class="nb">set_directory_properties</span><span class="p">(</span><span class="s">PROPERTIES</span> <span class="s">ADDITIONAL_MAKE_CLEAN_FILES</span>
- <span class="s2">"${FILES_TO_BE_REMOVED}"</span><span class="p">)</span>
+<span class="c"># additional packages/ headers/ etc.</span>
+<span class="c"># Eigen3 is mandatory right now but may vanish once OST switches to the same</span>
+<span class="c"># version.</span>
+<span class="nb">find_package</span><span class="p">(</span><span class="s">Eigen3</span> <span class="s">3.2.1</span> <span class="s">REQUIRED</span><span class="p">)</span>
+<span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">EIGEN3_FOUND</span><span class="p">)</span>
+ <span class="nb">message</span><span class="p">(</span><span class="s">FATAL_ERROR</span> <span class="s2">"Eigen3 is essential for building ${PROJECT_NAME}."</span><span class="p">)</span>
+<span class="nb">endif</span><span class="p">()</span>
- <span class="c">## sub dirs to be recognised by CMake</span>
- <span class="c">## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt</span>
- <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">config</span><span class="p">)</span>
- <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">core</span><span class="p">)</span>
- <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">meld</span><span class="p">)</span>
-<span class="hll"> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">sidechains</span><span class="p">)</span>
-</span> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">scripts</span><span class="p">)</span>
- <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">actions</span><span class="p">)</span>
- <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">extras</span><span class="p">)</span>
- <span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
- <span class="nb">add_changelog_to_doc</span><span class="p">(</span><span class="s">FILE</span> <span class="s2">"${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG"</span><span class="p">)</span>
- <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
- <span class="nb">endif</span><span class="p">()</span>
+<span class="c"># basic environment</span>
+<span class="nb">include_directories</span><span class="p">(</span><span class="o">${</span><span class="nv">Boost_INCLUDE_DIRS</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">OST_INCLUDE_DIR</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">QMEAN_INCLUDE_DIR</span><span class="o">}</span>
+ <span class="o">${</span><span class="nv">EIGEN3_INCLUDE_DIR</span><span class="o">}</span><span class="p">)</span>
- <span class="c">## report setup</span>
- <span class="nb">message</span><span class="p">(</span><span class="s">STATUS</span> <span class="s2">"PROMOD3 will be built with the following options:\n"</span>
- <span class="s2">" OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"</span>
- <span class="s2">" QMEAN (-DQMEAN_ROOT) : ${QMEAN_ROOT}\n"</span>
- <span class="s2">" Optimized (-DOPTIMIZE) : ${_OPT}\n"</span>
- <span class="s2">" Python : ${PYTHON_BINARY}\n"</span><span class="p">)</span>
+<span class="nb">set</span><span class="p">(</span><span class="s">FILES_TO_BE_REMOVED</span> <span class="o">${</span><span class="nv">PROJECT_BINARY_DIR</span><span class="o">}</span><span class="s">/stage</span><span class="p">)</span>
+<span class="nb">set_directory_properties</span><span class="p">(</span><span class="s">PROPERTIES</span> <span class="s">ADDITIONAL_MAKE_CLEAN_FILES</span>
+ <span class="s2">"${FILES_TO_BE_REMOVED}"</span><span class="p">)</span>
+
+<span class="c">## sub dirs to be recognised by CMake</span>
+<span class="c">## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">config</span><span class="p">)</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">core</span><span class="p">)</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">meld</span><span class="p">)</span>
+<span class="hll"><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">sidechains</span><span class="p">)</span>
+</span><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">loop</span><span class="p">)</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">scripts</span><span class="p">)</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">actions</span><span class="p">)</span>
+<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">extras</span><span class="p">)</span>
+<span class="nb">if</span><span class="p">(</span><span class="s">NOT</span> <span class="s">DISABLE_DOCUMENTATION</span><span class="p">)</span>
+ <span class="nb">add_changelog_to_doc</span><span class="p">(</span><span class="s">FILE</span> <span class="s2">"${CMAKE_CURRENT_SOURCE_DIR}/CHANGELOG"</span><span class="p">)</span>
+ <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
+<span class="nb">endif</span><span class="p">()</span>
+
+<span class="c">## report setup</span>
+<span class="nb">message</span><span class="p">(</span><span class="s">STATUS</span> <span class="s2">"${PROJECT_NAME} will be built with the following options:\n"</span>
+ <span class="s2">" OpenStructure (-DOST_ROOT) : ${OST_ROOT}\n"</span>
+ <span class="s2">" QMEAN (-DQMEAN_ROOT) : ${QMEAN_ROOT}\n"</span>
+ <span class="s2">" Optimized (-DOPTIMIZE) : ${_OPT}\n"</span>
+ <span class="s2">" Python : ${PYTHON_BINARY}\n"</span>
+ <span class="s2">" Eigen3 : ${EIGEN3_INCLUDE_DIR}\n"</span><span class="p">)</span>
</pre></div>
</td></tr></table></div>
<p>All that needs to be done for CMake to recognise your module is adding its
-directory as shown in line 83.</p>
+directory as shown in line 103.</p>
<p>This was the final step to set up the build system. Running CMake at this
point would create the build environment in place. But building software in
your code repository has several drawbacks. First of all, it puts all kind of
@@ -635,12 +679,17 @@ by extending the list of sub-directories in <tt class="file docutils literal"><s
<p>Then fill <tt class="file docutils literal"><span class="pre">sidechains/tests/CMakeLists.txt</span></tt> with your new test script and
<tt class="docutils literal"><span class="pre">make</span></tt> will recognise the changes next time it is run and fix the rest for
you.</p>
-<div class="highlight-cmake"><pre> set(SIDECHAINS_UNIT_TESTS
+<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+2
+3
+4
+5</pre></div></td><td class="code"><div class="highlight"><pre> set(SIDECHAINS_UNIT_TESTS
test_something.py
)
- promod3_unittest(MODULE sidechains SOURCES "${SIDECHAINS_UNIT_TESTS}")</pre>
-</div>
+ promod3_unittest(MODULE sidechains SOURCES "${SIDECHAINS_UNIT_TESTS}")
+</pre></div>
+</td></tr></table></div>
<p>Now tests should be available by <tt class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></tt>, <tt class="docutils literal"><span class="pre">make</span> <span class="pre">codetest</span></tt> and
<tt class="docutils literal"><span class="pre">make</span> <span class="pre">test_something.py_run</span></tt>.</p>
</div>
@@ -745,8 +794,8 @@ contributions to web pages using ProMod3.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 08:42, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:30, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index e8079353..e75d016e 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -217,8 +217,8 @@ shell. <tt class="docutils literal"><span class="pre">0</span></tt> is tradition
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 09:05, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 15:50, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index a8b9ea0c..34e940fa 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -123,8 +123,8 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 11 09:05, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 15:50, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 49595aa9..819b82bb 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -140,8 +140,8 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 14 13:38, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:30, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 47425e61..ac9b0837 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -334,8 +334,8 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 14 13:38, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:30, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/index.html b/doc/html/index.html
index ba8d5b87..86233655 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -86,9 +86,7 @@
<div class="sphinxsidebarwrapper">
<h3><a href="#">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#">Welcome to ProMod3’s documentation!</a><ul>
-</ul>
-</li>
+<li><a class="reference internal" href="#">Welcome to ProMod3’s documentation!</a></li>
<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li>
</ul>
@@ -134,8 +132,8 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 14 13:38, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:30, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/meld/index.html b/doc/html/meld/index.html
index a322cb8e..6dd1af16 100644
--- a/doc/html/meld/index.html
+++ b/doc/html/meld/index.html
@@ -127,8 +127,8 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 14 13:38, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:17, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/meld/loop.html b/doc/html/meld/loop.html
index 2cfc4fdc..75bbf769 100644
--- a/doc/html/meld/loop.html
+++ b/doc/html/meld/loop.html
@@ -160,7 +160,7 @@ gap.start to gap.end.</p>
<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"><tt class="xref py py-class docutils literal"><span class="pre">BackboneList</span></tt></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><tt class="xref py py-class docutils literal"><span class="pre">BackboneList</span></tt></td>
</tr>
</tbody>
</table>
@@ -263,7 +263,7 @@ extension of the gap.</p>
<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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a></td>
</tr>
</tbody>
</table>
@@ -338,8 +338,8 @@ extension of the gap.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 14 13:38, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:17, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/meld/rawmodel.html b/doc/html/meld/rawmodel.html
index b28a127b..79038f45 100644
--- a/doc/html/meld/rawmodel.html
+++ b/doc/html/meld/rawmodel.html
@@ -108,7 +108,7 @@ as information about insertions and deletions in the gaps list.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>calpha_only</strong> – If true, only Calpha atoms will be copied. Sidechains and
other backbone atoms are completely ignored.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises :</th><td class="field-body">A <tt class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></tt> when the second sequence does not have an
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body">A <tt class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></tt> when the second sequence does not have an
attached structure</td>
</tr>
</tbody>
@@ -129,7 +129,7 @@ report.</p>
<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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><tt class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></tt></a></td>
</tr>
</tbody>
</table>
@@ -145,7 +145,7 @@ missing or incomplete backbone coordinates in the template structure.</p>
<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"><tt class="xref py py-class docutils literal"><span class="pre">StructuralGapList</span></tt></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><tt class="xref py py-class docutils literal"><span class="pre">StructuralGapList</span></tt></td>
</tr>
</tbody>
</table>
@@ -221,8 +221,8 @@ missing or incomplete backbone coordinates in the template structure.</p>
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 14 13:38, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:17, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index fa69201d044980768da879cf410081d7f709e4d1..9c6f756aba1760165d3008b970d3d82700805f0a 100644
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diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index f3ff581b..f8a56c37 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -113,8 +113,8 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 14 13:38, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:30, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/search.html b/doc/html/search.html
index 58fbeca2..3a763dc1 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -99,8 +99,8 @@
</div>
<div class="footer">
© Copyright 2013, Bienchen.
- Last updated on Aug 14 13:38, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 16:30, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
</body>
</html>
\ No newline at end of file
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 47c98e6e..87a89139 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
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diff --git a/doc/html/users.html b/doc/html/users.html
index c8ec2e27..bfc1fc68 100644
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@@ -110,8 +110,8 @@
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© Copyright 2013, Bienchen.
- Last updated on Aug 11 08:42, 2014.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2b1.
+ Last updated on Sep 18 15:50, 2014.
+ Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
</div>
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\ No newline at end of file
--
GitLab