diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index a922908435f7092c5dc4de3ab3ca5942ab9b1665..d238522457178efa74686fef82a8822eea44acef 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -11,6 +11,7 @@ developers.rst
users.rst
buildsystem.rst
contributing.rst
+gettingstarted.rst
)
diff --git a/doc/buildsystem.rst b/doc/buildsystem.rst
index 7255812924497d2c233d1efb66153de5151810de..b90f9f10ba78b33ccbfe3f476c74c63e2fdba4c6 100644
--- a/doc/buildsystem.rst
+++ b/doc/buildsystem.rst
@@ -1,3 +1,5 @@
+.. _building-promod:
+
Building |project|
================================================================================
@@ -5,7 +7,8 @@ Building |project|
Dependencies
--------------------------------------------------------------------------------
|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version
-1.4. To create the build system, |cmake|_ is required in version
+1.4. |ost_s| must be configured and compiled with ``ENABLE_MM=1`` to use |openmm|_.
+To create the build system, |cmake|_ is required in version
2.8.7 or higher. |python|_ works well from version 2.7. For |ost_s| and the
|C++| bit of |project|, |boost|_ is required in version 1.47.0 (the same as
used for |ost_s|). Also |eigen3|_ and |lapack|_ are needed. To build
@@ -14,6 +17,7 @@ documentation, |sphinx|_ 1.2b1 is used.
The currently (Nov. 2015) preferred versions are:
* |ost_s|_ 1.4
+* |openmm|_ 6.1
* |cmake|_ 2.8.12
* |python|_ 2.7.5
* |boost|_ 1.53.0
@@ -114,6 +118,7 @@ special targets:
.. |qmean| replace:: QMEAN
.. |eigen3| replace:: Eigen 3
.. |lapack| replace:: LAPACK
+.. |openmm| replace:: OpenMM
.. _qmean: http://swissmodel.expasy.org/qmean/cgi/index.cgi?
.. _ost_l: http://www.OpenStructure.org
.. _cmake: https://cmake.org/
@@ -121,6 +126,7 @@ special targets:
.. _boost: http://www.boost.org/
.. _eigen3: http://eigen.tuxfamily.org/index.php?title=Main_Page
.. _lapack: http://www.netlib.org/lapack/
+.. _openmm: https://simtk.org/home/openmm
.. LocalWords: cmake makefiles CMakeLists txt DOCTEST LINKCHECK conf html
.. LocalWords: doctest linkcheck qmean DQMEAN eigen CMakeCache lapack
diff --git a/doc/contributing.rst b/doc/contributing.rst
index 6e52ea34c1a646019682c007de48c488ee41400d..2d60c8f5cf8aabb566ff765c597fb934ebd6d59a 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -14,6 +14,8 @@ one is a bit special and provides core functionality to everybody else.
In the end of this chapter you will find a little walk-through on how to get
started.
+.. _git-branches:
+
--------------------------------------------------------------------------------
|git| Branches
--------------------------------------------------------------------------------
diff --git a/doc/developers.rst b/doc/developers.rst
index de46b810cf47a872440ad2f2f2e8e6a052701482..dff318493e4df8f418a3531be599552144cdf76f 100644
--- a/doc/developers.rst
+++ b/doc/developers.rst
@@ -9,6 +9,7 @@ Contents:
.. toctree::
:maxdepth: 2
+ gettingstarted
core/setcompoundschemlib
core/index
pipeline/index
diff --git a/doc/gettingstarted.rst b/doc/gettingstarted.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c29dbd8b7ff950e5dcd3b8419aaff787e291845a
--- /dev/null
+++ b/doc/gettingstarted.rst
@@ -0,0 +1,48 @@
+Getting Started
+================================================================================
+
+Get and Run |project|
+--------------------------------------------------------------------------------
+First steps to get |project| up and running:
+
+#. Get |ost_s|_.
+#. Get |project| from the ``git`` repository (see :ref:`here <git-branches>`).
+#. Compile |project| with ``cmake`` and ``make`` (see :ref:`here <building-promod>`).
+#. Ensure that you have a ``stage/bin`` folder which includes a ``pm`` executable.
+ For convenience, add the folder to your ``PATH`` env. variable.
+#. You can now execute |project| by running the following in your terminal:
+
+ .. code-block:: console
+
+ $ pm <COMMAND>
+
+ Here ``<COMMAND>`` can be:
+
+ - a predefined "action" (execute ``pm help`` for a list of possible actions)
+ - the path to a python script, such as the following example:
+
+ .. code-block:: python
+
+ from ost import io
+ from promod3 import loop
+
+ # generate backbone with dihedrals of a helix and store it
+ sequence = "HELLYEAH"
+ bb_list = loop.BackboneList(sequence)
+ io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+ The execution of this script should generate a ``test.pdb`` file, which you
+ can visualize with any pdb reader (e.g. ``dng`` from |ost_s|).
+
+
+Modelling pipeline
+--------------------------------------------------------------------------------
+|project| is meant to help you perform operations for protein homology modelling.
+Commonly, your input is a template structure and an alignment of the template to
+the desired target sequence. The modelling steps then are:
+
+- Build a raw model from the template (see :mod:`~promod3.rawmodel` module)
+- Perform loop modelling to close all gaps (see :mod:`~promod3.loop` module)
+- Reconstruct sidechains (see :mod:`~promod3.sidechain` module)
+- Minimize energy of final model using molecular mechanics
+ (using :mod:`ost.mol.mm` from |ost_s|)
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index 064d5229abcf2048395a90f21c49bd38e72a503e..c0e209e755eca28d496cc6f426d4526b5a61b0c3 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -29,19 +29,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -54,6 +42,7 @@
<li><a href="BackboneList.html">BackboneList</a></li>
<li><a href="BackboneLoopScorer.html">BackboneLoopScorer</a></li>
<li><a href="BackboneRelaxer.html">BackboneRelaxer</a></li>
+<li><a href="CCD.html">CCD</a></li>
<li><a href="CCDCloser.html">CCDCloser</a></li>
<li><a href="DirtyCCDCloser.html">DirtyCCDCloser</a></li>
<li><a href="ExponentialCooler.html">ExponentialCooler</a></li>
@@ -61,9 +50,12 @@
<li><a href="FRMRotamerGroup.html">FRMRotamerGroup</a></li>
<li><a href="FragDB.html">FragDB</a></li>
<li><a href="Fragger.html">Fragger</a></li>
+<li><a href="FraggerScoreParameters.html">FraggerScoreParameters</a></li>
+<li><a href="FragmentSampler.html">FragmentSampler</a></li>
<li><a href="Frame.html">Frame</a></li>
<li><a href="FrameResidue.html">FrameResidue</a></li>
<li><a href="Graph.html">Graph</a></li>
+<li><a href="KIC.html">KIC</a></li>
<li><a href="KICCloser.html">KICCloser</a></li>
<li><a href="LinearScorer.html">LinearScorer</a></li>
<li><a href="LoopCandidate.html">LoopCandidate</a></li>
@@ -72,6 +64,7 @@
<li><a href="PhiPsiSampler.html">PhiPsiSampler</a></li>
<li><a href="RRMRotamer.html">RRMRotamer</a></li>
<li><a href="RRMRotamerGroup.html">RRMRotamerGroup</a></li>
+<li><a href="RotamerLib.html">RotamerLib</a></li>
<li><a href="RotamerLibEntry.html">RotamerLibEntry</a></li>
<li><a href="SoftSampler.html">SoftSampler</a></li>
<li><a href="StructureDB.html">StructureDB</a></li>
@@ -82,7 +75,6 @@
<li><a href="promod3/loop.html">promod3.loop</a></li>
<ul><li><a href="promod3/loop/_loop.html">promod3.loop._loop</a></li>
</ul><li><a href="promod3/pipeline/run_engine.html">promod3.pipeline.run_engine</a></li>
-<li><a href="promod3/rawmodel/_closedels.html">promod3.rawmodel._closedels</a></li>
<li><a href="promod3/rawmodel/_closegaps.html">promod3.rawmodel._closegaps</a></li>
<li><a href="promod3/rawmodel/_rawmodel.html">promod3.rawmodel._rawmodel</a></li>
<li><a href="promod3/sidechain/_sidechain.html">promod3.sidechain._sidechain</a></li>
@@ -94,7 +86,13 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ </ul></li>
+</ul>
+</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
@@ -117,7 +115,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/_modules/promod3.html b/doc/html/_modules/promod3.html
index 401f21a8a4c1d6e86f05b49bd8216a494148ff20..e54deac726f7a6c98d6369d9e954c3e38b82c24b 100644
--- a/doc/html/_modules/promod3.html
+++ b/doc/html/_modules/promod3.html
@@ -30,20 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="index.html" accesskey="U">Module code</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -59,7 +46,7 @@
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<div class="viewcode-block" id="SetCompoundsChemlib"><a class="viewcode-back" href="../core/setcompoundschemlib.html#promod3.SetCompoundsChemlib">[docs]</a><span class="k">def</span> <span class="nf">SetCompoundsChemlib</span><span class="p">(</span><span class="n">path_to_chemlib</span><span class="o">=</span><span class="s">"/import/bc2/home/schwede/bienert/git/naccess_smtl.git/compounds.chemlib"</span><span class="p">):</span>
+<div class="viewcode-block" id="SetCompoundsChemlib"><a class="viewcode-back" href="../core/setcompoundschemlib.html#promod3.SetCompoundsChemlib">[docs]</a><span class="k">def</span> <span class="nf">SetCompoundsChemlib</span><span class="p">(</span><span class="n">path_to_chemlib</span><span class="o">=</span><span class="s">"/users/staff/bioz/taurielg/GT/Code/ost/build/stage/share/openstructure/compounds.chemlib"</span><span class="p">):</span>
<span class="sd">"""SetCompoundsChemlib(path_to_chemlib)</span>
<span class="sd"> Load a compounds library. Does not return anything, the library is just</span>
<span class="sd"> enabled globally.</span>
@@ -76,7 +63,7 @@
<span class="k">try</span><span class="p">:</span>
<span class="n">ost</span><span class="o">.</span><span class="n">GetSharedDataPath</span><span class="p">()</span>
<span class="k">except</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">rt_err</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">SetPrefixPath</span><span class="p">(</span><span class="s">"/import/bc2/home/schwede/bienert/git/ost_newenv.git/build_mm/stage"</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">SetPrefixPath</span><span class="p">(</span><span class="s">"/users/staff/bioz/taurielg/GT/Code/ost/build/stage"</span><span class="p">)</span>
<span class="k">except</span><span class="p">:</span>
<span class="k">raise</span>
@@ -95,7 +82,15 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="index.html">Module code</a><ul>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
@@ -118,7 +113,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index 26a25b8bccbc719d9b953ba8e1badfe18f0fb53d..766b65160c547ebd7a519bee683c98c29cf1bbc9 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -30,21 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../../../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../../../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="../../../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> »</li>
- <li class="nav-item nav-item-2"><a href="../../promod3.html" accesskey="U">promod3</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -217,7 +203,17 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../../../index.html">Documentation overview</a><ul>
+ <li><a href="../../index.html">Module code</a><ul>
+ <li><a href="../../promod3.html">promod3</a><ul>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<form class="search" action="../../../search.html" method="get">
@@ -240,7 +236,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/_modules/promod3/core/pm3argparse.html b/doc/html/_modules/promod3/core/pm3argparse.html
index 212e0bae5bc5a9b7f5a4cce34a71b4eee1ab5d21..1e8bf8e5d716c5bd4a69c500a59953a047438610 100644
--- a/doc/html/_modules/promod3/core/pm3argparse.html
+++ b/doc/html/_modules/promod3/core/pm3argparse.html
@@ -30,21 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../../../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../../../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="../../../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> »</li>
- <li class="nav-item nav-item-2"><a href="../../promod3.html" accesskey="U">promod3</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -342,9 +328,9 @@
<span class="sd"> .. attribute:: action</span>
-<span class="sd"> Indicates if the calling script is a |project| action.</span>
+<span class="sd"> Indicates if the calling script is a |project| action.</span>
-<span class="sd"> :type: :class:`bool`</span>
+<span class="sd"> :type: :class:`bool`</span>
<span class="sd"> """</span>
<div class="viewcode-block" id="PM3ArgumentParser.__init__"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.__init__">[docs]</a> <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">description</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -580,7 +566,17 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../../../index.html">Documentation overview</a><ul>
+ <li><a href="../../index.html">Module code</a><ul>
+ <li><a href="../../promod3.html">promod3</a><ul>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<form class="search" action="../../../search.html" method="get">
@@ -603,7 +599,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/_modules/promod3/loop.html b/doc/html/_modules/promod3/loop.html
index 5408f9511ea523824804d5a023089aa04462bfcb..abcce1ead6af48fe858515a17893778ce13ad27e 100644
--- a/doc/html/_modules/promod3/loop.html
+++ b/doc/html/_modules/promod3/loop.html
@@ -30,21 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="../../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../index.html" >Module code</a> »</li>
- <li class="nav-item nav-item-2"><a href="../promod3.html" accesskey="U">promod3</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -83,7 +69,17 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../../index.html">Documentation overview</a><ul>
+ <li><a href="../index.html">Module code</a><ul>
+ <li><a href="../promod3.html">promod3</a><ul>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<form class="search" action="../../search.html" method="get">
@@ -106,7 +102,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/_modules/promod3/pipeline/run_engine.html b/doc/html/_modules/promod3/pipeline/run_engine.html
index 81612ee7c6681b98cc46ade5bad36a97508adb45..7eb11f3bbb1355af9fd8a1a9c0da63e5d57f8774 100644
--- a/doc/html/_modules/promod3/pipeline/run_engine.html
+++ b/doc/html/_modules/promod3/pipeline/run_engine.html
@@ -30,21 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../../../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../../../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="../../../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> »</li>
- <li class="nav-item nav-item-2"><a href="../../promod3.html" accesskey="U">promod3</a> »</li>
- </ul>
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+ <body role="document">
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@@ -115,7 +101,17 @@
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<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../../../index.html">Documentation overview</a><ul>
+ <li><a href="../../index.html">Module code</a><ul>
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<div id="searchbox" style="display: none" role="search">
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@@ -138,7 +134,7 @@
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Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
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diff --git a/doc/html/_modules/promod3/rawmodel/_closedels.html b/doc/html/_modules/promod3/rawmodel/_closedels.html
deleted file mode 100644
index a0a0b425bf023496ca053b7a1ebf6fabe444fa83..0000000000000000000000000000000000000000
--- a/doc/html/_modules/promod3/rawmodel/_closedels.html
+++ /dev/null
@@ -1,250 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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- <title>promod3.rawmodel._closedels — ProMod3 0 documentation</title>
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-
- <h1>Source code for promod3.rawmodel._closedels</h1><div class="highlight"><pre>
-<span class="sd">'''Single function to be 'injected' into the RawModellingResult class in the</span>
-<span class="sd">__init__.py file.</span>
-<span class="sd">'''</span>
-
-<span class="kn">import</span> <span class="nn">ost</span>
-<span class="c">#pylint: disable=no-name-in-module</span>
-<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">_rawmodel</span> <span class="k">as</span> <span class="n">rawmodel</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
-
-<span class="k">def</span> <span class="nf">_CloseSmallDeletions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">scorer</span><span class="p">,</span> <span class="n">extension_steps</span><span class="o">=</span><span class="mi">9</span><span class="p">,</span> <span class="n">clash_thresh</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
- <span class="n">e_thresh</span><span class="o">=</span><span class="mi">200</span><span class="p">):</span>
- <span class="sd">'''Close small deletions by relaxing neighbouring residues.</span>
-
-<span class="sd"> Small deletions in the template from the target-template alignment have a</span>
-<span class="sd"> good chance to be bridged just by relaxing neighbours around a tiny gap.</span>
-<span class="sd"> Before diving into the more demanding tasks in modeling, those may be closed</span>
-<span class="sd"> already in the raw-model. After closure some checks are done to see if the</span>
-<span class="sd"> solution is stereochemically sensible.</span>
-
-<span class="sd"> Closed gaps are removed from :attr:`self.gaps`.</span>
-
-<span class="sd"> .. testcode:: closesmalldel</span>
-<span class="sd"> :hide:</span>
-
-<span class="sd"> from promod3 import rawmodel</span>
-<span class="sd"> from promod3 import loop</span>
-
-<span class="sd"> tpl = ost.io.LoadPDB('../tests/rawmodel/data/raw-modeling/gly.pdb')</span>
-<span class="sd"> aln = ost.seq.CreateAlignment(ost.seq.CreateSequence('trg', 'GGG-GGG'),</span>
-<span class="sd"> ost.seq.CreateSequence('tpl', 'GGGAGGG'))</span>
-<span class="sd"> aln.AttachView(1, tpl.CreateFullView())</span>
-<span class="sd"> rmodel = rawmodel.BuildRawModel(aln)</span>
-<span class="sd"> assert len(rmodel.gaps) == 1</span>
-<span class="sd"> scorer = loop.SetupBackboneScorer(rmodel)</span>
-<span class="sd"> rmodel.CloseSmallDeletions(scorer)</span>
-<span class="sd"> assert len(rmodel.gaps) == 0</span>
-
-<span class="sd"> .. doctest:: closesmalldel</span>
-
-<span class="sd"> import ost</span>
-<span class="sd"> from promod3 import rawmodel</span>
-<span class="sd"> from promod3 import loop</span>
-
-<span class="sd"> tpl = ost.io.LoadPDB('gly.pdb')</span>
-<span class="sd"> aln = ost.io.LoadAlignment('seq.fasta')</span>
-<span class="sd"> aln.AttachView(1, tpl.CreateFullView())</span>
-<span class="sd"> rmodel = rawmodel.BuildRawModel(aln)</span>
-<span class="sd"> scorer = loop.SetupBackboneScorer(rmodel)</span>
-<span class="sd"> rmodel.CloseSmallDeletions(scorer)</span>
-
-<span class="sd"> :param scorer: A scorer dedicated to this raw model.</span>
-<span class="sd"> :type scorer: :class:`~promod3.loop.BackboneLoopScorer`</span>
-
-<span class="sd"> :param extension_steps: Iterations allowed for gap extension. This does not</span>
-<span class="sd"> directly mean 'extended size of gap' but no. of</span>
-<span class="sd"> attempts to extend. Extension works like trying to</span>
-<span class="sd"> increase left, then right, then try more on the</span>
-<span class="sd"> left side again...</span>
-<span class="sd"> :type extension_steps: :class:`int`</span>
-
-<span class="sd"> :param clash_thresh: Threshold for the clash score, acceptance means being</span>
-<span class="sd"> lower than this.</span>
-<span class="sd"> :type clash_thresh: :class:`float`</span>
-
-<span class="sd"> :param e_thresh: Potential energy should be lower than this.</span>
-<span class="sd"> :type e_thresh: :class:`float`</span>
-
-<span class="sd"> :return: If gaps are deleted, the scorer needs to be updated and is</span>
-<span class="sd"> returned.</span>
-<span class="sd"> :rtype: :class:`~promod3.loop.BackboneLoopScorer`</span>
-<span class="sd"> '''</span>
- <span class="n">current_gap_index</span> <span class="o">=</span> <span class="mi">0</span>
-
- <span class="c"># iterating self.gaps. The number of gaps may change during the process,</span>
- <span class="c"># hence we run by 'while', breaking out once we've seen all gaps. If a gap</span>
- <span class="c"># gets closed, it is deleted from self.gaps, otherwise, current_gap_index</span>
- <span class="c"># as a counter is increased.</span>
- <span class="k">while</span> <span class="bp">True</span><span class="p">:</span>
- <span class="c"># check if all gaps were visited</span>
- <span class="k">if</span> <span class="n">current_gap_index</span> <span class="o">>=</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">):</span>
- <span class="k">break</span>
-
- <span class="c"># in the end this determines if a gap was closed or not</span>
- <span class="n">success</span> <span class="o">=</span> <span class="bp">False</span>
-
- <span class="c"># A deletion is a gap of size 0 in the template, this means that to</span>
- <span class="c"># transform the template sequence into the target sequence, aa's vanish,</span>
- <span class="c"># so the target sequence has gap caracters, the template not.</span>
- <span class="c"># If we are not looking at a deletion, do nothing.</span>
- <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">]</span><span class="o">.</span><span class="n">seq</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
- <span class="c"># work on a copy of the gap, if not closed in the end, no harm done</span>
- <span class="n">current_gap</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
- <span class="n">current_chain</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">GetChain</span><span class="p">()</span>
- <span class="n">current_chain_index</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
-
- <span class="c"># Try to close gap by relaxation: by checking how far we may extend</span>
- <span class="c"># the gap, we get the backbone to be stretched. If no more extension</span>
- <span class="c"># is possible, break out. On first successful relaxation for an</span>
- <span class="c"># extension, we successfully stop.</span>
- <span class="n">extender</span> <span class="o">=</span> <span class="n">rawmodel</span><span class="o">.</span><span class="n">GapExtender</span><span class="p">(</span><span class="n">current_gap</span><span class="p">)</span>
- <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">extension_steps</span><span class="p">):</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">extender</span><span class="o">.</span><span class="n">Extend</span><span class="p">():</span>
- <span class="k">break</span>
- <span class="c"># gather residues for backbone relaxation, check that we get a</span>
- <span class="c"># bunch of actual residues, otherwise jump to next extension</span>
- <span class="n">res_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
- <span class="n">current_resnum</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
- <span class="n">after_resnum</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
- <span class="n">found_residues</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="k">while</span> <span class="bp">True</span><span class="p">:</span>
- <span class="k">if</span> <span class="n">current_resnum</span> <span class="o">></span> <span class="n">after_resnum</span><span class="p">:</span>
- <span class="k">break</span>
- <span class="n">res</span> <span class="o">=</span> <span class="n">current_chain</span><span class="o">.</span><span class="n">FindResidue</span><span class="p">(</span><span class="n">current_resnum</span><span class="p">)</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">res</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
- <span class="n">found_residues</span> <span class="o">=</span> <span class="bp">False</span>
- <span class="k">break</span>
- <span class="n">res_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res</span><span class="p">)</span>
- <span class="n">current_resnum</span> <span class="o">+=</span> <span class="mi">1</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">found_residues</span><span class="p">:</span>
- <span class="k">continue</span>
- <span class="c"># backbone relaxation, for now we allow 300 steps or stop at</span>
- <span class="c"># max. force of 0.1</span>
- <span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">current_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span> <span class="n">res_list</span><span class="p">)</span>
- <span class="n">bb_relaxer</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneRelaxer</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)</span>
- <span class="n">potential_e</span> <span class="o">=</span> <span class="n">bb_relaxer</span><span class="o">.</span><span class="n">Run</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="mi">300</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">)</span>
- <span class="c"># check for clashes</span>
- <span class="n">score</span> <span class="o">=</span> <span class="n">scorer</span><span class="o">.</span><span class="n">CalculateClashScore</span><span class="p">(</span>\
- <span class="n">bb_list</span><span class="p">,</span>
- <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
- <span class="n">current_chain_index</span><span class="p">)</span>
- <span class="c"># if there is no clash and potential energy is low enough we</span>
- <span class="c"># just solved a gap, delete it and update the scorer for the</span>
- <span class="c"># changed model</span>
- <span class="k">if</span> <span class="n">score</span> <span class="o"><</span> <span class="n">clash_thresh</span> <span class="ow">and</span> \
- <span class="n">potential_e</span> <span class="o"><</span> <span class="n">e_thresh</span> <span class="ow">and</span> \
- <span class="n">scorer</span><span class="o">.</span><span class="n">TransOmegaTorsions</span><span class="p">(</span><span class="n">bb_list</span><span class="p">):</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Closed: </span><span class="si">%s</span><span class="s"> by relaxing </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> \
- <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">],</span> <span class="n">current_gap</span><span class="p">))</span>
- <span class="n">chain</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetChain</span><span class="p">()</span>
- <span class="n">bb_list</span><span class="o">.</span><span class="n">InsertInto</span><span class="p">(</span><span class="n">chain</span><span class="p">,</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">(),</span>
- <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">())</span>
- <span class="n">scorer</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span>\
- <span class="n">bb_list</span><span class="p">,</span>
- <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">())</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">ClearGaps</span><span class="p">(</span><span class="n">current_gap</span><span class="p">)</span>
- <span class="n">success</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="k">break</span>
- <span class="c"># On closed gap, it is removed so the no. of gaps goes down by itself.</span>
- <span class="c"># In case of no success, counter needs to be increased to jump to the</span>
- <span class="c"># next gap.</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">success</span><span class="p">:</span>
- <span class="n">current_gap_index</span> <span class="o">+=</span> <span class="mi">1</span>
-
- <span class="k">return</span> <span class="n">scorer</span>
-
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s">'_CloseSmallDeletions'</span><span class="p">]</span>
-
-<span class="c"># LocalWords: modeling stereochemically param</span>
-</pre></div>
-
- </div>
- </div>
- </div>
- <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
-<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
- <form class="search" action="../../../search.html" method="get">
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- <input type="submit" value="Go" />
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
- </form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
- </div>
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- </div>
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- ©2015, Bienchen.
-
- |
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
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diff --git a/doc/html/_modules/promod3/rawmodel/_closegaps.html b/doc/html/_modules/promod3/rawmodel/_closegaps.html
index 57caaa23627609b77e7d50e41c58cec0b3290915..cbfe4e58fa98d21e678c8f838eea70cac3f8b7a1 100644
--- a/doc/html/_modules/promod3/rawmodel/_closegaps.html
+++ b/doc/html/_modules/promod3/rawmodel/_closegaps.html
@@ -30,21 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../../../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../../../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="../../../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> »</li>
- <li class="nav-item nav-item-2"><a href="../../promod3.html" accesskey="U">promod3</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -192,8 +178,8 @@
<span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Closed: </span><span class="si">%s</span><span class="s"> by relaxing </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> \
<span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">],</span> <span class="n">current_gap</span><span class="p">))</span>
<span class="n">chain</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetChain</span><span class="p">()</span>
- <span class="n">bb_list</span><span class="o">.</span><span class="n">InsertInto</span><span class="p">(</span><span class="n">chain</span><span class="p">,</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">(),</span>
- <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">())</span>
+ <span class="n">bb_list</span><span class="o">.</span><span class="n">InsertInto</span><span class="p">(</span><span class="n">chain</span><span class="p">,</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
+ <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">())</span>
<span class="n">scorer</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span>\
<span class="n">bb_list</span><span class="p">,</span>
<span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">())</span>
@@ -292,7 +278,17 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../../../index.html">Documentation overview</a><ul>
+ <li><a href="../../index.html">Module code</a><ul>
+ <li><a href="../../promod3.html">promod3</a><ul>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<form class="search" action="../../../search.html" method="get">
@@ -315,7 +311,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/_modules/promod3/sidechain/reconstruct_sidechains.html b/doc/html/_modules/promod3/sidechain/reconstruct_sidechains.html
index a8b80d59240acbbca393a538cfda75de7838d33c..4d82f763b7de42d2c928034bea1f6f4b5572b878 100644
--- a/doc/html/_modules/promod3/sidechain/reconstruct_sidechains.html
+++ b/doc/html/_modules/promod3/sidechain/reconstruct_sidechains.html
@@ -30,21 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../../../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../../../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="../../../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> »</li>
- <li class="nav-item nav-item-2"><a href="../../promod3.html" accesskey="U">promod3</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -57,7 +43,7 @@
<div class="viewcode-block" id="Reconstruct"><a class="viewcode-back" href="../../../sidechain/index.html#promod3.sidechain.reconstruct_sidechains.Reconstruct">[docs]</a><span class="k">def</span> <span class="nf">Reconstruct</span><span class="p">(</span><span class="n">ent</span><span class="p">,</span> <span class="n">keep_sidechains</span> <span class="o">=</span> <span class="bp">False</span><span class="p">,</span> <span class="n">build_disulfids</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span>
<span class="n">rotamer_model</span> <span class="o">=</span> <span class="s">"frm"</span><span class="p">,</span> <span class="n">consider_hbonds</span> <span class="o">=</span> <span class="bp">True</span><span class="p">,</span>
- <span class="n">rotamer_library</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span><span class="n">add_all_polar_hydrogens</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
+ <span class="n">rotamer_library</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">add_polar_hydrogens</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="n">name_id_mapper</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
<span class="n">name_id_mapper</span><span class="p">[</span><span class="s">"ARG"</span><span class="p">]</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ARG</span>
@@ -96,6 +82,9 @@
<span class="n">rotamer_settings</span><span class="o">.</span><span class="n">consider_hbonds</span> <span class="o">=</span> <span class="n">consider_hbonds</span>
<span class="k">if</span> <span class="n">rotamer_library</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">rotamer_library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadDunbrackLib</span><span class="p">()</span>
+ <span class="n">bbdep</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">rotamer_library</span><span class="p">)</span> <span class="ow">is</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">BBDepRotamerLib</span><span class="p">:</span>
+ <span class="n">bbdep</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">residues_with_rotamer_group</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="n">rotamer_groups</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="n">prot</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"peptide=true"</span><span class="p">)</span>
@@ -218,25 +207,45 @@
<span class="k">if</span> <span class="n">use_frm</span><span class="p">:</span>
- <span class="n">rot_group_one</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructFRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
- <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
- <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
- <span class="n">phi_angles</span><span class="p">[</span><span class="n">i_index</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">i_index</span><span class="p">])</span>
-
- <span class="n">rot_group_two</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructFRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
- <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
- <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
- <span class="n">phi_angles</span><span class="p">[</span><span class="n">j_index</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">j_index</span><span class="p">])</span>
- <span class="k">else</span><span class="p">:</span>
- <span class="n">rot_group_one</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructRRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
- <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
- <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
- <span class="n">phi_angles</span><span class="p">[</span><span class="n">i_index</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">i_index</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">bbdep</span><span class="p">:</span>
+ <span class="n">rot_group_one</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructFRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
+ <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
+ <span class="n">phi_angles</span><span class="p">[</span><span class="n">i_index</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">i_index</span><span class="p">])</span>
+
+ <span class="n">rot_group_two</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructFRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
+ <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
+ <span class="n">phi_angles</span><span class="p">[</span><span class="n">j_index</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">j_index</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">rot_group_one</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructFRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
+ <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">)</span>
+
+ <span class="n">rot_group_two</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructFRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
+ <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">)</span>
+
- <span class="n">rot_group_two</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructRRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
- <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
- <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
- <span class="n">phi_angles</span><span class="p">[</span><span class="n">j_index</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">j_index</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">bbdep</span><span class="p">:</span>
+ <span class="n">rot_group_one</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructRRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
+ <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
+ <span class="n">phi_angles</span><span class="p">[</span><span class="n">i_index</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">i_index</span><span class="p">])</span>
+
+ <span class="n">rot_group_two</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructRRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
+ <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
+ <span class="n">phi_angles</span><span class="p">[</span><span class="n">j_index</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">j_index</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">rot_group_one</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructRRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
+ <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">)</span>
+
+ <span class="n">rot_group_two</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructRRMRotamerGroup</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">]]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span>
+ <span class="n">sidechain</span><span class="o">.</span><span class="n">CYD</span><span class="p">,</span><span class="n">cystein_info</span><span class="p">[</span><span class="n">j</span><span class="p">][</span><span class="mi">2</span><span class="p">],</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">)</span>
<span class="n">frame</span><span class="o">.</span><span class="n">AddFrameEnergy</span><span class="p">(</span><span class="n">rot_group_one</span><span class="p">)</span>
@@ -342,13 +351,21 @@
<span class="k">try</span><span class="p">:</span>
<span class="k">if</span> <span class="n">use_frm</span><span class="p">:</span>
- <span class="n">rot_group</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructFRMRotamerGroup</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span><span class="n">rot_id</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
- <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
- <span class="n">phi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">bbdep</span><span class="p">:</span>
+ <span class="n">rot_group</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructFRMRotamerGroup</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span><span class="n">rot_id</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
+ <span class="n">phi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">rot_group</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructFRMRotamerGroup</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span><span class="n">rot_id</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">rot_group</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructRRMRotamerGroup</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span><span class="n">rot_id</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
- <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
- <span class="n">phi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
+ <span class="k">if</span> <span class="n">bbdep</span><span class="p">:</span>
+ <span class="n">rot_group</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructRRMRotamerGroup</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span><span class="n">rot_id</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">,</span>
+ <span class="n">phi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">],</span><span class="n">psi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="n">rot_group</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ConstructRRMRotamerGroup</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span><span class="n">rot_id</span><span class="p">,</span><span class="n">i</span><span class="p">,</span>
+ <span class="n">rotamer_library</span><span class="p">,</span><span class="n">rotamer_settings</span><span class="p">)</span>
<span class="k">except</span><span class="p">:</span>
<span class="k">continue</span>
@@ -370,11 +387,12 @@
<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">rot_group</span><span class="p">,</span><span class="n">sol</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">residues_with_rotamer_group</span><span class="p">,</span><span class="n">rotamer_groups</span><span class="p">,</span><span class="n">solution</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
- <span class="n">rot_group</span><span class="p">[</span><span class="n">sol</span><span class="p">]</span><span class="o">.</span><span class="n">ApplyOnResidue</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span><span class="n">consider_hydrogens</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+ <span class="n">rot_group</span><span class="p">[</span><span class="n">sol</span><span class="p">]</span><span class="o">.</span><span class="n">ApplyOnResidue</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">GetHandle</span><span class="p">(),</span><span class="n">consider_hydrogens</span><span class="o">=</span><span class="n">add_polar_hydrogens</span><span class="p">)</span>
<span class="k">except</span><span class="p">:</span>
<span class="k">print</span> <span class="s">"there is a backbone atom missing... "</span><span class="p">,</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">GetQualifiedName</span><span class="p">()</span>
- <span class="k">if</span> <span class="n">add_all_polar_hydrogens</span><span class="p">:</span>
+ <span class="c">#if we want to add polar hydrogens, we also have to consider the backbone...</span>
+ <span class="k">if</span> <span class="n">add_polar_hydrogens</span><span class="p">:</span>
<span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">frame_residues</span><span class="p">:</span>
<span class="n">i</span><span class="o">=</span><span class="n">r</span><span class="o">.</span><span class="n">GetResidueIndex</span><span class="p">()</span>
<span class="k">if</span> <span class="n">i</span><span class="o">==</span><span class="mi">100000</span><span class="p">:</span><span class="k">continue</span><span class="c">#These are cysteins that were already handled</span>
@@ -386,7 +404,17 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../../../index.html">Documentation overview</a><ul>
+ <li><a href="../../index.html">Module code</a><ul>
+ <li><a href="../../promod3.html">promod3</a><ul>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<form class="search" action="../../../search.html" method="get">
@@ -409,7 +437,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/_modules/test_actions.html b/doc/html/_modules/test_actions.html
index d4ba959b6bb3ddb3fa7c78a596866caf98cab419..60893b7d893f94f8c176c3434fd52e6faf9acc0f 100644
--- a/doc/html/_modules/test_actions.html
+++ b/doc/html/_modules/test_actions.html
@@ -30,20 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="index.html" accesskey="U">Module code</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -73,18 +60,18 @@
<span class="sd"> .. attribute:: pm_bin</span>
-<span class="sd"> This is the path of the ``pm`` binary. Automatically set by calling</span>
-<span class="sd"> :meth:`~ActionTestCase.__init__` inside the initialisation of your class.</span>
+<span class="sd"> This is the path of the ``pm`` binary. Automatically set by calling</span>
+<span class="sd"> :meth:`~ActionTestCase.__init__` inside the initialisation of your class.</span>
-<span class="sd"> :type: :class:`str`</span>
+<span class="sd"> :type: :class:`str`</span>
<span class="sd"> .. attribute:: pm_action</span>
-<span class="sd"> The action to be tested. Needs to be set by your initialisation routine,</span>
-<span class="sd"> **after** calling :meth:`~ActionTestCase.__init__` from here. Skip the</span>
-<span class="sd"> "pm-" in front of the action name.</span>
+<span class="sd"> The action to be tested. Needs to be set by your initialisation routine,</span>
+<span class="sd"> **after** calling :meth:`~ActionTestCase.__init__` from here. Skip the</span>
+<span class="sd"> "pm-" in front of the action name.</span>
-<span class="sd"> :type: :class:`str`</span>
+<span class="sd"> :type: :class:`str`</span>
<span class="sd"> """</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -185,7 +172,15 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="index.html">Module code</a><ul>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<form class="search" action="../search.html" method="get">
@@ -208,7 +203,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/_sources/actions/index_dev.txt b/doc/html/_sources/actions/index_dev.txt
index 8594a9dd4480a51680093fbc15db84995fc9d2ef..d9b667f1dd27451affaf9c98db0cff407083db1c 100644
--- a/doc/html/_sources/actions/index_dev.txt
+++ b/doc/html/_sources/actions/index_dev.txt
@@ -172,7 +172,7 @@ Must Have Tests
--------------------------------------------------------------------------------
What needs testing without exclusion are the exit codes of actions. Those
states will be placed in the userlevel documentation. This topic is already
-covered in :class:`test_actions.ActionTestCase` by :meth:`RunExitStatusTest`.
+covered in :class:`test_actions.ActionTestCase` by :meth:`~ActionTestCase.RunExitStatusTest`.
As an example, testing for ``$?=0`` could work like this:
.. testcode:: actiontest
@@ -202,7 +202,7 @@ happens if a user throws dirty input data in.
Making the Script Executable
--------------------------------------------------------------------------------
-In |project|, unit tests are run via |ost_s|_ and |python|'s
+In |project|, unit tests are run via |ost_s|_'s :mod:`ost.testutils` and |python|'s
:class:`unittest.TestCase`. Those are called when the test module is executed
as a script:
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
index 2dfe453889d674c51753096eb21d7aae1757f201..b90f9f10ba78b33ccbfe3f476c74c63e2fdba4c6 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -1,3 +1,5 @@
+.. _building-promod:
+
Building |project|
================================================================================
@@ -5,20 +7,23 @@ Building |project|
Dependencies
--------------------------------------------------------------------------------
|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version
-1.4, and |qmean|_. To create the build system, |cmake|_ is required in version
+1.4. |ost_s| must be configured and compiled with ``ENABLE_MM=1`` to use |openmm|_.
+To create the build system, |cmake|_ is required in version
2.8.7 or higher. |python|_ works well from version 2.7. For |ost_s| and the
|C++| bit of |project|, |boost|_ is required in version 1.47.0 (the same as
used for |ost_s|). Also |eigen3|_ and |lapack|_ are needed. To build
documentation, |sphinx|_ 1.2b1 is used.
+The currently (Nov. 2015) preferred versions are:
+
* |ost_s|_ 1.4
-* |qmean|_
-* |cmake|_ 2.8.7
-* |python|_ 2.7
-* |boost|_ 1.47.0
-* |sphinx|_ 1.3.1
+* |openmm|_ 6.1
+* |cmake|_ 2.8.12
+* |python|_ 2.7.5
+* |boost|_ 1.53.0
* |eigen3|_ 3.2.1
-* |lapack|_ 3.0
+* |lapack|_ 3.4.2
+* |sphinx|_ 1.3.1
--------------------------------------------------------------------------------
Using |cmake|
@@ -26,20 +31,25 @@ documentation, |sphinx|_ 1.2b1 is used.
|cmake| is used to configure the build system and in the end produces makefiles
and certain directories needed for building |project|. Basically it is called
right from a shell with the directory containing the top-level
-:file:`CMakeLists.txt` as an argument:
+:file:`CMakeLists.txt` as an argument. The preferred approach is to generate a
+build folder and configure and compile in there:
.. code-block:: console
- $ cmake . -DOST_ROOT=<PATH TO OST> -DQMEAN_ROOT=<PATH TO QMEAN>
+ # execute this in the ProMod3 root folder
+ $ mkdir build
+ $ cd build
+ $ cmake .. -DOST_ROOT=<PATH TO OST>
+
+For us, at least pointer to the |ost_s| installation directory is needed,
+handed over to |cmake| by ``-D`` into the variable ``OST_ROOT`` (e.g. |ost_s|
+headers would be located in ``OST_ROOT/include/ost``).
-For us, at least pointers to the |ost_s| and |qmean| installation directories
-are needed, handed over to |cmake| by ``-D`` into the variables ``OST_ROOT``
-and ``QMEAN_ROOT``. Other important variables would be ``BOOST_ROOT``, set to
-the same path as for |ost_s| and probably ``PYTHON_ROOT`` if you want to use a
-certain |python|. Also |eigen3| can be pulled in like this, e.g. if you have to
-download it by yourself because its not installed on your system. Just point
-``EIGEN3_INCLUDE_DIR`` to the path which provides the :file:`Eigen` header
-directory. Don't forget to put a ``-D`` in front of options.
+Similarly, one can specify folders for |boost|, |python|, |eigen3| and |lapack|
+if multiple versions exist and/or they are not installed in a default location.
+These are set with the ``BOOST_ROOT`` (make sure that's the same as for |ost_s|),
+``PYTHON_ROOT``, ``EIGEN3_INCLUDE_DIR``, ``BLAS_blas_LIBRARY`` (BLAS library used
+by |lapack|) and ``LAPACK_lapack_LIBRARY``.
Here is a list of more options used within |project|:
@@ -58,17 +68,23 @@ in the :file:`CMakeCache.txt` of |ost_s|:
* ``OPTIMIZE``
* ``OST_DOUBLE_PRECISION``
+.. doesn't work (yet?)
+ Instead of providing all those options at the command line, you can also use
+ ``ccmake`` instead of ``cmake``, which allows you to set the |cmake| variables
+ interactively. Press 'c' to try to configure the build. If it fails, enter the
+ requested paths and configure again. Advanced settings can be edited by
+ pressing 't'.
+
Instead of calling |cmake| by yourself, there is the :file:`conf-scripts`
directory, providing smallish scripts to invoke |cmake| the right way for
-various systems. Usually those scripts just need the |ost_s| and |qmean| paths
+various systems. Usually those scripts just need the |ost_s| path
and the location of the top-level :file:`CMakeLists.txt`.
-What we highly recommend is going for out-of-source builds. This means creating
-a dedicated directory for building |project| and calling |cmake| or a
-configuration script from there. This way, you can have several builds with
-different configurations. Also if anything goes wrong, just remove the build
-directory to get to a clean state again. No searching for |cmake| cache files or
-checking if certain files really got rebuild and similar things required.
+As mentioned earlier, we highly recommend to use out-of-source builds.
+This way, you can have several builds with different configurations. Also if
+anything goes wrong, just remove the build directory to get to a clean state
+again. No searching for |cmake| cache files or checking if certain files
+really got rebuild and similar things required.
Running Make
@@ -102,13 +118,15 @@ special targets:
.. |qmean| replace:: QMEAN
.. |eigen3| replace:: Eigen 3
.. |lapack| replace:: LAPACK
+.. |openmm| replace:: OpenMM
.. _qmean: http://swissmodel.expasy.org/qmean/cgi/index.cgi?
.. _ost_l: http://www.OpenStructure.org
-.. _cmake: http://www.cmake.org/
+.. _cmake: https://cmake.org/
.. _python: https://www.python.org/
.. _boost: http://www.boost.org/
.. _eigen3: http://eigen.tuxfamily.org/index.php?title=Main_Page
.. _lapack: http://www.netlib.org/lapack/
+.. _openmm: https://simtk.org/home/openmm
.. LocalWords: cmake makefiles CMakeLists txt DOCTEST LINKCHECK conf html
.. LocalWords: doctest linkcheck qmean DQMEAN eigen CMakeCache lapack
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index 6d263eb393e230ee26d774f1877834f32c64d6b2..2d60c8f5cf8aabb566ff765c597fb934ebd6d59a 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -1,7 +1,7 @@
Contributing
================================================================================
The following should explain, in a coarse grain manner, how to add new
-features/ your project to |project|. Important topics are |git| branches, the
+features or your project to |project|. Important topics are |git| branches, the
directory structure and tightly linked with this also |cmake|. The most general
advice would be to use existing bits and pieces as examples and to be
consistent with what you already find here. As an example, documentation
@@ -14,6 +14,8 @@ one is a bit special and provides core functionality to everybody else.
In the end of this chapter you will find a little walk-through on how to get
started.
+.. _git-branches:
+
--------------------------------------------------------------------------------
|git| Branches
--------------------------------------------------------------------------------
diff --git a/doc/html/_sources/core/pm3argparse.txt b/doc/html/_sources/core/pm3argparse.txt
index a20dbf70a86524e322c3561ac2dd7293d2a4c305..8800b4def55411a909be3777bcfa012a4bf776e5 100644
--- a/doc/html/_sources/core/pm3argparse.txt
+++ b/doc/html/_sources/core/pm3argparse.txt
@@ -23,25 +23,29 @@ input.
from promod3.core import pm3argparse
- parser = pm3argparse.PM3ArgumentParser('Dummy')
- parser.AddAlignment()
- parser.AssembleParser()
+ testparser = pm3argparse.PM3ArgumentParser('Dummy')
+ testparser.AddAlignment()
+ testparser.AssembleParser()
try:
- opts = parser.Parse(['-h'])
+ opts = testparser.Parse(['-h'])
except SystemExit, sysex:
if sysex.code == 0:
pass
.. doctest:: pm3argparse
- '''\
+ '''
Place the description of your script right in the file and import
- it via '__doc__' as description to the parser ('-h', '--help').\
+ it via '__doc__' as description to the parser ('-h', '--help').
'''
from promod3.core import pm3argparse
+ # make sure we see output when passing '-h'
+ import ost
+ ost.PushVerbosityLevel(2)
+
parser = pm3argparse.PM3ArgumentParser(__doc__)
parser.AddAlignment()
parser.AssembleParser()
diff --git a/doc/html/_sources/developers.txt b/doc/html/_sources/developers.txt
index 260a2e5cc2d0150f0dd528f36ed55cbdbe67c2bb..dff318493e4df8f418a3531be599552144cdf76f 100644
--- a/doc/html/_sources/developers.txt
+++ b/doc/html/_sources/developers.txt
@@ -1,4 +1,4 @@
-Documentation For Developes
+Documentation For Developers
===============================================================================
.. give an intro on what will be stored here
.. topics: how to create a new module, how to do doc (rst_epillog),
@@ -9,6 +9,7 @@ Contents:
.. toctree::
:maxdepth: 2
+ gettingstarted
core/setcompoundschemlib
core/index
pipeline/index
diff --git a/doc/html/_sources/gettingstarted.txt b/doc/html/_sources/gettingstarted.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c29dbd8b7ff950e5dcd3b8419aaff787e291845a
--- /dev/null
+++ b/doc/html/_sources/gettingstarted.txt
@@ -0,0 +1,48 @@
+Getting Started
+================================================================================
+
+Get and Run |project|
+--------------------------------------------------------------------------------
+First steps to get |project| up and running:
+
+#. Get |ost_s|_.
+#. Get |project| from the ``git`` repository (see :ref:`here <git-branches>`).
+#. Compile |project| with ``cmake`` and ``make`` (see :ref:`here <building-promod>`).
+#. Ensure that you have a ``stage/bin`` folder which includes a ``pm`` executable.
+ For convenience, add the folder to your ``PATH`` env. variable.
+#. You can now execute |project| by running the following in your terminal:
+
+ .. code-block:: console
+
+ $ pm <COMMAND>
+
+ Here ``<COMMAND>`` can be:
+
+ - a predefined "action" (execute ``pm help`` for a list of possible actions)
+ - the path to a python script, such as the following example:
+
+ .. code-block:: python
+
+ from ost import io
+ from promod3 import loop
+
+ # generate backbone with dihedrals of a helix and store it
+ sequence = "HELLYEAH"
+ bb_list = loop.BackboneList(sequence)
+ io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+ The execution of this script should generate a ``test.pdb`` file, which you
+ can visualize with any pdb reader (e.g. ``dng`` from |ost_s|).
+
+
+Modelling pipeline
+--------------------------------------------------------------------------------
+|project| is meant to help you perform operations for protein homology modelling.
+Commonly, your input is a template structure and an alignment of the template to
+the desired target sequence. The modelling steps then are:
+
+- Build a raw model from the template (see :mod:`~promod3.rawmodel` module)
+- Perform loop modelling to close all gaps (see :mod:`~promod3.loop` module)
+- Reconstruct sidechains (see :mod:`~promod3.sidechain` module)
+- Minimize energy of final model using molecular mechanics
+ (using :mod:`ost.mol.mm` from |ost_s|)
diff --git a/doc/html/_sources/loop/backbone.txt b/doc/html/_sources/loop/backbone.txt
index 136b870131242c5de878a7601b3f7e6a1dd5e43f..13befcdcbfc4bb2f97cde23c802cd302f872aec1 100644
--- a/doc/html/_sources/loop/backbone.txt
+++ b/doc/html/_sources/loop/backbone.txt
@@ -12,6 +12,7 @@ a residue. For simple structural manipulations they can be gathered to a
.. code-block:: python
+ from ost import io
from promod3 import loop
sequence = "AAAAAAAA"
@@ -47,19 +48,7 @@ a residue. For simple structural manipulations they can be gathered to a
The Basic Building Blocks
--------------------------------------------------------------------------------
-
-.. class:: DihedralPair()
-
- The DihedralPair class only serves as a helper to initialize a
- :class:`BackboneList` given consecutive dihedral angles.
-
- .. method:: DihedralPair(phi,psi)
-
- :param phi: Phi dihedral angle
- :param psi: Psi dihedral angle
-
-
-.. class:: Backbone()
+.. class:: Backbone
Container for the positions of the backbone atoms (N,CA,CB,C and O) of a residue.
@@ -167,8 +156,12 @@ Editing Full Stretches Of Backbone Residues
Creates a BackboneList from given **sequence** and **dihedral_angles**
:param sequence: Sequence of created BackboneList
- :param dihedral_angles: List of :class:`DihedralAngle` objects defining the phi/psi
- angles of created BackboneList
+ :param dihedral_angles: List of :class:`tuple` objects defining the backbone dihedral
+ angles of created BackboneList. Every :class:`tuple` 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.
:type sequence: :class:`str`
:type dihedral_angles: :class:`list`
@@ -195,7 +188,7 @@ Editing Full Stretches Of Backbone Residues
.. method:: ToEntity()
- Transforms the backbone list into an :class:`ost.mol.EntityHandle`.
+ Transforms the backbone list into an :class:`ost.mol.EntityHandle`.
:return: The entity
:rtype: :class:`ost.mol.EntityHandle`
@@ -204,7 +197,7 @@ Editing Full Stretches Of Backbone Residues
:return: The amino acid sequence
- .. method:: InsertInto(chain,n_stem,c_stem [,reset_stem_positions=True])
+ .. method:: InsertInto(chain,n_stem,c_stem,[remodel_cterminal_o = True])
Inserts the backbone list into the **chain**. If the residues corresponding
to the :class:`BackboneList` are already present in the entity, they will
@@ -213,12 +206,31 @@ Editing Full Stretches Of Backbone Residues
:param chain: The chain
:param n_stem: The residue number of the n_stem
:param c_stem: The residue number of the c_stem
- :param reset_stem_positions: Whether *n_stem* and *c_stem* residues'positions whould be set to the positions of the :class:`BackboneList`
+ :param remodel_cterminal_o: The position of the cterminal o is dependent
+ on the residue after the c_stem. If this flag
+ is set and the residue after the cterminus is
+ present in **chain**, the according oxygen
+ position gets recalculated.
:type entity: :class:`ost.mol.ChainHandle`
- :type n_stem: :class:`ost.mol.ResNum`
- :type c_stem: :class:`ost.mol.ResNum`
- :type reset_stem_positions: :class:`Bool`
+ :type n_stem: :class:`int`
+ :type c_stem: :class:`int`
+ :type remodel_cterminal_o: :class:`bool`
+
+ .. method:: ReconstructCBetaPositions()
+
+ Does a simple reconstruction of all CBeta positions based on the actual
+ n, ca, and c positions.
+ .. method:: ReconstructOxygenPositions([last_psi = -0.78540])
+
+ 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.
+
+ :param last_psi: Psi angle of the last BackboneList residue,
+ the default value corresponds to a typical alpha-helix
+
+ :type last_psi: :class:`float`
.. method:: ApplyTransform(transformation_matrix)
@@ -238,7 +250,7 @@ Editing Full Stretches Of Backbone Residues
Sets the *phi* torsion angle of the backbone at position **index** in the :class:`BackboneList`.
- :param index: The index of the residue in the :class:`BackboneList` for which the angle shout be set.
+ :param index: The index of the residue in the :class:`BackboneList` for which the angle should be set.
:param angle: The angle
:param sequential: If *True*, the rotation will be propagated to all residues after the one with **index**. Otherwise it will be propagated in the direction where it will affect the least number of residues.
@@ -250,7 +262,7 @@ Editing Full Stretches Of Backbone Residues
Sets the *psi* torsion angle of the backbone at position **index** in the :class:`BackboneList`.
- :param index: The index of the residue in the :class:`BackboneList` for which the angle shout be set.
+ :param index: The index of the residue in the :class:`BackboneList` for which the angle should be set.
:param angle: The angle
:param sequential: If *True*, the rotation will be propagated to all residues after the one with **index**. Otherwise it will be propagated in the direction where it will affect the least number of residues.
@@ -262,7 +274,7 @@ Editing Full Stretches Of Backbone Residues
Sets the *omega* torsion angle of the backbone at position **index** in the :class:`BackboneList`.
- :param index: The index of the residue in the :class:`BackboneList` for which the angle shout be set.
+ :param index: The index of the residue in the :class:`BackboneList` for which the angle should be set.
:param angle: The angle
:param sequential: If *True*, the rotation will be propagated to all residues after the one with **index**. Otherwise it will be propagated in the direction where it will affect the least number of residues.
@@ -270,11 +282,25 @@ Editing Full Stretches Of Backbone Residues
:type angle: :class:`float`
:type sequential: :class:`bool`
+ .. method:: SetPhiPsiTorsion(index,phi, psi[,sequential=False])
+
+ Sets the *phi* and *psi* torsion angle of the backbone at position **index** in the :class:`BackboneList`.
+
+ :param index: The index of the residue in the :class:`BackboneList` for which the angle should be set.
+ :param phi: The phi angle
+ :param psi: The psi angle
+ :param sequential: If *True*, the rotation will be propagated to all residues after the one with **index**. Otherwise it will be propagated in the direction where it will affect the least number of residues.
+
+ :type index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type sequential: :class:`bool`
+
.. method:: RotateAroundPhiTorsion(index,angle[,sequential=False])
Rotates the *phi* torsion angle of the backbone at position **index** in the :class:`BackboneList` by **angle**.
- :param index: The index of the residue in the :class:`BackboneList` for which the angle shout be set.
+ :param index: The index of the residue in the :class:`BackboneList` for which the angle should be set.
:param angle: The angle
:param sequential: If *True*, the rotation will be propagated to all residues after the one with **index**. Otherwise it will be propagated in the direction where it will affect the least number of residues.
@@ -286,7 +312,7 @@ Editing Full Stretches Of Backbone Residues
Rotates the *psi* torsion angle of the backbone at position **index** in the :class:`BackboneList` by **angle**.
- :param index: The index of the residue in the :class:`BackboneList` for which the angle shout be set.
+ :param index: The index of the residue in the :class:`BackboneList` for which the angle should be set.
:param angle: The angle
:param sequential: If *True*, the rotation will be propagated to all residues after the one with **index**. Otherwise it will be propagated in the direction where it will affect the least number of residues.
@@ -298,7 +324,7 @@ Editing Full Stretches Of Backbone Residues
Rotates the *omega* torsion angle of the backbone at position **index** in the :class:`BackboneList` by **angle**.
- :param index: The index of the residue in the :class:`BackboneList` for which the angle shout be set.
+ :param index: The index of the residue in the :class:`BackboneList` for which the angle should be set.
:param angle: The angle
:param sequential: If *True*, the rotation will be propagated to all residues after the one with **index**. Otherwise it will be propagated in the direction where it will affect the least number of residues.
@@ -306,6 +332,20 @@ Editing Full Stretches Of Backbone Residues
:type angle: :class:`float`
:type sequential: :class:`bool`
+ .. method:: RotateAroundPhiPsiTorsion(index,phi, psi[,sequential=False])
+
+ Rotates the *phi* and *psi* torsion angle of the backbone at position **index** in the :class:`BackboneList` by **phi** and **psi**.
+
+ :param index: The index of the residue in the :class:`BackboneList` for which the angle should be set.
+ :param phi: The phi angle
+ :param psi: The psi angle
+ :param sequential: If *True*, the rotation will be propagated to all residues after the one with **index**. Otherwise it will be propagated in the direction where it will affect the least number of residues.
+
+ :type index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type sequential: :class:`bool`
+
.. method:: GetPhiTorsion(index)
Get the *phi* torsion angle of the residue with **index** in the :class:`BackboneList`
@@ -327,14 +367,26 @@ Editing Full Stretches Of Backbone Residues
:param index: The index
:type index: :class:`int`
- .. method:: ReplaceFragment(sub_fragment,index)
+ .. method:: ReplaceFragment(sub_fragment,index,superpose_stems)
Replaces a fragment of the :class:`BackboneList` starting at position **index** by the **sub_fragment**.
:param sub_fragment: The fragment to be inserted
- :param index: The position at which the fragment replacement will begin
+ :param index: The position at which the fragment
+ replacement will begin
+ :param superpose_stems: If set to false, the function will simply
+ replace the according
+ :class:`Backbone` objects. If set to true,
+ the n-terminal and c-terminal tails are superposed onto the **sub_fragment**
+ stems using the positions at **index** and
+ **index** + len( **sub_fragment** )-1.
:type sub_fragment: :class:`BackboneList`
:type index: :class:`int`
+ :type superpose_stems: :class:`bool`
+
+ :raises: :class:`RuntimeError` If **sub_fragment**
+ does not fully fit into actual fragment at
+ specified **index**
.. method:: CARMSD(other[,superposed_rmsd=False])
@@ -363,15 +415,6 @@ Editing Full Stretches Of Backbone Residues
:param other: The other backbone list
:type other: :class:`BackboneList`
- .. method:: insert(index,bb)
-
- Insert the backbone **bb** into the :class:`BackboneList` at position **index**.
-
- :param index: The index
- :param bb: The backbone
- :type index: :class:`int`
- :type bb: :class:`Backbone`
-
.. method:: append(bb)
Appends the backbone **bb** at the end of the :class:`BackboneList`.
diff --git a/doc/html/_sources/loop/index.txt b/doc/html/_sources/loop/index.txt
index 121692f633e26bd0f2cb4280dc7fd5f37afbc99a..4d7e4abf1979161b2b1bba9e59590f11892f5d1c 100644
--- a/doc/html/_sources/loop/index.txt
+++ b/doc/html/_sources/loop/index.txt
@@ -6,7 +6,76 @@
.. currentmodule:: promod3.loop
-Tools and algorithms to for loop modelling.
+Tools and algorithms for loop modelling.
+This module provides ways for representation and manipulation of peptides and
+finally connect them to larger structures. The following example should give
+you a starting point to get an idea of what can be done.
+
+.. code-block:: python
+
+ from ost import io
+ from promod3 import loop
+
+ #let's load a crambin structure from the pdb
+ crambin = io.LoadPDB("1crn",remote=True)
+ SEQRES = ''.join([r.one_letter_code for r in crambin.residues])
+
+ #this is the sequence we want to remodel
+ loop_seq = SEQRES[23:31]
+
+ #let's define the stem residues
+ n_stem = crambin.residues[23]
+ c_stem = crambin.residues[30]
+
+ #we use the StructureDB as source for structural information
+ structure_db = loop.LoadStructureDB()
+
+ #the FragDB allows to access the StructureDB based on geometric
+ #features of the loop stem residue
+ frag_db = loop.LoadFragDB()
+
+ #the LoopCandidates allow to handle several loops at once
+ #we directly want to find potential loop candidates from the
+ #previously loaded databases
+ loop_candidates = loop.LoopCandidates.FillFromDatabase(n_stem,
+ c_stem,
+ loop_seq,
+ frag_db,
+ structure_db)
+
+ #The candidates usually don't match exactly the required stem coordinates
+ #CCD (Cyclic Coordinate Descent) is one way to enforce this match.
+ loop_candidates.ApplyCCD()
+
+ #now it's time to select one candidate, we load a scorer object to do that
+ scorer = loop.LoadBackboneLoopScorer()
+
+ #initialize scorer with the environment given by the crambin structure
+ scorer.Initialize(SEQRES)
+ scorer.SetEnvironment(crambin)
+
+ #the scorer can then be attached to the LoopCandidates object
+ #to calculate several different scores, we go for a distance dependent
+ #statistical potential considering the CBeta positions of each residue
+ #and a clash score
+ loop_candidates.AttachScorer(scorer)
+ loop_candidates.CalculateCBetaScores()
+ loop_candidates.CalculateClashScores()
+
+ #we simply sum up the previously calculated scores and search for the
+ #loop with minimal score
+ min_score = float("inf")
+ min_candidate = 0
+ for i,lc in enumerate(loop_candidates):
+ score = lc.cbeta_score + lc.clash_score
+ if score < min_score:
+ min_score = score
+ min_candidate = i
+
+ #let's insert that loop and save the structure down to disk
+ loop_candidates.InsertInto(crambin,min_candidate)
+ io.SavePDB(crambin,"remodeled_crambin.pdb")
+
Contents:
diff --git a/doc/html/_sources/loop/loop_candidate.txt b/doc/html/_sources/loop/loop_candidate.txt
index e5c970ac83fa209022f9c51e9ff262876a97171b..8ddf97898d623b9fba69f4ff552409c69d007ce0 100644
--- a/doc/html/_sources/loop/loop_candidate.txt
+++ b/doc/html/_sources/loop/loop_candidate.txt
@@ -94,7 +94,7 @@ Loop Candidates
.. class:: LoopCandidates(n_stem,c_stem,seq)
- The *LoopCandidates* is the basic object used for loop modelling. It contains the positions of the two anchor residues, the *n_stem* and *c_stem* residues, and thes sequence of the residues to be modelled in between these anchor residues.
+ The *LoopCandidates* is the basic object used for loop modelling. It contains the positions of the two anchor residues, the *n_stem* and *c_stem* residues, and the sequence of the residues to be modelled in between these anchor residues.
It also contains a list of :class:`LoopCandidate`, which are possible conformations of the backbone between the stem residues.
@@ -137,11 +137,11 @@ Loop Candidates
:param initial_bb: Initial configuration used for the sampling
:param seq: The sequence of residues to be added between the *n_stem* and *c_stem*
:param num_loops: Number of loop candidates to return
- :param steps: Number of MC steps to perform for each loop candidate generated.
+ :param steps: Number of MC steps to perform for each loop candidate generated
+ :param sampler: Used to generate a new configuration at each MC step
+ :param closer: Used to close the loop (make it match the *n_stem* and *c_stem* geometry) after each MC step
+ :param scorer: Used to score the generated configurations at each MC step
:param cooler: Controls the temperature profile of the simulated annealing
- :param scorer: Used to score the generated configurations at each MC step.
- :param sampler: Used to generate a new configuration at each MC step.
- :param closer: Used to close the loop (make it match the *n_stem* and *c_stem* geometry) after each MC step.
:type n_stem: :class:`ost.mol.ResidueHandle`
:type c_stem: :class:`ost.mol.ResidueHandle`
@@ -149,10 +149,10 @@ Loop Candidates
:type initial_bb: :class:`BackboneList`
:type num_loops: :class:`int`
:type steps: :class:`int`
- :type sampler: :class:`MonteCarloSampler`
- :type closer: :class:`MonteCarloCloser`
- :type scorer: :class:`MonteCarloScorer`
- :type cooler: :class:`MonteCarloCooler`
+ :type sampler: :ref:`mc-sampler-object`
+ :type closer: :ref:`mc-closer-object`
+ :type scorer: :ref:`mc-scorer-object`
+ :type cooler: :ref:`mc-cooler-object`
:returns: A list of loop candidates
:rtype: :class:`LoopCandidates`
@@ -165,21 +165,21 @@ Loop Candidates
:param c_stem: The residue at the C-terminal end of the loop
:param seq: The sequence of residues to be added between the *n_stem* and *c_stem*
:param num_loops: Number of loop candidates to return
- :param steps: Number of MC steps to perform for each loop candidate generated.
+ :param steps: Number of MC steps to perform for each loop candidate generated
+ :param sampler: Used to generate a new configuration at each MC step
+ :param closer: Used to close the loop (make it match the *n_stem* and *c_stem* geometry) after each MC step
+ :param scorer: Used to score the generated configurations at each MC step
:param cooler: Controls the temperature profile of the simulated annealing
- :param scorer: Used to score the generated configurations at each MC step.
- :param sampler: Used to generate a new configuration at each MC step.
- :param closer: Used to close the loop (make it match the *n_stem* and *c_stem* geometry) after each MC step.
:type n_stem: :class:`ost.mol.ResidueHandle`
:type c_stem: :class:`ost.mol.ResidueHandle`
:type seq: :class:`str`
:type num_loops: :class:`int`
:type steps: :class:`int`
- :type sampler: :class:`MonteCarloSampler`
- :type closer: :class:`MonteCarloCloser`
- :type scorer: :class:`MonteCarloScorer`
- :type cooler: :class:`MonteCarloCooler`
+ :type sampler: :ref:`mc-sampler-object`
+ :type closer: :ref:`mc-closer-object`
+ :type scorer: :ref:`mc-scorer-object`
+ :type cooler: :ref:`mc-cooler-object`
:returns: A list of loop candidates
:rtype: :class:`LoopCandidates`
@@ -245,7 +245,7 @@ Loop Candidates
.. method:: ApplyKIC(pivot_one,pivot_two,pivot_three)
- Closes all :class:`LoopCandidate` in :class:`LoopCandidates` (i.e. modifies the :class:`LoopCandidate` so that its stem residues match those of the :class:`LoopCandidates`, which are the stem residues of the loop being modelled), using the KIC algorithm. This algorithm finds analytical solutions for closing the loop by modifying the torsion angles of just three pivot residues.
+ Closes all :class:`LoopCandidate` in :class:`LoopCandidates` (i.e. modifies the :class:`LoopCandidate` so that its stem residues match those of the :class:`LoopCandidates`, which are the stem residues of the loop being modelled), using the KIC algorithm. This 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.
:param pivot_one: Maximum number of iteration
:param pivot_two: Cutoff in stem residue RMSD used
diff --git a/doc/html/_sources/loop/loop_closing.txt b/doc/html/_sources/loop/loop_closing.txt
index 00fd52ae8a77085167002797145808817818db68..a43ec1fc9ad71cf642fc0b0237913ea1d984c735 100644
--- a/doc/html/_sources/loop/loop_closing.txt
+++ b/doc/html/_sources/loop/loop_closing.txt
@@ -8,11 +8,11 @@ Loops, represented as :class:`BackboneList` objects, often need to undergo
conformational changes to fit into gaps defined by stem residues.
|project| implements two algorithms performing this task.
-There is cyclic coordinate descent (CCD):
-Adrian A. Canutescu and Roland L. Dunbrack Jr. "Cyclic coordinate descent: A robotics algorithm for protein loop closure." Protein Sci. 12(5):963–972. (2003)
+ * There is cyclic coordinate descent (CCD) [canutescu2003]_
+
+
+ * and kinematic closure (KIC) [mandell2009]_
-and kinematic closure (KIC):
-Mandell DJ, Coutsias EA and Kortemme T. "Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling." Nat Methods. 6(8):551-2. (2009)
In case of small gaps or small issues in the :class:`BackboneList` you might
also consider the :class:`BackboneRelaxer`.
@@ -41,179 +41,75 @@ after/before is smaller than a random number in range [0;1[, the proposed
dihedral pair gets rejected and the next iteration starts. Please note, that
this increases the probability of non-convergence.
-.. method:: CCD(bb_list, n_stem, c_stem, [max_steps=1000,rmsd_cutoff=0.1,random_seed=0])
- :param bb_list: Loop to be closed
- :param n_stem: Residue from which the desired n-stem positions are
- extracted
- :param c_stem: Residue from which the desired c-stem positions are
- extracted
- :param max_steps: Max number of iterations
- :param rmsd_cutoff: Iterations abort when this RMSD between the c-stem of
- the loop and the desired c-stem is reached
- :param random_seed: Seed for internal randomness
- :type bb_list: :class:`BackboneList`
- :type n_stem: :class:`ost.mol.ResidueHandle`
- :type c_stem: :class:`ost.mol.ResidueHandle`
- :type max_steps: :class:`int`
- :type rmsd_cutoff: :class:`float`
- :type random_seed: :class:`int`
+.. class:: CCD
- :returns: :class:`bool` whether the RMSD threshold has been reached
+ Class, that sets up everything you need to perform a particular loop closing
+ action.
+ .. method:: CCD(sequence, n_stem, c_stem, torsion_sampler, max_steps, rmsd_cutoff, seed)
-.. method:: CCD(bb_list, n_stem_pos, c_stem_pos, [max_steps=1000,rmsd_cutoff=0.1,random_seed=0])
+ All runs with this CCD object will be with application of torsion samplers
+ to avoid moving into unfavourable regions of the backbone dihedrals.
- :param bb_list: Loop to be closed
- :param n_stem_pos: 3 positions describing the desired
- N, CA and C positions of the n_stem
- :param c_stem_pos: 3 positions describing the desired
- N, CA and C positions of the c_stem
- :param max_steps: Max number of iterations
- :param rmsd_cutoff: Iterations abort when this RMSD between the c-stem of
- the loop and the desired c-stem is reached
- :param random_seed: Seed for internal randomness
+ :param sequence: Sequence of the backbones to be closed
+ :param n_stem: Residue defining the n_stem
+ :param c_stem: Residue defining the c_stem
+ :param torsion_sampler: To extract probabilities for the analysis of the backbone
+ dihedrals. You either pass a list with :class:`TorsionSampler`
+ objects for every residue of the loop to be closed or a single
+ :class:`TorsionSampler`, that will be applied on all residues.
+ :param max_steps: Maximal number of iterations
+ :param rmsd_cutoff: The algorithm stops as soon as the c_stem of the loop to be
+ closed has RMSD below the **c_stem**
+ :param seed: Seed of random number generator to decide whether new phi/psi pair
+ should be accepted.
- :type bb_list: :class:`BackboneList`
- :type n_stem_pos: :class:`ost.geom.Vec3List`
- :type c_stem_pos: :class:`ost.geom.Vec3List`
- :type max_steps: :class:`int`
- :type rmsd_cutoff: :class:`float`
- :type random_seed: :class:`int`
- :returns: :class:`bool` whether the RMSD threshold has been reached
+ :type sequence: :class:`str`
+ :type n_stem: :class:`ost.mol.ResidueHandle`
+ :type c_stem: :class:`ost.mol.ResidueHandle`
+ :type torsion_sampler: :class:`TorsionSampler` / :class:`list`
+ :type max_steps: :class:`int`
+ :type rmsd_cutoff: :class:`float`
+ :type seed: :class:`int`
+ :raises: :class:`RuntimeError` if a list of torsion samplers is given
+ with inconsistent length regarding the sequence. Another
+ requirement is that the residue before **n_stem** and
+ after **c_stem** must be valid and all backbone atoms
+ are present.
+ .. method:: CCD(n_stem, c_stem, max_steps, rmsd_cutoff)
+ All runs with this CCD object will be without application of torsion samplers.
+ This is faster but might lead to weird backbone dihedral pairs.
-.. method:: CCD(bb_list, n_stem, c_stem, torsion_sampler [max_steps=1000,rmsd_cutoff=0.1,random_seed=0])
+ :param n_stem: Residue defining the n_stem
+ :param c_stem: Residue defining the c_stem
+ :param max_steps: Maximal number of iterations
+ :param rmsd_cutoff: The algorithm stops as soon as the c_stem of the loop to be
+ closed has RMSD below the **c_stem**
- :param bb_list: Loop to be closed
- :param n_stem: Residue from which the desired n-stem positions are
- extracted
- :param c_stem: Residue from which the desired c-stem positions are
- extracted
- :param torsion_sampler: For extracting probabilities to decide whether a new
- dihedral pair should be accepted or not. This sampler
- gets applied to all residues of the loop.
- :param max_steps: Max number of iterations
- :param rmsd_cutoff: Iterations abort when this RMSD between the c-stem of
- the loop and the desired c-stem is reached
- :param random_seed: Seed for internal randomness
+ :type n_stem: :class:`ost.mol.ResidueHandle`
+ :type c_stem: :class:`ost.mol.ResidueHandle`
+ :type max_steps: :class:`int`
+ :type rmsd_cutoff: :class:`float`
- :type bb_list: :class:`BackboneList`
- :type n_stem: :class:`ost.mol.ResidueHandle`
- :type c_stem: :class:`ost.mol.ResidueHandle`
- :type torsion_sampler: :class:`TorsionSampler`
- :type max_steps: :class:`int`
- :type rmsd_cutoff: :class:`float`
- :type random_seed: :class:`int`
-
- :returns: :class:`bool` whether the RMSD threshold has been reached
-
- :raises: :class:`RuntimeError` when assigining of histogram
- indices for torsion sampler fails. This is the case
- when the residue before the given n-stem or the
- residue after the given c-stem is not present.
-
-
-.. method:: CCD(bb_list, n_stem, c_stem, torsion_sampler[max_steps=1000,rmsd_cutoff=0.1,random_seed=0])
-
- :param bb_list: Loop to be closed
- :param n_stem: Residue from which the desired n-stem positions are
- extracted
- :param c_stem: Residue from which the desired c-stem positions are
- extracted
- :param torsion_sampler: List of :class:`TorsionSampler` For extracting
- probabilities to decide whether a new dihedral pair
- should be accepted or not. There must be one sampler
- for every residue.
- :param max_steps: Max number of iterations
- :param rmsd_cutoff: Iterations abort when this RMSD between the c-stem of
- the loop and the desired c-stem is reached
- :param random_seed: Seed for internal randomness
+ .. method:: Close(bb_list)
- :type bb_list: :class:`BackboneList`
- :type n_stem: :class:`ost.mol.ResidueHandle`
- :type c_stem: :class:`ost.mol.ResidueHandle`
- :type torsion_sampler: :class:`list`
- :type max_steps: :class:`int`
- :type rmsd_cutoff: :class:`float`
- :type random_seed: :class:`int`
-
- :returns: :class:`bool` whether the RMSD threshold has been
- reached
-
- :raises: :class:`RuntimeError` when assigining of histogram
- indices for torsion sampler fails. This is the case
- when the residue before the given n-stem or the
- residue after the given c-stem is not present.
-
-
-.. method:: CCD(bb_list, n_stem_pos, c_stem_pos, torsion_sampler, dihedral_indices[max_steps=1000,rmsd_cutoff=0.1,random_seed=0])
-
- :param bb_list: Loop to be closed
- :param n_stem_pos: 3 positions describing the desired
- N, CA and C positions of the n_stem
- :param c_stem_pos: 3 positions describing the desired
- N, CA and C positions of the c_stem
- :param torsion_sampler: List of :class:`TorsionSampler` For extracting
- probabilities to decide whether a new dihedral pair
- should be accepted or not. There must be one sampler
- for every residue.
- :param dihedral_indices: If no stem residues are given, there is no
- possibility to figure out the torsion sampler indices
- for the stem residues. All indices must therefore be
- given.
- :param max_steps: Max number of iterations
- :param rmsd_cutoff: Iterations abort when this RMSD between the c-stem of
- the loop and the desired c-stem is reached
- :param random_seed: Seed for internal randomness
+ Closes given **bb_list** with the settings set at initialization.
- :type bb_list: :class:`BackboneList`
- :type n_stem_pos: :class:`ost.geom.Vec3List`
- :type c_stem_pos: :class:`ost.geom.Vec3List`
- :type torsion_sampler: :class:`TorsionSampler`
- :param dihedral_indices: :class:`list`
- :type max_steps: :class:`int`
- :type rmsd_cutoff: :class:`float`
- :type random_seed: :class:`int`
-
- :returns: :class:`bool` whether the RMSD threshold has been
- reached
-
-
-.. method:: CCD(bb_list, n_stem_pos, c_stem_pos, torsion_sampler, dihedral_indices[max_steps=1000,rmsd_cutoff=0.1,random_seed=0])
-
- :param bb_list: Loop to be closed
- :param n_stem_pos: 3 positions describing the desired
- N, CA and C positions of the n_stem
- :param c_stem_pos: 3 positions describing the desired
- N, CA and C positions of the c_stem
- :param torsion_sampler: For extracting probabilities to decide whether a new
- dihedral pair should be accepted or not. This sampler
- gets applied to all residues of the loop.
- :param dihedral_indices: If no stem residues are given, there is no
- possibility to figure out the torsion sampler indices
- for the stem residues. All indices must therefore be
- given.
- :param max_steps: Max number of iterations
- :param rmsd_cutoff: Iterations abort when this RMSD between the c-stem of
- the loop and the desired c-stem is reached
- :param random_seed: Seed for internal randomness
+ :param bb_list: Loop to be closed
- :type bb_list: :class:`BackboneList`
- :type n_stem_pos: :class:`ost.geom.Vec3List`
- :type c_stem_pos: :class:`ost.geom.Vec3List`
- :type torsion_sampler: :class:`list`
- :param dihedral_indices: :class:`list`
- :type max_steps: :class:`int`
- :type rmsd_cutoff: :class:`float`
- :type random_seed: :class:`int`
+ :type bb_list: :class:`BackboneList`
+
+ :returns: :class:`bool` Whether **rmsd_cutoff** has been reached
- :returns: :class:`bool` whether the RMSD threshold has been
- reached
+ :raises: :class:`RuntimeError` if the CCD object has been initialized
+ with :class:`TorsionSampler` support and the length of the
+ **bb_list** is not consistent with the initial sequence.
@@ -226,57 +122,37 @@ at these pivot residues. Due to the internal mathematical formalism, up to
16 solutions can be found for a given loop closing problem.
-.. method:: KIC(bb_list, n_stem, c_stem, pivot_one, pivot_two, pivot_three)
+.. class:: KIC
- :param bb_list: Loop to be closed
- :param n_stem: Residue from which the desired n-stem positions are
- extracted
- :param c_stem: Residue from which the desired c-stem positions are
- extracted
- :param pivot_one: Index of first pivot residue
- :param pivot_two: Index of second pivot residue
- :param pivot_three: Index of third pivot residue
+ Class, that sets up everything you need to perform a particular loop closing
+ action.
- :type bb_list: :class:`BackboneList`
- :type n_stem: :class:`ost.mol.ResidueHandle`
- :type c_stem: :class:`ost.mol.ResidueHandle`
- :type pivot_one: :class:`int`
- :type pivot_two: :class:`int`
- :type pivot_three: :class:`int`
+ .. method:: KIC(n_stem, c_stem)
+ All runs of this KIC closing object will adapt the input loops to these
+ stem residues.
- :returns: List of :class:`BackboneList` objects representing
- the closed loops. There is a maximum of 16 entries.
+ :param n_stem: Residue describing the stem towards n_ter
+ :param c_stem: Residue describing the stem towards c_ter
- :raises: :class:`RuntimeError` in case of invalid pivot indices.
+ .. method:: Close(bb_list, pivot_one, pivot_two, pivot_three)
+ Applies KIC algorithm, so that the output loops match the given stem residues
-.. method:: KIC(bb_list, n_stem_pos, c_stem_pos, pivot_one, pivot_two, pivot_three)
+ :param bb_list: Loop to be closed
+ :param pivot_one: Index of first pivot residue
+ :param pivot_two: Index of second pivot residue
+ :param pivot_three: Index of third pivot residue
- :param bb_list: Loop to be closed
+ :type bb_list: :class:`BackboneList`
+ :type pivot_one: :class:`int`
+ :type pivot_two: :class:`int`
+ :type pivot_three: :class:`int`
+ :returns: List of :class:`BackboneList` objects representing
+ the closed loops. There is a maximum of 16 entries.
- :param n_stem_pos: 3 positions describing the desired
- N, CA and C positions of the n_stem
- :param c_stem_pos: 3 positions describing the desired
- N, CA and C positions of the c_stem
- :param pivot_one: Index of first pivot residue
- :param pivot_two: Index of second pivot residue
- :param pivot_three: Index of third pivot residue
-
- :type bb_list: :class:`BackboneList`
- :type n_stem_pos: :class:`ost.geom.Vec3List`
- :type c_stem_pos: :class:`ost.geom.Vec3List`
- :type pivot_one: :class:`int`
- :type pivot_two: :class:`int`
- :type pivot_three: :class:`int`
-
-
- :returns: List of :class:`BackboneList` objects representing
- the closed loops. There is a maximum of 16 entries.
-
- :raises: :class:`RuntimeError` in case of invalid pivot indices.
-
+ :raises: :class:`RuntimeError` in case of invalid pivot indices.
@@ -300,7 +176,7 @@ can be relaxed by the relaxer.
:param bb_list: Basis for topology creation
:param fix_nterm: Whether n-terminal backbone positions should kept
rigid during relaxation.
- :param fix_cterm: Whether c-termainl backbone positions should kept
+ :param fix_cterm: Whether c-terminal backbone positions should kept
rigid during relaxation.
:type bb_list: :class:`BackboneList`
@@ -324,7 +200,14 @@ can be relaxed by the relaxer.
:type steps: :class:`steps`
:type stop_criterion: :class:`float`
- :returns: Forcefield energy
+ :returns: Forcefield energy upon relaxation
:raises: :class:`RuntimeError` if **bb_list** has not the same
size or sequence as the initial one.
+
+
+
+
+.. [canutescu2003] Canutescu AA and Dunbrack RL Jr. (2003). Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12(5):963–972.
+
+.. [mandell2009] Mandell DJ, Coutsias EA and Kortemme T (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 6(8):551-2.
\ No newline at end of file
diff --git a/doc/html/_sources/loop/monte_carlo.txt b/doc/html/_sources/loop/monte_carlo.txt
index fb7973e19b6e68dd74868b86ec235a353d964fb2..11dbd3e03fe5d76d3f9ad42c40732f626912e69a 100644
--- a/doc/html/_sources/loop/monte_carlo.txt
+++ b/doc/html/_sources/loop/monte_carlo.txt
@@ -28,13 +28,13 @@ provided by |project|.
temperature given by the **cooler**
=> acceptance probability: exp(-delta_score/T)
- :param cooler: Cooler object to control the temperature of the
- monte carlo trajectory
- :param scorer: Scorer object to score new loop conformations
:param sampler: Sampler object capable of initializing and altering
conformations.
:param closer: Closer object to adapt a new conformation to
the environment
+ :param scorer: Scorer object to score new loop conformations
+ :param cooler: Cooler object to control the temperature of the
+ monte carlo trajectory
:param steps: Number of monte carlo iterations to be performed
:param bb_list: The lowest scoring conformation of the trajectory
gets stored in here
@@ -43,10 +43,10 @@ provided by |project|.
The input **bb_list** gets used otherwise.
:param seed: Seed for internal random number generator.
- :type cooler: :class:`CoolerObject`
- :type scorer: :class:`ScorerObject`
- :type sampler: :class:`SamplerObject`
- :type closer: :class:`CloserObject`
+ :type sampler: :ref:`mc-sampler-object`
+ :type closer: :ref:`mc-closer-object`
+ :type scorer: :ref:`mc-scorer-object`
+ :type cooler: :ref:`mc-cooler-object`
:type steps: :class:`int`
:type bb_list: :class:`BackboneList`
:type initialize: :class:`bool`
@@ -62,6 +62,7 @@ provided by |project|.
#Example script, that applies monte-carlo sampling to the n-terminal
#part of crambin
+ from ost import io
from promod3 import loop
import numpy as np
@@ -77,7 +78,7 @@ provided by |project|.
#setup mc_sampler
torsion_sampler = loop.LoadTorsionSampler()
- mc_sampler = loop.SoftSampler(terminal_sequence,torsion_sampler,20.0/180*np.pi)
+ mc_sampler = loop.SoftSampler(terminal_sequence,torsion_sampler,10.0/180*np.pi)
#setup mc_closer
mc_closer = loop.NTerminalCloser(prot.residues[n_terminal_length-1])
@@ -89,7 +90,6 @@ provided by |project|.
weights = dict()
weights["cbeta"]=10.0
- weights["cb_packing"]=1.0
weights["clash"]=0.1
mc_scorer = loop.LinearScorer(scorer,start_resnum,chain_index,weights)
@@ -107,8 +107,9 @@ provided by |project|.
+.. _mc-sampler-object:
-Sampler Objects
+Sampler Object
--------------------------------------------------------------------------------
The sampler objects can be used to generate initial conformations and
@@ -254,8 +255,53 @@ for any monte carlo sampling pipeline.
efficiency reasons.
+.. class:: FragmentSampler(sequence, fraggers, [init_fragments = 3, seed = 0])
+
+ The FragmentSampler samples by replacing full fragments originating from a list
+ of :class:`Fragger` objects.
+
+ :param sequence: Sequence that should be sampled
+ :param fraggers: A list of :class:`Fragger` objects. The first fragger
+ covers the region starting at the first letter of the
+ **sequence** and so on. All fraggers must contain fragments
+ of equal size an exactly cover the full sequence to
+ be sampled.
+ :param init_fragments: When calling the Initialize function, a completely helical
+ conformation gets created. This is the number of fragments
+ that gets randomly selected and inserted.
+ :param seed: Seed for the internal random number generators
+
+ :type sequence: :class:`str`
+ :type fraggers: :class:`str`
+ :type init_fragments: :class:`int`
+ :type seed: :class:`int`
+
+
+ .. method:: Initialize(bb_list)
+
+ Sets up a new :class:`BackboneList` by creating a helix and replace n fragments
+ with n = **init_fragments** as given at the samplers initialization
+
+ :param bb_list: The newly created conformation gets stored in here
+ :type bb_list: :class:`BackboneList`
+
+
+ .. method:: ProposeStep(actual_step, proposed_position)
+
+ Randomly selects a position and selects a random fragment from the according
+ fragger object to alter the conformation.
-Closer Objects
+ :param actual_positions: Conformation to be changed
+ :param proposed_positions: Changed conformation gets stored in here
+
+ :type actual_positions: :class:`BackboneList`
+ :type proposed_positions: :class:`BackboneList`
+
+
+
+.. _mc-closer-object:
+
+Closer Object
--------------------------------------------------------------------------------
After the proposal of new conformations by the sampler objects, the
@@ -307,7 +353,7 @@ or simple stem superposition in case of terminal sampling.
:returns: Whether CCD converged
-.. class:: DirtyCCDCloser(n_stem, c_stem, seed)
+.. class:: DirtyCCDCloser(n_stem, c_stem)
The DirtyCCDCloser applies the CCD algorithm to the sampled conformation
to enforce the match between the conformations stem residue and
@@ -319,11 +365,8 @@ or simple stem superposition in case of terminal sampling.
:param c_stem: Defining stem positions the closed conformation
should adapt.
- :param seed: Seed for internal random generators.
-
:type n_stem: :class:`ost.mol.ResidueHandle`
:type c_stem: :class:`ost.mol.ResidueHandle`
- :type seed: :class:`int`
.. method:: Close(actual_positions,closed_positions)
@@ -387,8 +430,9 @@ or simple stem superposition in case of terminal sampling.
:returns: Whether closing was successful
+.. _mc-scorer-object:
-Scorer Objects
+Scorer Object
--------------------------------------------------------------------------------
The scorer asses a proposed conformation and are intended to return a pseudo
@@ -418,21 +462,18 @@ energy, the lower the better.
:raises: :class:`RuntimeError` If there is an invalid weight name.
- .. method:: GetScore(temperature, bb_list)
+ .. method:: GetScore(bb_list)
- :param temperature: Current temperature in the monte carlo trajectory.
- This has no effect on the score of the LinearScorer
- and is only there to fulfill the requirements of the
- abstract baseclass.
:param bb_list: Current loop conformation to be scored.
- :type temperature: :class:`float`
:type bb_list: :class:`BackboneList`
:returns: A linear combination of the scores
-Cooler Objects
+.. _mc-cooler-object:
+
+Cooler Object
--------------------------------------------------------------------------------
The cooler objects control the temperature of the monte carlo trajectory.
diff --git a/doc/html/_sources/loop/structure_db.txt b/doc/html/_sources/loop/structure_db.txt
index 0746bf2c6f62f65ab5fab6251b6892e9f8e557ae..0f792588a93a6c6198fa4b9a22d4faad8a08c8d2 100644
--- a/doc/html/_sources/loop/structure_db.txt
+++ b/doc/html/_sources/loop/structure_db.txt
@@ -5,8 +5,29 @@ Structural Database
The structural database serves as a container for structural backbone
and profile data. It can be filled with chains of pdb structures with their
-corresponding profiles as they are produced by the HHSuite tools.
-
+corresponding profiles as they are produced by the HHSuite tools [soding2005]_.
+Some of the extracted features expect the secondary structure, as well as the solvent
+accessibility to be assigned using dssp [kabsch1983]_.
+Following features get stored on a per residue basis:
+
+* The amino acid one letter code
+* The coordinates of the backbone atoms (N,CA,C,O)
+* The phi/psi dihedral angles
+* The secondary structure state as defined by dssp
+* The solvent accessibility in square Angstrom as calculated by dssp
+* The residue depth defined as the average distance from all atoms of a
+ residue to the closest surface vertex as calculated by msms [sanner1996]_
+ - This is a simplified version of
+ the residue depth as discussed in [chakravarty1999]_ and gets directly calculated
+ when structural information gets added to the StructureDB
+* The amino acid frequencies as given by an input HMM
+* The amino acid frequency derived from structural alignments as described
+ in [zhou2005]_ - 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).
Defining Chains and Fragments
--------------------------------------------------------------------------------
@@ -20,38 +41,127 @@ Defining Chains and Fragments
.. attribute:: pdb_id
A character residue string containing the 4 character pdb_id and the
- 1 character chain_id.
+ 1 character chain_id. (:class:`str`)
.. attribute:: offset
All residues of the added structures are stored in a linear memory layout.
- The offset parameter tells us where it exactly starts...
+ The offset parameter tells us where it exactly starts. (:class:`int`)
.. attribute:: size
- The length of the stretch of residues.
+ The length of the stretch of residues. (:class:`int`)
.. class:: FragmentInfo(chain_index, offset, length)
The FragmentInfo defines a fragment in the structural database.
- :param chain_index: The index of the chain in the structure db this particle
- belongs to.
+ :param chain_index: Fills :attr:`chain_index`
- :param offset: Index of residue in **chain** the fragment starts.
+ :param offset: Fills :attr:`offset`
- :param length: Length of the fragment, which is limited to 255
+ :param length: Fills :attr:`length`
.. attribute:: chain_index
+
+ The index of the chain (defined by :class:`CoordInfo`) in the structure db this particle belongs to. (:class:`int`)
+
.. attribute:: offset
+
+ Index of residue in **chain** the fragment starts. (:class:`int`)
+
.. attribute:: length
-
+ Length of the fragment (:class:`int`)
+
The Database
--------------------------------------------------------------------------------
+
+
+.. code-block:: python
+
+ #this code example demonstrates how to create a structural database and
+ #fill it with content
+
+ from promod3 import loop
+ import os
+
+ #we also need the external tools dssp and msms, you have to make sure
+ #that they are somewhere in your PATH
+ from ost.bindings import dssp
+ from ost.bindings import msms
+
+ structure_db = loop.StructureDB()
+
+ #lets fill in some structures. It gets assumed, that all required data lies
+ #in following directories
+ structure_dir = "foo"
+ hmm_dir = "bar"
+
+ #the first 4 letters are suposed to be the pdb id, and the last one
+ #the corresponding chain name. The naming of the files in the
+ #directories is e.g. 1CRN.pdb for the structure and 1CRNA.hhm for the
+ #hmm. Please note, that the structure can contain several chains, whereas
+ #an hmm is considered unique for one particular sequence.
+ ids = [1CRNA,1AKEA]
+
+ for i in ids:
+
+ pdb_id = i[:4]
+ chain_id = i[4]
+
+ #join together the data paths
+ structure_path = os.path.join(structure_dir,pdb_id+".pdb")
+ hmm_path = os.path.join(hmm_dir,pdb_id+chain_id+".hhm")
+
+ #let's load the structure
+ structure = io.LoadPDB(structure_path).Select("cname="+chain_id+" and peptide=True")
+ #and the according HMM, that has to be in hhm format
+ hmm = ost.seq.HMM.Load(hmm_path)
+ #we run dssp in a way, that the secondary structure, as well as
+ #the solvent accessibily gets assigned
+ dssp.AssignDSSP(structure,extract_burial_status=True)
+
+ #as a final step we need the surface as calculated by msms
+ surf = msms.CalculateSurface(structure)[0]
+
+ #let's add it
+ structure_db.AddCoordinates(pdb_id,chain_id,structure.chains[0],surf,hmm)
+
+ #we Now have two structures in the database... Please note, that there
+ #is no profile derived from structures assigned yet. You might consider to use
+ #the default StructureDB to derive such profiles
+ default_db = loop.LoadStructureDB()
+
+ for i in range(structure_db.GetNumCoords()):
+ #get the CoordInfo for chain with index i
+ coord_info = structure_db.GetCoordInfo(i)
+ #define a fragment, that covers the full length
+ fragment_info = loop.FragmentInfo(i,0,coord_info.size)
+ #extract the according BackboneList and the residue depths
+ bb_list = structure_db.GetBackboneList(bb_list,fragment_info)
+ depths = structure_db.GetResidueDepths(fragment_info)
+ #generate a profile based on the structural data in the default_db
+ hmm = default_db.GenerateStructureProfile(bb_list,depths)
+ #and add it to the previously created structure_db
+ structure_db.SetStructureProfile(i,hmm)
+
+ #That's it! Let's save it down...
+ structure_db.Save("my_db.dat")
+
+ #Calculating the structural profiles is highly expensive and heavily depends
+ #on the size of the database used as source...
+ #If you want to do this for a larger database, you might consider two things:
+ #
+ # 1. Use a database of limited size as structural source (something in
+ # between 5000 and 10000 nonredundant chains is enough)
+ # 2. Use the ost.seq.HMMDB to gather hmms produced from jobs running
+ # in parallel
+
+
.. class:: StructureDB()
.. method:: Load(filename,[load_frequencies=False])
@@ -82,7 +192,7 @@ The Database
databases to be saved down.
- .. method:: AddCoordinates(pdb_id, chain_name, chain, hmm)
+ .. method:: AddCoordinates(pdb_id, chain_name, chain, surf, hmm)
This method takes a structural chain and searches the longest stretch of
connected residues containing all necessary backbone atoms. This stretch
@@ -92,11 +202,13 @@ The Database
:param pdb_id: 4-letter code of the structure the chain belongs to
:param chain_name: Name of the chain consisting of one letter
:param chain: The actual chain
+ :param surf: A surface describint the solvent accessible surface
:param hmm: An HMM containing profile information.
- :type pdb_id: :class:`String`
- :type chain_name: :class:'String`
+ :type pdb_id: :class:`str`
+ :type chain_name: :class:`str`
:type chain: :class:`ost.mol.ChainView`
+ :type surf: :class:`ost.mol.SurfaceHandle`
:type hmm: :class:`ost.seq.HMM`
:returns: DB Index of added chain.
@@ -125,25 +237,22 @@ The Database
index **idx**.
- .. method:: FillBackbone(bb_list, fragment)
+ .. method:: GetBackboneList(fragment)
-
- :param bb_list: Structural data will be filled in here.
:param fragment: Description of the fragment from which a
:class:`BackboneList` should be built.
- :type bb_list: :class:`BackboneList`
:type fragment: :class:`FragmentInfo`
+ :returns: :class:`BackboneList`
+
:raises: :class:`RuntimeError` If fragment is invalid. This is
the case when the fragment does not fully fit into one
- of chains in the database.
+ of the chains in the database.
- .. method:: FillBackbone(bb_list, n_stem, c_stem, fragment)
+ .. method:: GetBackboneList(n_stem, c_stem, fragment)
-
- :param bb_list: Structural data will be filled in here.
:param n_stem: Positions on which the bb_list n-terminus should be
superposed onto.
:param c_stem: Positions on which th ebb_list c_terminus should be
@@ -151,14 +260,15 @@ The Database
:param fragment: Description of the fragment from which a
:class:`BackboneList` should be built.
- :type bb_list: :class:`BackboneList`
:type n_stem: :class:`ost.mol.ResidueHandle`
:type c_stem: :class:`ost.mol.ResidueHandle`
:type fragment: :class:`FragmentInfo`
+ :returns: :class:`BackboneList`
+
:raises: :class:`RuntimeError` If fragment is invalid. This is
the case when the fragment does not fully fit into one
- of chains in the database.
+ of the chains in the database.
.. method:: GetNumCoords()
@@ -166,7 +276,7 @@ The Database
:returns: Number of chains, that have been added to the database.
- .. method:: PrindStatistics()
+ .. method:: PrintStatistics()
Prints out some information about the db.
@@ -180,7 +290,7 @@ The Database
:raises: :class:`RuntimeError` If fragment is invalid. This is
the case when the fragment does not fully fit into one
- of chains in the database.
+ of the chains in the database.
.. method:: GetDSSPStates(fragment)
@@ -192,7 +302,7 @@ The Database
:raises: :class:`RuntimeError` If fragment is invalid. This is
the case when the fragment does not fully fit into one
- of chains in the database.
+ of the chains in the database.
.. method:: GetDihedralAngles(fragment)
@@ -200,107 +310,110 @@ The Database
:param fragment: Fragment definition from which to extract the dihedrals.
:type fragment: :class:`FragmentInfo`
- :returns: A list of pairs containing the dihedral angles of every
+ :returns: A list of pairs containing the phi and psi dihedral angles of every
residue of the **fragment**.
:raises: :class:`RuntimeError` If fragment is invalid. This is
the case when the fragment does not fully fit into one
- of chains in the database.
+ of the chains in the database.
- .. method:: GetSeqSim(fragment, seq, subst_matrix)
+ .. method:: GetResidueDepths(fragment)
- :param fragment: Fragment from the database.
- :param seq: The sequence to which the sequence similarity should be
- calculated.
- :param subst_matrix: Source for substitution scores.
+ :param fragment: Fragment definition from which to extract the residue
+ depths
:type fragment: :class:`FragmentInfo`
- :type seq: :class:`str`
- :type subst_matrix: :class:`ost.seq.alg.SubstWeightMatrix`
- :returns: Sequence similarity between **fragment** and **seq**
- normalized to a range [0,1]
+ :returns: A :class:`list` of :class:`float` values describing
+ the per residue depth
:raises: :class:`RuntimeError` If fragment is invalid. This is
the case when the fragment does not fully fit into one
- of chains in the database.
+ of the chains in the database.
- .. method:: GetSeqID(fragment, seq)
+ .. method:: GetSolventAccessibilitites(fragment)
- :param fragment: Fragment from the database.
- :param seq: The sequence to which the sequence identity should be
- calculated.
+ :param fragment: Fragment definition from which to extract the solvent
+ accessibilities
:type fragment: :class:`FragmentInfo`
- :type seq: :class:`str`
- :returns: Sequence identity between **fragment** and **seq**
+ :returns: A :class:`list` of :class:`float` values describing
+ the per residue solvent accessibilities in square A as
+ calculated by dssp
:raises: :class:`RuntimeError` If fragment is invalid. This is
the case when the fragment does not fully fit into one
- of chains in the database.
+ of the chains in the database.
- .. method:: GetSSAgreement(fragment,predicted_ss, confidence)
+ .. method:: GetSequenceProfile(fragment)
- :param fragment: Fragment from the database.
- :param predicted_ss: Predicted secondary structure from psipred with
- every element being in ['H','E','C'].
- :param confidence: Confidence values of psipred predictions,
- with every element being in range [0,9].
+ :param fragment: Fragment definition from which to extract the sequence
+ profile
:type fragment: :class:`FragmentInfo`
- :type predicted_ss: :class:`list`
- :type confidence: :class:`list`
- :returns: Average sequence similarity with parameters also used
- in QMEAN.
+ :returns: The sequence profile for the residues defined by
+ **fragment**, represented as a :class:`ost.seq.HMM`
+ with the BLOSUM62 probabilities as NULL model
:raises: :class:`RuntimeError` If fragment is invalid. This is
the case when the fragment does not fully fit into one
- of chains in the database. It also throws an error if
- one of the psipred values is invalid.
+ of the chains in the database.
+
+ .. method:: GetStructureProfile(fragment)
-
- .. method:: GetTorsionProbability(fragment, seq, torsion_sampler)
-
- :param fragment: Fragment from the database
- :param seq: Sequence the fragment is assumed to have.
- :param torsion_sampler: The source of the probability
+ :param fragment: Fragment definition from which to extract the structure
+ profile
:type fragment: :class:`FragmentInfo`
- :type seq: :class:`str`
- :type torsion_sampler: :class:`TorsionSampler`
-
- :returns: The average probablity of observing the dihedral angles
- from **fragment** assuming the sequence **seq**.
- Note, that the torsion sampler considers amino acid
- triplets, the torsion angles of the flanking residues
- are therefore neglected.
+ :returns: The structure profile for the residues defined by
+ **fragment**, represented as a :class:`ost.seq.HMM`
+ with the BLOSUM62 probabilities as NULL model
:raises: :class:`RuntimeError` If fragment is invalid. This is
the case when the fragment does not fully fit into one
- of chains in the database.
+ of the chains in the database.
+ .. method:: GenerateStructureProfile(bb_list, residue_depths)
- .. method:: GetProfileScore(fragment, hmm)
+ Takes the **bb_list** with its corresponding **residue_depths** to
+ calculate a structure profile using the full internal structural data
+ with their corresponding residue depths.
- :param fragment: Fragment from the database
- :param hmm: Hmm to be aligned with fragment.
+ :param bb_list: Structural data from which do extract structural
+ profile
- :type fragment: :class:`FragmentInfo`
- :type hmm: :class:`ost.seq.HMM`
+ :param residue_depths: Residue depth values for **bb_list**
- :returns: The average column alignment score between the columns
- in the **hmm** and the corresponding positions in
- the database.
+ :type bb_list: :class:`BackboneList`
+ :type residue_depths: :class:`list` of :class:`float` values
+ :returns: The structure profile for the input,
+ represented as a :class:`ost.seq.HMM`
+ with the BLOSUM62 probabilities as NULL model
+
+ :raises: :class:`RuntimeError` if **bb_list** and
+ **residue_depths** differ in size or when
+ their size is 0
+
+ .. method:: SetStructureProfile(chain_idx, hmm)
+
+ Takes the **hmm** and sets the corresponding StructureProfile
+ frequencies in entry with **chain_idx**
+
+ :param hmm: Source of profile frequencies
+ :param chain_idx: idx of entry for which to set the frequencies
+
+ :type hmm: :class:`ost.seq.HMM`
+ :type chain_idx: :class:`int`
+
+ :raises: :class:`RuntimeError` If **chain_idx** does not match
+ any entry in the db or when the size of the **hmm**
+ does not exactly match the size of entry at
+ **chain_idx**
- :raises: :class:`RuntimeError` If fragment is invalid. This is
- the case when the fragment does not fully fit into one
- of chains in the database. The function also raises
- and error if the database has been loaded with
- load_frequencies=False.
@@ -317,7 +430,48 @@ The bins are accessed through a hash table, making searching the database
ultra fast.
-.. class:: FragDB()
+.. code-block:: python
+
+ #This example should illustrate how to create a custom FragDB
+ #based on a StructureDB
+
+ from promod3 import loop
+
+ #let's load the default structure_db
+ structure_db = loop.LoadStructureDB()
+
+ #and our beloved crambin...
+ structure = io.LoadPDB('1crn',remote=True)
+
+ #we now want to connect the residue with index 17 and 21
+ n_stem = structure.residues[17]
+ c_stem = structure.residues[21]
+
+ #A custom FragDB can be build to identify fragments
+ #fulfilling these particular geometric constraints
+ frag_db = loop.FragDB(1.0,20)
+
+ #At this point we add all possible fragments of length 5
+ #with an RMSD threshold of 0.5
+ frag_db.AddFragments(5,0.5,structure_db)
+
+ #The FragDB can now be used to extract FragmentInfo objects to finally query
+ #the StructureDB
+ fragment_infos = frag_db.SearchDB(n_stem,c_stem,5)
+
+ #let's get the fragments in form of BackboneList objects and save the down
+ for i,f_i in enumerate(fragment_infos):
+ bb_list = structure_db.GetBackboneList(n_stem,c_stem,f_i)
+ io.SavePDB(bb_list.ToEntity(),str(i)+".pdb")
+
+
+
+.. class:: FragDB(dist_bin_size, angle_bin_size)
+
+ :param dist_bin_size: Size of the distance parameter binning in A
+ :param angle_bin_size: Size of the angle parameter binning in degree
+ :type dist_bin_size: :class:`float`
+ :type angle_bin_size: :class:`int`
.. method:: Load(filename)
@@ -369,7 +523,7 @@ ultra fast.
Prints statistics about the fragment databse, notably:
1. the number of different stem groups (number of bins used to group the fragments according to the geometry of their stem residues)
- 2. The total number of fragments in the databse
+ 2. The total number of fragments in the database
3. The minimal and maximal number of fragments found in a stem group.
@@ -411,7 +565,7 @@ ultra fast.
.. method:: SearchDB(n_stem, c_stem,frag_size,[extended_search=False])
- Search the database for fragments matching the geometry of the **n_stem** and **c_stem** and of the same length as the **sequence**.
+ Search the database for fragments matching the geometry of the **n_stem** and **c_stem** and of the same length as the **frag_size**.
:param n_stem: The N-stem
:param c_stem: The C-stem
@@ -428,39 +582,45 @@ ultra fast.
-
-
Finding Fragments based on Sequence Features
--------------------------------------------------------------------------------
In some cases you might want to use the :class:`StructureDB` to search
for fragments that possibly represent the structural conformation of interest.
-The :class:`Fragger` allows to perform this task for several different
-features. It searches a :class:`StructureDB` for n fragments, that maximize
-a certain score and gathers a set of fragments with a guaranteed structural
-diversity based on an rmsd_threshold. The final score gets built using an
-arbitrary linear combination of the available scores as controlled by
-the :class:`FraggerScoreParameters`. There are five scores available:
-
-* **SequenceSimilarityScore**: Takes a substitution matrix and calculates for
- every possible fragment the normalized sequence similarity in a range [0,1].
-
-* **SequenceIdentityScore**: Calculates for every possible fragment the
- sequence identity.
-
-* **SSAgreementScore**: Takes the predicted secondary structure by PSIPRED
- with its confidence and calculates an agreement score based on the
- actually observed secondary structure in the :class:`StructureDB`.
-
-* **TorsionProbabilityScore**: Calculates for every possible fragment the
- average probablity of the backbone dihedral angles in the
- :class:`StructureDB` given the input sequence.
-
-* **ProfileScore**: Calculates for every possible fragment the profile-profile
- alignment score given an input :class:`ost.seq.HMM` and the amino acid
- frequencies in the :class:`StructureDB`.
-
-
+The :class:`Fragger` searches a :class:`StructureDB` for n fragments,
+that maximize a certain score and gathers a set of fragments with a guaranteed
+structural diversity based on an rmsd_threshold. The score can be built using an
+arbitrary linear combination of following components:
+
+* **SeqID**:
+ Calculates the fraction of amino acids being identical when comparing
+ a potential fragment from the :class:`StructureDB` and the target sequence
+
+* **SeqSim**:
+ Calculates the avg. substitution matrix based sequence similarity of amino acids
+ when comparing a potential fragment from the :class:`StructureDB` and the target
+ sequence
+
+* **SSAgree**:
+ Calculates the avg. agreement of the predicted secondary structure by PSIPRED [Jones1999]_
+ and the dssp [kabsch1983]_ assignment stored in the :class:`StructureDB`.
+ The Agreement term is based on a probabilistic approach also used in HHSearch [soding2005]_.
+
+* **TorsionProbability**:
+ Calculates the avg. probability of observing the phi/psi dihedral angles of a potential
+ fragment from the :class:`StructureDB` given the target sequence. The probabilities are
+ extracted from the :class:`TorsionSampler` class.
+
+* **SequenceProfile**:
+ Calculates the avg. profile score between the amino acid frequencies of a potential
+ fragment from the :class:`StructureDB` and a target profile assuming a gapfree alignment
+ in between them. The scores are calculated as described for HHSearch [soding2005]_.
+
+* **StructureProfile**:
+ Calculates the avg. profile score between the amino acid frequencies of a potential
+ fragment from the :class:`StructureDB` and a target profile assuming a gapfree alignment
+ in between them. The scores are calculated as described for HHSearch [soding2005]_.
+ In this case, the amino acid frequencies extracted from structural alignments are used.
.. code-block:: python
@@ -482,14 +642,15 @@ the :class:`FraggerScoreParameters`. There are five scores available:
db = loop.LoadStructureDB()
subst_matrix = ost.seq.alg.BLOSUM62
- #to fill the fragger we need a list of parameters
- #we only add a parametrization for the sequence similarity
- parameters = list()
- parameters.append(loop.FraggerScoreParameters(frag_seq,subst_matrix,1.0))
-
- #let's finally fill the fragger
- fragger = loop.Fragger()
- fragger.Fill(db,parameters,1.0,100)
+ #the fragger object needs to be initialized with its target sequence
+ fragger = loop.Fragger(frag_seq)
+
+ #we could now add an arbitrary number of parameters from different features
+ #for now we only go for the sequence similarity score
+ fragger.AddSeqSimParameters(1.0, subst_matrix)
+
+ #the Fragger can finally be filled by providing a StructureDB
+ fragger.Fill(db,1.0,100)
#let's see how good the fragments are...
below_three = 0
@@ -502,98 +663,83 @@ the :class:`FraggerScoreParameters`. There are five scores available:
print "Fraction of fragments below 3A: ", float(below_three)/len(fragger)
-.. class:: FraggerScoreParameters
-
- Controls the parametrization and linear weights of the available
- fragger scores.
+.. class:: Fragger
- .. method:: FraggerScoreParameters(seq, matrix, w)
+ .. method:: Fragger(seq)
- Parametrization of sequence similarity score
+ Initialize a Fragger object to search a :class:`StructureDB` for fragments with
+ **seq** as target sequence. You need to add some score components before
+ you can finally call the Fill function.
- :param seq: Sequence of fragment
- :param matrix: Source of substitution scores
- :param w: Linear weight for sequence similarity score
+ :param seq: Sequence of fragments to be searched
:type seq: :class:`str`
- :type matrix: :class:`ost.seq.alg.SubstWeightMatrix`
- :type w: :class:`float`
-
- .. method:: FraggerScoreParameters(seq, w)
+ .. method:: Fill(db, rmsd_thresh, num_fragments)
- Parametrization of sequence identity score
-
- :param seq: Sequence of fragment
- :param w: Linear weight for sequence identity score
+ Searches **db** for **num_fragments** fragments with maximal
+ score based on the defined score components.
+ There will be no pair of fragments with RMSD below **rmsd_thresh**.
- :type seq: :class:`str`
- :type w: :class:`float`
+ :param db: Source of structural data
+ :param rmsd_thresh: To guarantee structural diversity
+ :param num_fragments: Number of fragments to be extracted
+ :type db: :class:`StructureDB`
+ :type rmsd_thresh: :class:`float`
+ :type num_fragments: :class:`int`
- .. method:: FraggerScoreParameters(seq, psipred_prediction, psipred_confidence, w)
+ .. method:: AddSeqIDParameters(w)
- Parametrization of secondary structure agreement score
+ Add SeqID score component with linear weight **w**
- :param seq: Sequence of fragment
- :param psipred_prediction: Per AA psipred prediction, every element
- must be in ['H','E','C']
- :param psipred_confidence: Per AA psipred confidence values, every element
- must be in [0,9]
- :param w: Linear weight for secondary structure agreement score
+ :param w: linear weight
- :type seq: :class:`str`
- :type psipred_prediction: :class:`list`
- :type psipred_confidence: :class:`list`
:type w: :class:`float`
+ .. method:: AddSeqSimParameters(w, subst)
- .. method:: FraggerScoreParameters(seq, torsion_sampler, w)
-
- Parametrization of torsion angle probablity score
+ Add SeqSim score component with linear weight **w**
- :param seq: Sequence of fragment
- :param torsion_sampler: Torsion sampler to get sequence specific backbone
- dihedral probabilities
- :param w: Linear weight for torsion probability score
+ :param w: linear weight
+ :param subst: Substitution matrix to calculate sequence similarity
- :type seq: :class:`str`
- :type torsion_sampler: :class:`TorsionSampler`
:type w: :class:`float`
+ :type subst: :class:`ost.seq.SubstWeightMatrix`
+ .. method:: AddSSAgreeParameters(w, psipred_prediction, psipred_confidence)
- .. method:: FraggerScoreParameters(seq, hmm, w)
+ Add SSAgree score component with linear weight **w**
- Parametrization of profile score
+ :param w: linear weight
+ :param psipred_prediction: Secondary structure state ('H','E','C') as predicted
+ by PSIPRED for every item in the Fraggers target sequence
+ :param psipred_confidence: Confidence for secondary structure state ([0,9]) as predicted
+ by PSIPRED for every item in the Fraggers target sequence
- :param seq: Sequence of fragment
- :param hmm: HMM of same size as the sequence to extract
- the according amino acid frequencies
- :param w: Linear weight for profile score
+ :type w: :class:`str`
+ :type psipred_prediction: :class:`list`
+ :type psipred_confidence: :class:`list`
- :type seq: :class:`str`
- :type hmm: :class:`ost.seq.HMM`
- :type w: :class:`float`
+ .. method:: AddSequenceProfileParameters(w, hmm)
+ Add SequenceProfile component of linear weight **w**
-.. class:: Fragger
+ :param w: linear weight
+ :param hmm: Profile for the fraggers target_sequence
- .. method:: Fill(db, parameters, rmsd_thresh, num_fragments)
+ :type w: :class:`float`
+ :type hmm: :class:`ost.seq.HMM`
- Searches **db** for **num_fragments** fragments with maximal
- score as defined by the **parameters**.
- There will be no pair of fragments with RMSD below
- **rmsd_thresh**.
+ .. method:: AddStructureProfileParameters(w, hmm)
- :param db: Source of structural data
- :param parameters: Parameters to build a per fragment score
- :param rmsd_thresh: To guarantee structural diversity
- :param num_fragments: Number of fragments to be extracted
+ Add StructureProfile component of linear weight **w**
- :type db: :class:`StructureDB`
- :type parameters: :class:`list`
- :type rmsd_thresh: :class:`float`
- :type num_fragments: :class:`int`
+ :param w: linear weight
+ :param hmm: Profile for the fraggers target_sequence
+
+ :type w: :class:`float`
+ :type hmm: :class:`ost.seq.HMM`
.. method:: __len__()
@@ -612,3 +758,33 @@ the :class:`FraggerScoreParameters`. There are five scores available:
:type index: :class:`int`
:returns: :class:`FragmentInfo` of fragment at position **index**
+
+ .. method:: GetScore(index)
+
+ Returns the final score of fragment defined by **index**
+
+ :param index: Index of fragment
+
+ :type index: :class:`int`
+
+ :returns: Score of fragment at position **index**
+
+ .. method:: GetScore(parameter_index, index)
+
+ Returns the single feature score defined by **parameter_index** of
+ fragment defined by **index** with parameter indexing based on the order
+ you added them to the :class:`Fragger`
+
+ :param parameter_index: Index of score
+ :param index: Index of fragment
+
+ :type parameter_index: :class:`int`
+ :type index: :class:`int`
+
+
+.. [soding2005] Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.
+.. [sanner1996] Sanner M, Olson AJ, Spehner JC (1996). Reduced Surface: an Efficient Way to Compute Molecular Surfaces. Biopolymers 38 (3): 305-320.
+.. [chakravarty1999] Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.
+.. [zhou2005] Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.
+.. [Jones1999] Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.
+.. [kabsch1983] Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 2577-2637.
diff --git a/doc/html/_sources/loop/torsion_sampler.txt b/doc/html/_sources/loop/torsion_sampler.txt
index 4a5a4ebe60333408b71c1ff133fe413f40bd8dde..d297dddfc166a0c961ef9c60aa4f1a49ebbb520c 100644
--- a/doc/html/_sources/loop/torsion_sampler.txt
+++ b/doc/html/_sources/loop/torsion_sampler.txt
@@ -12,18 +12,47 @@ It uses distributions specific for triplets of residues, so that when drawing
a phi/psi pair for a certain residue, the distribution from which the pair is
drawn also depends on the identity of the residues before and after the residue
in question.
-The distributions of the sampler are stored in a vector, so that
+The distributions of the sampler are internally stored in a vector, so that
most methods which need to access a specific distribution can either take 3
residue names or an index as input.
+.. code-block:: python
+
+ from promod3 import loop
+ import matplotlib.pyplot as plt
+ import numpy as np
+
+ #load a default sampler
+ t_sampler = loop.LoadTorsionSampler()
+
+ #dihedral angles will be stored in here
+ phi = list()
+ psi = list()
+
+ #draw from a random distribution
+ for i in range(1000):
+ dihedral_pair = t_sampler.Draw("ALA","PRO","ALA")
+ phi.append(dihedral_pair[0])
+ psi.append(dihedral_pair[1])
+
+ #and plot it
+ plt.xlim((-np.pi,np.pi))
+ plt.ylim((-np.pi,np.pi))
+ plt.plot(phi,psi,'.')
+ plt.xlabel("phi",fontsize='large')
+ plt.ylabel("psi",fontsize='large')
+ plt.title("ALA-PRO-ALA")
+
+ plt.show()
+
Defining Amino Acid triplets
--------------------------------------------------------------------------------
Since the torsion sampler considers triplets of amino acids, we need to define
them. This is done with the so called torsion group definitions.
-Three strings represent the according positions of the consecu-
-tive amino acids. They are combined by "-". It is either possible to
+Three strings represent the according positions of the consecutive
+amino acids. They are combined by "-". It is either possible to
use the keyword "all", or write out all allowed amino acids by their
three letter code and separate them by ",". An example would be: "all-
VAL,ILE-PRO". There are cases where a tripeptide can match several
@@ -37,18 +66,21 @@ decisive.
The Torsion Sampler Class
--------------------------------------------------------------------------------
-.. class:: TorsionSampler(group_definitions, bin_size,seed)
-
+.. class:: TorsionSampler(group_definitions, bin_size, seed)
- :param group_definitions: List of group definitions defining
- amino acid triplets.
- :param bin_size: Size of bins in distributions
- :param seed:
+ Basic object used to sample the backbone torsion angles phi and psi.
+
+ :param group_definitions: List of group definitions defining amino acid triplets
+ :param bin_size: Size of bins in distributions (in degrees)
+ :param seed: Seed for random number generator
- :type bin_size: :class:`float`
- :raises: :class:`RuntimeException` when there is a
- possible combination of the 20 standard amino
- acids not matching any of the group definitions.
+ :type group_definitions: :class:`list` of :class:`str`
+ :type bin_size: :class:`int`
+ :type seed: :class:`int`
+
+ :raises: :class:`RuntimeException` when there is a
+ possible combination of the 20 standard amino
+ acids not matching any of the group definitions.
.. method:: ExtractStatistics(view)
@@ -180,31 +212,35 @@ The Torsion Sampler Class
:returns: An angle
- .. method:: GetProbability(before,central,after,dihedrals)
+ .. method:: GetProbability(before,central,after,phi,psi)
- Returns the probability of a specific pair of phi/psi dihedrals for the central residue from the corresponding distribution.
+ Returns the probability of a specific pair of phi/psi angles for the central residue from the corresponding distribution.
:param before: Name (3 letter code) of the residue before *central*
:param central: Name (3 letter code) of the residue for which the probability is calculated.
:param after: Name (3 letter code) of the residue after *central*
- :param dihedrals: pair of phi/psi angles
+ :param phi: phi angle
+ :param psi: psi angle
:type before: :class:`str`
:type central: :class:`str`
:type after: :class:`str`
- :type dihedrals: (:class:`float`, :class:`float`)
+ :type phi: :class:`float`
+ :type psi: :class:`float`
:returns: A probability
- .. method:: GetProbability(index,dihedrals)
+ .. method:: GetProbability(index,phi,psi)
- Returns the probability of a specific pair of phi/psi dihedrals calulated form the distribution specified by *index*.
+ Returns the probability of a specific pair of phi/psi angles calulated form the distribution specified by *index*.
:param index: The index of the distribution.
- :param dihedrals: pair of phi/psi angles
+ :param phi: phi angle
+ :param psi: psi angle
:type index: :class:`int`
- :type dihedrals: (:class:`float`, :class:`float`)
+ :type phi: :class:`float`
+ :type psi: :class:`float`
:returns: A probability
@@ -276,12 +312,12 @@ The Torsion Sampler Class
.. method:: GetBinsPerDimension()
- Returns the number of bins in one dimension of the distributions.
+ Returns the number of bins per dimension of the distributions.
:rtype: :class:`int`
.. method:: GetBinSize()
- Returns the size of the bins of the distributions.
+ Returns the size of the bins (in radians) of the distributions.
:rtype: :class:`float`
diff --git a/doc/html/_sources/rawmodel/index.txt b/doc/html/_sources/rawmodel/index.txt
index 939917b507cad5862f19d5d9a8d94125b99b7e8b..e1c3630597ff54466a9ab97b7e5577a235e30456 100644
--- a/doc/html/_sources/rawmodel/index.txt
+++ b/doc/html/_sources/rawmodel/index.txt
@@ -1,4 +1,4 @@
-:mod:`~promod3.rawmodel` - Coordinate Modeling
+:mod:`~promod3.rawmodel` - Coordinate Modelling
================================================================================
.. module:: promod3.rawmodel
@@ -38,7 +38,7 @@ Here is an example of how to build a model from an alignment and a structure.
io.SavePDB(result.model, 'model.pdb')
-Raw Coordinate Modeling API
+Raw Coordinate Modelling API
--------------------------------------------------------------------------------
.. function:: BuildRawModel(alignment, calpha_only=False)
@@ -48,7 +48,7 @@ Raw Coordinate Modeling API
alignment handle or an alignment handle list. Every list item is treated as a
single chain in the final raw model.
- This is a basic protein core modeling algorithm that copies backbone
+ This is a basic protein core modelling algorithm that copies backbone
coordinates based on the sequence alignment. For matching residues, the
side chain coordinates are also copied. Gaps are ignored. Hydrogen an
deuterium atoms are not copied into the model.
@@ -62,7 +62,7 @@ Raw Coordinate Modeling API
phosphoserine are copied as a whole with the modifications stripped off.
Residue numbers are set such that missing residue in gaps are honoured and
- subsequent loop modeling can insert new residues without having to
+ subsequent loop modelling can insert new residues without having to
renumber.
The returned :class:`RawModelingResult` stores the obtained raw model as well
@@ -98,7 +98,7 @@ Raw Coordinate Modeling API
.. automethod:: MergeGapsByDistance
.. LocalWords: currentmodule promod aln AttachView BuildRawModel pdb calpha
-.. LocalWords: RawModelingResult StructuralGapList rawmodel Modeling os ost
+.. LocalWords: RawModelingResult StructuralGapList rawmodel Modelling os ost
.. LocalWords: testcode tempfile io LoadAlignment LoadPDB fh fn doctest API
-.. LocalWords: modeling phosphoserine param exc RuntimeError automethod
+.. LocalWords: modelling phosphoserine param exc RuntimeError automethod
.. LocalWords: CloseSmallDeletions
diff --git a/doc/html/_sources/sidechain/disulfid.txt b/doc/html/_sources/sidechain/disulfid.txt
index b86b5152f471daf949a4f2933a7971dd7f742537..9a63016ec1e15e38bd139d0b20fd3965b7183c99 100644
--- a/doc/html/_sources/sidechain/disulfid.txt
+++ b/doc/html/_sources/sidechain/disulfid.txt
@@ -7,12 +7,8 @@ When calculating the pairwise interaction energy between two rotamers building
a disulfid bond, one would get an unfavourable energy due to "clashes" between
the sulfur atoms. It is possible to improve performance in sidechain
reconstruction regarding cysteins when finding and separately handle
-disulfid bonds. PROMOD3 implements a simple geometrical description of
-disulfid bonds described in:
-
-Canutescu AA, Shelenkov AA, Dunbrack RL Jr.
-A graph-theory algorithm for rapid protein side-chain prediction.
-Protein Sci (2003).
+disulfid bonds. PROMOD3 implements a simple geometrical description
+[canutescu2003]_ .
Two methods are implemented to evaluate this disulfid score on either rigid of
flexible rotamers. The above paper proposes two rotamers to be in a disulfid
@@ -27,8 +23,8 @@ bonded state, if the resulting score is below 45.
:param ca_pos_two: CA position of second rotamer
:param cb_pos_two: CB position of second rotamer
- :type rotamer_one: :class:`RRMRotamer`
- :type rotamer_two: :class:`RRMRotamer`
+ :type rotamer_one: :class:`RRMRotamer` , :class:`FRMRotamer`
+ :type rotamer_two: :class:`RRMRotamer` , :class:`FRMRotamer`
:type ca_pos_one: :class:`ost.geom.Vec3`
:type cb_pos_one: :class:`ost.geom.Vec3`
:type ca_pos_two: :class:`ost.geom.Vec3`
@@ -37,33 +33,9 @@ bonded state, if the resulting score is below 45.
:raises: :class:`RuntimeError` if given rotamers do not contain
exactly one particle representing the gamma sulfur.
- :returns: The disulfid score based on geometric features.
-
-
-.. method:: DisulfidScore(rotamer_one,rotamer_two,ca_pos_one,cb_pos_one,ca_pos_two,cb_pos_two)
-
- :param rotamer_one: First rotamer
- :param rotamer_two: Second rotamer
- :param ca_pos_one: CA position of first rotamer
- :param cb_pos_one: CB position of first rotamer
- :param ca_pos_two: CA position of second rotamer
- :param cb_pos_two: CB position of second rotamer
-
- :type rotamer_one: :class:`FRMRotamer`
- :type rotamer_two: :class:`FRMRotamer`
- :type ca_pos_one: :class:`ost.geom.Vec3`
- :type cb_pos_one: :class:`ost.geom.Vec3`
- :type ca_pos_two: :class:`ost.geom.Vec3`
- :type cb_pos_two: :class:`ost.geom.Vec3`
-
- :raises: :class:`RuntimeError` if given subrotamers do not contain
- exactly one particle representing the gamma sulfur.
-
- :returns: The disulfid score based on geometric features. Scores
- are calculated for all possible subrotamer combinations
- and the minimal score gets returned.
-
-
-
-
+ :returns: The disulfid score based on geometric features. In case
+ of :class:`FRMRotamer` as input, the minimal score
+ between all possible subrotamer combinations gets
+ returned.
+.. Already in other module .. [canutescu2003] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
diff --git a/doc/html/_sources/sidechain/frame.txt b/doc/html/_sources/sidechain/frame.txt
index eff17bab505ec61fad8542cf9c031e5d5b7153b1..06af9c3adbed83e96a256eb4035e15beec22d10f 100644
--- a/doc/html/_sources/sidechain/frame.txt
+++ b/doc/html/_sources/sidechain/frame.txt
@@ -13,6 +13,66 @@ enters the frame energy calculation, all interaction with particles
belonging to the frame residue with the same residue index are neglected.
+The Frame Objects
+--------------------------------------------------------------------------------
+
+.. class:: FrameResidue(particles, residue_index)
+
+ The most simple way of constructing a frame residue is the usage
+ of the convenient functions provided by PROMOD3.
+
+ :param particles: particles building frame residue
+ :param residue_index: Interaction energies between the constructed frame
+ residue and any rotamer associated to the same
+ residue index are neglected
+
+ :type particles: :class:`list` of :class:`Particle`
+ :type residue_index: :class:`int`
+
+ .. method:: __len__()
+
+ :returns: Number of particles in :class:`FrameResidue`
+
+
+ .. method:: __getitem__(index)
+
+ :param index: :class:`Particle` index
+ :type index: :class:`int`
+
+ :returns: :class:`Particle` at position **index**
+
+ :raises: :class:`RuntimeError` if index is invalid
+
+
+
+.. class:: Frame(frame_residues)
+
+ The :class:`Frame` object allows to calculate frame energies for rotamers.
+ Due to technical reasons, this is only possible if the rotamers are
+ part of rotamer groups.
+
+ :param frame_residues: residues building the frame.
+ :type frame_residues: :class:`list` of :class:`FrameResidue`
+
+ .. method:: SetFrameEnergy(rotamer_group)
+
+ Calculates and sets frame energies for all rotamers in the rotamer group.
+
+ :param rotamer_group: group of rotamers for energy calculation
+
+ :type rotamer_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+
+ .. method:: AddFrameEnergy(rotamer_group)
+
+ Calculates and adds frame energies to the already existing frame
+ energy values for all rotamers in the rotamer group.
+ This is useful if you have several :class:`Frame` objects.
+
+ :param rotamer_group: group of rotamers for energy calculation
+
+ :type rotamer_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+
+
Convenient functions for constructing frame residues
--------------------------------------------------------------------------------
@@ -107,106 +167,21 @@ and sidechain frame residues.
:raises: :class:`RuntimeError` when not all required atoms
atoms are present in **residue**
-.. method:: ConstructFrameResidue(residue,residue_index,settings,[radius=[],emin=[]])
+ :returns: :class:`FrameResidue`
+
+.. method:: ConstructFrameResidue(residue,residue_index)
Constructs a :class:`FrameResidue` from a :class:`ost.mol.ResidueHandle`.
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.
+ there won't be any parametrization of hbonds in this function. All
+ Atoms of the residue will be represented as carbons.
- :param residue: Reside from which all atoms will be taken to
+ :param residue: Residue from which all atoms will be taken to
construct a :class:`FrameResidue`.
:param residue_index: Index this :class:`FrameResidue` belongs to.
- :param settings: Settings to control parametrization of the single
- particles.
- :param radius: Radius for pseudo Lennard-Jones term in energy
- evaluation for every particle. If left empty,
- radius of carbon will be used for all particles.
-
- :param emin: Min energy for pseudo Lennard-Jones term in energy
- evaluation for every particle. If left empty,
- emin of carbon will be used for all particles.
:type residue: :class:`ost.mol.ResidueHandle`
:type residue_index: :class:`int`
- :type settings: :class:`RotamerSettings`
- :type radius: :class:`list`
- :type emin: :class:`list`
-
- :raises: :class:`RuntimeError` if size of radius and emin is not
- consistent.
-
-The Frame Objects
---------------------------------------------------------------------------------
-
-.. class:: FrameResidue(particles, residue_index)
-
- The most simple way of constructing a frame residue is the usage
- of the convenient functions provided by PROMOD3.
- :param particles: :class:`list` of :class:`Particle` objects building
- up the :class:`FrameResidue`
- :param residue_index: Interaction energies between the constructed frame
- residue and any rotamer associated to the same
- residue index are neglected.
-
- .. method:: __len__()
-
- :returns: Number of particles in :class:`FrameResidue`
-
-
- .. method:: __getitem__(index)
-
- :param index: :class:`Particle` index
-
- :returns: :class:`Particle` at position **index**
-
- :raises: :class:`RuntimeError` if index is invalid
-
-
-
-.. class:: Frame(frame_residues)
-
- :param frame_residues:
-
- :type frame_residues:
-
- The :class:`Frame` object allows to calculate frame energies for rotamers.
- Due to technical reasons, this is only possible if the rotamers are
- part of rotamer groups.
-
- .. method:: SetFrameEnergy(rotamer_group)
-
- Calculates and sets frame energies
-
- :param rotamer_group: group of rotamers for energy calculation
-
- :type rotamer_group: :class:`RRMRotamerGroup`
-
- .. method:: SetFrameEnergy(rotamer_group)
-
- Calculates and sets frame energies
-
- :param rotamer_group: group of rotamers for energy calculation
-
- :type rotamer_group: :class:`FRMRotamerGroup`
-
- .. method:: AddFrameEnergy(rotamer_group)
-
- Calculates and adds frame energies to the already existing frame
- energy values. This might be useful if you have several :class:`Frame`
- objects.
-
- :param rotamer_group: group of rotamers for energy calculation
-
- :type rotamer_group: :class:`RRMRotamerGroup`
-
- .. method:: AddFrameEnergy(rotamer_group)
-
- Calculates and adds frame energies to the already existing frame
- energy values. This might be useful if you have several :class:`Frame`
- objects.
-
- :param rotamer_group: group of rotamers for energy calculation
-
- :type rotamer_group: :class:`FRMRotamerGroup`
+ :returns: :class:`FrameResidue`
diff --git a/doc/html/_sources/sidechain/graph.txt b/doc/html/_sources/sidechain/graph.txt
index 0797b9312003d03db85dcab10e879173404aa3ce..f7d4802311d89a3786fefc360c2134db35fd1e11 100644
--- a/doc/html/_sources/sidechain/graph.txt
+++ b/doc/html/_sources/sidechain/graph.txt
@@ -20,7 +20,7 @@ The Interaction Graph
The Graph object has no constructor exported to python. It is meant to be
constructed using the static create functions.
- .. method:: CreateFromRRMList(rotamer_groups)
+ .. staticmethod:: CreateFromRRMList(rotamer_groups)
:param rotamer_groups: :class:`RRMRotamerGroup` objects representing the
possible sidechain conformations for every amino
@@ -29,7 +29,7 @@ The Interaction Graph
:type rotamer_groups: :class:`list`
- .. method:: CreateFromFRMList(rotamer_groups)
+ .. staticmethod:: CreateFromFRMList(rotamer_groups)
:param rotamer_groups: :class:`FRMRotamerGroup` objects representing the
possible sidechain conformations for every amino
@@ -44,7 +44,8 @@ The Interaction Graph
and edge decomposition until the number of possible permutations, that
have to be enumerated in the resulting tree, fall below
**max_complecity**. In every iteration the epsilon value gets doubled to
- enforce more edges to be approximated by edge decomposition.
+ enforce more edges to be approximated by edge decomposition. This function
+ assumes all self energies of the rotamers to be calculated and properly set!
:param max_complexity: Max number of possible permutations, that have to
be enumerated in the resulting tree after tree
@@ -94,7 +95,7 @@ The Interaction Graph
.. method:: GetNumActiveNodes()
- :returns: The number of nodes havind at least one edge, even
+ :returns: The number of nodes having at least one edge, even
after performing pruning operations
.. method:: GetNumActiveEdges()
@@ -105,8 +106,3 @@ The Interaction Graph
-
-
-
-
-
diff --git a/doc/html/_sources/sidechain/index.txt b/doc/html/_sources/sidechain/index.txt
index 78a1a2ce2a570874ca8e8523ee7ae04dde273c23..6a1bee166fe33f04d6109aae26314fc3b7c574d3 100644
--- a/doc/html/_sources/sidechain/index.txt
+++ b/doc/html/_sources/sidechain/index.txt
@@ -7,21 +7,33 @@
.. currentmodule:: promod3.sidechain
Tools and algorithms to model sidechains given backbone coordinates.
-The full module is heavily based on SCWRL4:
+The full module is heavily based on SCWRL4 [krivov2009]_ .
+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.
-G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr.
-Improved prediction of protein side-chain conformations with SCWRL4.
-Proteins (2009).
+Reconstruct Function
+--------------------------------------------------------------------------------
-The 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.
+.. currentmodule:: promod3.sidechain.reconstruct_sidechains
-The most simple way though is the usage of following function:
+The simplest usage of the module is provided by the :func:`Reconstruct` function:
-.. currentmodule:: promod3.sidechain.reconstruct_sidechains
+.. code-block:: python
-.. method:: Reconstruct(prot,[,keep_sidechains=False,build_disulfids,rotamer_model="frm",consider_hbonds=True,rotamer_library=None])
+ from ost import io,mol
+ from promod3.sidechain import reconstruct_sidechains
+
+ #load a protein
+ prot = io.LoadPDB('1eye',remote=True)
+ #get only amino acids
+ prot = mol.CreateEntityFromView(prot.Select("peptide=true"),True)
+ io.SavePDB(prot,"sidechain_test_orig.pdb")
+ #reconstruct sidechains
+ reconstruct_sidechains.Reconstruct(prot)
+ io.SavePDB(prot,"sidechain_test_rec.pdb")
+
+.. method:: Reconstruct(prot,[,keep_sidechains=False,build_disulfids,rotamer_model="frm",consider_hbonds=True,rotamer_library=None,add_polar_hydrogens=False])
.. currentmodule:: promod3.sidechain
@@ -45,36 +57,49 @@ The most simple way though is the usage of following function:
:param consider_hbonds: Flag, whether hbonds should be evaluated in the energy
function. If set to False, no hydrogens will be built
- when building rotamers and frame.
+ when building rotamers and frame and the **add_polar_hydrogens**
+ flag won't have any consequences.
- :param rotamer_library: A backbone dependent rotamer library to extract the
+ :param rotamer_library: A rotamer library to extract the
rotamers from.
+ :param add_polar_hydrogens: All polar hydrogens will be constructed if
+ **consider_hbonds** is True.
+ If this flag is activated, they'll be added to the
+ structure.
+
+
:type prot: :class:`ost.mol.EntityHandle`
:type keep_sidechains: :class:`bool`
:type build_disulfids: :class:`bool`
:type rotamer_model: :class:`str`
:type consider_hbonds: :class:`bool`
- :type rotamer_library: :class:`BBDepRotamerLib`
+ :type rotamer_library: :class:`BBDepRotamerLib` / :class:`RotamerLib`
+ :type add_polar_hydrogens: :class:`bool`
-Following code fragment shows an example of a basic sidechain reconstruction
+Sidechain Module Functionality
+--------------------------------------------------------------------------------
+
+.. currentmodule:: promod3.sidechain
+
+The following code fragment shows an example of a basic sidechain reconstruction
algorithm using the functionality in the module. Note, that this code will
crash as soon as you have structures containing all the weirdness the PDB throws
-at us. In this case you should use the Reconstruct function above. An overview
-of the full provided functionality can be found at the bottom of this page.
+at us. In this case, you should use the :func:`~promod3.sidechain.reconstruct_sidechains.Reconstruct` function above. An overview of the full provided functionality can be found at the bottom of this page.
.. code-block:: python
-
+
+ from ost import io,mol
from promod3 import sidechain
#load a protein, the rotamer library and the settings with default values
- prot= io.LoadPDB('1eye',remote=True)
+ prot = io.LoadPDB('1eye',remote=True)
settings = sidechain.RotamerSettings()
library = sidechain.LoadDunbrackLib()
#let's create a new entity from the protein only containing the amino acids
- prot = ost.mol.CreateEntityFromView(prot.Select("peptide=true"),True)
+ prot = mol.CreateEntityFromView(prot.Select("peptide=true"),True)
#gather some data, the rotamer ids and backbone torsion angles
torsion_angles = list()
@@ -104,10 +129,8 @@ of the full provided functionality can be found at the bottom of this page.
torsion_angles[i][0],
i == 1,
i == (len(rotamer_ids)-1))
-
frame_residues.append(frame_residue)
-
frame = sidechain.Frame(frame_residues)
@@ -127,7 +150,7 @@ of the full provided functionality can be found at the bottom of this page.
#internal and frame energy have to be calculated directly
rot_group.CalculateInternalEnergies()
frame.SetFrameEnergy(rot_group)
- #remove supper unlikely rotamer in rotamer group
+ #remove super unlikely rotamer in rotamer group
#e.g. those who clash with the frame
rot_group.ApplySelfEnergyThresh()
#finally add it and keep track of the indices
@@ -162,3 +185,5 @@ Contents:
Graph <graph>
The Settings - Control Things... <sidechain_settings>
Disulfid Bond Evaluation <disulfid>
+
+.. [krivov2009] Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.
diff --git a/doc/html/_sources/sidechain/rotamer.txt b/doc/html/_sources/sidechain/rotamer.txt
index 3ba2b20e36c9297923c962e424e115a755e2cfb5..ff201e334d0dd03bbf324f7d5b11d9821158f4c6 100644
--- a/doc/html/_sources/sidechain/rotamer.txt
+++ b/doc/html/_sources/sidechain/rotamer.txt
@@ -14,409 +14,111 @@ PROMOD3 offers a built-in construction function, directly accessing a
:class:`BBDepRotamerLib`.
-Convenient functions for constructing rotamers
+The Smallest Building Block - The Particle
--------------------------------------------------------------------------------
-PROMOD3 offers some functionality to directly access a
-:class:`BBDepRotamerLibrary` and build single rotamers as well as
-rotamer groups.
+Particles give raise to more complex objects such as rotamers and frame residues.
+They are the basis for calculating interaction energies based on a Lennard-Jones
+like term and an approximation of an hbond energy term.
+The Lennard-Jones term gets mainly controlled by the type of the particle, that
+has to be defined at initialization.
-.. method:: ConstructRRMRotamer(n_pos,ca_pos,cb_pos,rotamer_id,settings,probability,[chi1=NaN,chi2=NaN,chi3=NaN,chi4=NaN])
+.. class:: SidechainParticle
- :param n_pos: Position of nitrogen used as anchor for the rotamer
- :param ca_pos: Position of alpha carbon used as anchor for the rotamer
- :param cb_pos: Position of beta carbon used as anchor for the rotamer
- :param rotamer_id: Type of :class:`RRMRotamer`
- :param settings: Settings to control parametrization of the single
- particles.
- :param probability: Probability of occurence of this particular rotamer.
- :param chi1: First sidechain dihedral angle
- :param chi2: Second sidechain dihedral angle
- :param chi3: Third sidechain dihedral angle
- :param chi4: Fourth sidechain dihedral angle
+ Enumerates the types of particle. Possible values:
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
- :type rotamer_id: :class:`RotamerID`
- :type settings: :class:`RotamerSettings`
- :type probability: :class:`float`
- :type chi1: :class:`float`
- :type chi2: :class:`float`
- :type chi3: :class:`float`
- :type chi4: :class:`float`
+ * HParticle - represents hydrogen
+ * CParticle - default representation of a carbon
+ * CH1Particle - represents carbon bound to 1 hydrogen
+ * CH2Particle - represents carbon bound to 2 hydrogen
+ * CH3Particle - represents carbon bound to 3 hydrogen
+ * NParticle - represents nitrogen
+ * OParticle - default representation of oxygen
+ * OCParticle - represents carbonyl-oxygen for ASP/GLU
+ * SParticle - represents sulfur
- :raises: :class:`RuntimeError` if not all required chi angles
- for this particular **id** are given.
+.. class:: Particle(type, pos, charge, name)
+ :param type: Type of particle
+ :param pos: Positions of particle
+ :param charge: Charge of particle, will be used in case H-Bonds
+ :param name: Name of particle. This name will be given to an actual
+ :class:`ost.mol.AtomHandle` if a rotamer gets applied
+ to a :class:`ost.mol.ResidueHandle`
-.. method:: ConstructRRMRotamer(residue,rotamer_id,settings,probability,[chi1=NaN,chi2=NaN,chi3=NaN,chi4=NaN])
+ :type type: :class:`SidechainParticle`
+ :type pos: :class:`ost.geom.Vec3`
+ :type charge: :class:`float`
+ :type name: :class:`str`
- :param residue: Residue from which the anchor positions will be
- extracted
- :param rotamer_id: Type of :class:`RRMRotamer`
- :param settings: Settings to control parametrization of the single
- particles.
- :param probability: Probability of occurence of this particular rotamer.
- :param chi1: First sidechain dihedral angle
- :param chi2: Second sidechain dihedral angle
- :param chi3: Third sidechain dihedral angle
- :param chi4: Fourth sidechain dihedral angle
+ .. method:: PairwiseEnergy(other)
- :type residue: :class:`ost.mol.ResideHandle`
- :type rotamer_id: :class:`RotamerID`
- :type settings: :class:`RotamerSettings`
- :type probability: :class:`float`
- :type chi1: :class:`float`
- :type chi2: :class:`float`
- :type chi3: :class:`float`
- :type chi4: :class:`float`
+ Calculates the interaction energy between two particles.
- :raises: :class:`RuntimeError` if not all required chi angles
- for this particular **id** are given or when not
- all required anchor atoms are present in
- **residue**.
+ :param other: Interaction partner
+ :type other: :class:`Particle`
-.. method:: ConstructFRMRotamer(n_pos,ca_pos,cb_pos,rotamer_id,settings,probability,[chi1=NaN,sig1=NaN,chi2=NaN,sig2=NaN,chi3=NaN,sig3=NaN,chi4=NaN,sig4=NaN])
+ :returns: the interaction energy
- :param n_pos: Position of nitrogen used as anchor for the rotamer
- :param ca_pos: Position of alpha carbon used as anchor for the rotamer
- :param cb_pos: Position of beta carbon used as anchor for the rotamer
- :param rotamer_id: Type of :class:`FRMRotamer`
- :param settings: Settings to control parametrization of the single
- particles.
- :param probability: Probability of occurence of this particular rotamer.
- :param chi1: First sidechain dihedral angle
- :param sig1: Standard deviation of first dihedral angle
- :param chi2: Second sidechain dihedral angle
- :param sig2: Standard deviation of second dihedral angle
- :param chi3: Third sidechain dihedral angle
- :param sig3: Standard deviation of third dihedral angle
- :param chi4: Fourth sidechain dihedral angle
- :param sig4: Standard deviation of fourth dihedral angle
+ .. method:: GetPos()
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
- :type rotamer_id: :class:`RotamerID`
- :type settings: :class:`RotamerSettings`
- :type probability: :class:`float`
- :type chi1: :class:`float`
- :type sig1: :class:`float`
- :type chi2: :class:`float`
- :type sig2: :class:`float`
- :type chi3: :class:`float`
- :type sig3: :class:`float`
- :type chi4: :class:`float`
- :type sig4: :class:`float`
+ :returns: The Particle position
- :raises: :class:`RuntimeError` if not all required chi angles
- for this particular **id** are given.
+ .. method:: GetCharge()
-.. method:: ConstructFRMRotamer(residue,rotamer_id,settings,probability,[chi1=NaN,sig1=NaN,chi2=NaN,sig2=NaN,chi3=NaN,sig3=NaN,chi4=NaN,sig4=NaN])
+ :returns: Charge of particle used for HBond term
- :param residue: Residue from which the anchor positions will be
- extracted
- :param rotamer_id: Type of :class:`FRMRotamer`
- :param settings: Settings to control parametrization of the single
- particles.
- :param probability: Probability of occurence of this particular rotamer.
- :param chi1: First sidechain dihedral angle
- :param sig1: Standard deviation of first dihedral angle
- :param chi2: Second sidechain dihedral angle
- :param sig2: Standard deviation of second dihedral angle
- :param chi3: Third sidechain dihedral angle
- :param sig3: Standard deviation of third dihedral angle
- :param chi4: Fourth sidechain dihedral angle
- :param sig4: Standard deviation of fourth dihedral angle
+ .. method:: GetParticleType()
- :type residue: :class:`ost.mol.ResideHandle`
- :type rotamer_id: :class:`RotamerID`
- :type settings: :class:`RotamerSettings`
- :type probability: :class:`float`
- :type chi1: :class:`float`
- :type sig1: :class:`float`
- :type chi2: :class:`float`
- :type sig2: :class:`float`
- :type chi3: :class:`float`
- :type sig3: :class:`float`
- :type chi4: :class:`float`
- :type sig4: :class:`float`
+ :returns: Internal type of particle
- :raises: :class:`RuntimeError` if not all required chi angles
- or standard deviations for this particular **id**
- are given or when not all required anchor atoms are present in
- **residue**.
+ .. method:: GetName()
-Convenient functions for constructing rotamer groups
---------------------------------------------------------------------------------
+ :returns: Name of particle
-Instead of building single rotamers, following convenient functions query a
-rotamer library and build all possible rotamers for a particular residue
-position. If hbond scoring is enabled (**settings**) several rotamers might be
-constructed and added to the group per library instance:
-#. SER construct three rotamers with hydrogen chi angles 180,-60 and 60
-#. THR construct three rotamers with hydrogen chi angles 180,-60 and 60
-#. TYR construct two rotamers with hydrogen chi angles 180 and 0
-#. HIS construct both possible protonation states (HSE,HSD)
+ .. method:: IsHBondDonor()
-.. _rotamer_group_construction_label:
+ :returns: Whether particle has defined polar direction
-.. method:: ConstructRRMRotamerGroup(n_pos,ca_pos,cb_pos,rotamer_id,residue_index,rot_lib,settings,[phi=-1.0472,psi=1.0472])
- Constructs a full group of :class:`RRMRotamer` objects. It extracts rotamers
- from *rot_lib* and adds them to the group until the summed probability
- reaches the probability cutoff defined in **settings**.
+ .. method:: IsHBondAcceptor()
- :param n_pos: Position of nitrogen used as anchor for the rotamers
- :param ca_pos: Position of alpha carbon used as anchor for the rotamers
- :param cb_pos: Position of beta carbon used as anchor for the rotamers
- :param rotamer_id: Type of of the constructed :class:`RRMRotamer`
- :param residue_index: Index of :class:`RRMRotamer` objects in constructed
- :class:`RRMRotamerGroup`. This matters for calculating
- the frame energy. Interactions to frame residues with
- same index get neglected.
- :param rot_lib: Library from which the data is taken to construct the
- rotamers.
- :param settings: Settings to control parametrization of the single
- particles.
- :param phi: Phi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
- :param psi: Psi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
+ :returns: Whether particle has defined lone pairs
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
- :type rotamer_id: :class:`RotamerID`
- :type residue_index: :class:`int`
- :type rot_lib: :class:`BBDepRotamerLib`
- :type settings: :class:`RotamerSettings`
- :type phi: :class:`float`
- :type psi: :class:`float`
+ .. method:: AddLonePair(lone_pair)
-.. method:: ConstructRRMRotamerGroup(residue,rotamer_id,residue_index,rot_lib,settings,[phi=-1.0472,psi=1.0472])
+ Adds lone pair, that gets evaluated in the HBond term.
- Constructs a full group of :class:`RRMRotamer` objects. It extracts rotamers
- from *rot_lib* and adds them to the group until the summed probability
- reaches the probability cutoff defined in **settings**.
+ :param lone_pair: Lone pair direction
+ :type lone_pair: :class:`ost.geom.Vec3`
- :param residue: Residue from which the anchor positions will be
- extracted
- :param rotamer_id: Type of of the constructed :class:`RRMRotamer`
- :param residue_index: Index of :class:`RRMRotamer` objects in constructed
- :class:`RRMRotamerGroup`. This matters for calculating
- the frame energy. Interactions to frame residues with
- same index get neglected.
- :param rot_lib: Library from which the data is taken to construct the
- rotamers.
- :param settings: Settings to control parametrization of the single
- particles.
- :param phi: Phi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
- :param psi: Psi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
- :type rotamer_id: :class:`RotamerID`
- :type residue_index: :class:`int`
- :type rot_lib: :class:`BBDepRotamerLib`
- :type settings: :class:`RotamerSettings`
- :type phi: :class:`float`
- :type psi: :class:`float`
+ .. method:: SetPolarDirection(polar_direction)
- :raises: :class:`RuntimeError` if not all required anchor atoms
- are present in **residue**.
+ Sets the polar direction of particle. In case of backbone
+ hydrogen, this would be the direction of backbone-N to backbone-H.
+ :param polar_direction: Polar direction of particle
-.. method:: ConstructFRMRotamerGroup(n_pos,ca_pos,cb_pos,rotamer_id,residue_index,rot_lib,settings,[phi=-1.0472,psi=1.0472])
+ :type polar_direction: :class:`ost.geom.Vec3`
- Constructs a full group of :class:`FRMRotamer` objects. It extracts rotamers
- from *rot_lib* and adds them to the group until the summed probability
- reaches the probability cutoff defined in **settings**.
- :param n_pos: Position of nitrogen used as anchor for the rotamers
- :param ca_pos: Position of alpha carbon used as anchor for the rotamers
- :param cb_pos: Position of beta carbon used as anchor for the rotamers
- :param rotamer_id: Type of of the constructed :class:`FRMRotamer`
- :param residue_index: Index of :class:`FRMRotamer` objects in constructed
- :class:`RRMRotamerGroup`. This matters for calculating
- the frame energy. Interactions to frame residues with
- same index get neglected.
- :param rot_lib: Library from which the data is taken to construct the
- rotamers.
- :param settings: Settings to control parametrization of the single
- particles.
- :param phi: Phi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
- :param psi: Psi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
+Rotamers
+--------------------------------------------------------------------------------
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
- :type rotamer_id: :class:`RotamerID`
- :type residue_index: :class:`int`
- :type rot_lib: :class:`BBDepRotamerLib`
- :type settings: :class:`RotamerSettings`
- :type phi: :class:`float`
- :type psi: :class:`float`
+.. class:: RRMRotamer
-.. method:: ConstructFRMRotamerGroup(residue,rotamer_id,residue_index,rot_lib,settings,[phi=-1.0472,psi=1.0472])
-
- Constructs a full group of :class:`FRMRotamer` objects. It extracts rotamers
- from *rot_lib* and adds them to the group until the summed probability
- reaches the probability cutoff defined in **settings**.
-
- :param residue: Residue from which the anchor positions will be
- extracted
- :param rotamer_id: Type of of the constructed :class:`FRMRotamer`
- :param residue_index: Index of :class:`FRMRotamer` objects in constructed
- :class:`RRMRotamerGroup`. This matters for calculating
- the frame energy. Interactions to frame residues with
- same index get neglected.
- :param rot_lib: Library from which the data is taken to construct the
- rotamers.
- :param settings: Settings to control parametrization of the single
- particles.
- :param phi: Phi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
- :param psi: Psi backbone dihedral angle used as input for backbone
- dependent rotamer library. Default value is a typical
- alpha helical value.
-
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
- :type rotamer_id: :class:`RotamerID`
- :type residue_index: :class:`int`
- :type rot_lib: :class:`BBDepRotamerLib`
- :type settings: :class:`RotamerSettings`
- :type phi: :class:`float`
- :type psi: :class:`float`
-
- :raises: :class:`RuntimeError` if not all required anchor atoms
- are present in **residue**.
-
-
-
-
-The Smallest Building Block - The Particle
---------------------------------------------------------------------------------
-
-.. class:: Particle(pos, radius, r, emin, charge, name)
-
- :param pos: Positions of particle
- :param radius: Expected distance, this particle gives
- raise to nonzero interactions. This parameter is used
- for the internal collision detection algorithm.
- If two particles have a nonzero interaction energy up to
- 3 Angstrom, their radius should be at least 1.5.
- :param r: Distance for pseudo Lennard-Jones interaction term
- :param emin: Emin for pseudo Lennard-Jones interaction term
- :param charge: Charge of particle, will be used in case H-Bonds
- :param name: Name of particle. This name will be given to an actual
- :class:`ost.mol.AtomHandle` if a rotamer gets applied
- to a :class:`ost.mol.ResidueHandle`
-
- :type pos: :class:`ost.geom.Vec3`
- :type radius: :class:`float`
- :type r: :class:`float`
- :type emin: :class:`float`
- :type charge: :class:`float`
- :type name: :class:`str`
-
- .. method:: PairwiseEnergy(other)
-
- Calculates the interaction energy between two particles.
-
- :param other: Interaction partner
-
- :type other: :class:`Particle`
-
- :returns: the interaction energy
-
-
- .. method:: GetPos()
-
- :returns: The Particle position
-
-
- .. method:: GetRadius()
-
- :returns: The distance of pseudo Lennard-Jones Term
-
-
- .. method:: GetEMin()
-
- :returns: EMin of pseudo Lennart-Jones Term
-
-
- .. method:: GetCharge()
-
- :returns: Charge of particle used for HBond term
-
-
- .. method:: GetName()
-
- :returns: Name of particle
-
-
- .. method:: IsHBondDonor()
-
- :returns: Whether particle has defined polar direction
-
-
- .. method:: IsHBondAcceptor()
-
- :returns: Whether particle has defined lone pairs
-
-
- .. method:: AddLonePair(lone_pair)
-
- Adds lone pair, that gets evaluated in the HBond term.
-
- :param lone_pair: Lone pair direction
-
- :type lone_pair: :class:`ost.geom.Vec3`
-
-
- .. method:: SetPolarDirection(polar_direction)
-
- Sets the polar direction of particle. In case of backbone
- hydrogen, this would be the direction of backbone-N to backbone-H.
-
- :param polar_direction: Polar direction of particle
-
- :type polar_direction: :class:`ost.geom.Vec3`
-
-
-Rotamers
---------------------------------------------------------------------------------
-
-
-.. class:: RRMRotamer
-
- The RRMRotamer represents a rotamer of the so called rigid rotamer model.
- The class has no constructor exported to python, the rotamer is expected to
- be constructed with the convenient functions provided by PROMOD3.
+ The RRMRotamer represents a rotamer of the so called rigid rotamer model.
+ The class has no constructor exported to python, the rotamer is expected to
+ be constructed with the convenient functions provided by PROMOD3.
.. method:: __getitem__(index)
@@ -780,11 +482,11 @@ Rotamer Groups
:type other: :class:`RRMRotamerGroup`
- .. CalculateInternalEnergies()
+ .. method:: CalculateInternalEnergies()
Calculates internal energies of all rotamers in group
- .. ApplySelfEnergyThres([thresh=30])
+ .. method:: ApplySelfEnergyThres([thresh=30])
Searches rotamer with lowest self energy **l_e** and deletes all
rotamers with **self_energy** > **l_e** + **thresh**
@@ -856,6 +558,428 @@ Rotamer Groups
-
+
+
+
+
+Convenient functions for constructing rotamers
+--------------------------------------------------------------------------------
+
+PROMOD3 offers some functionality to directly access a
+:class:`BBDepRotamerLibrary` and build single rotamers as well as
+rotamer groups.
+
+.. method:: ConstructRRMRotamer(n_pos,ca_pos,cb_pos,rotamer_id,settings,probability,[chi1=NaN,chi2=NaN,chi3=NaN,chi4=NaN])
+
+ :param n_pos: Position of nitrogen used as anchor for the rotamer
+ :param ca_pos: Position of alpha carbon used as anchor for the rotamer
+ :param cb_pos: Position of beta carbon used as anchor for the rotamer
+ :param rotamer_id: Type of :class:`RRMRotamer`
+ :param settings: Settings to control parametrization of the single
+ particles.
+ :param probability: Probability of occurence of this particular rotamer.
+ :param chi1: First sidechain dihedral angle
+ :param chi2: Second sidechain dihedral angle
+ :param chi3: Third sidechain dihedral angle
+ :param chi4: Fourth sidechain dihedral angle
+
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type rotamer_id: :class:`RotamerID`
+ :type settings: :class:`RotamerSettings`
+ :type probability: :class:`float`
+ :type chi1: :class:`float`
+ :type chi2: :class:`float`
+ :type chi3: :class:`float`
+ :type chi4: :class:`float`
+
+ :raises: :class:`RuntimeError` if not all required chi angles
+ for this particular **id** are given.
+
+
+.. method:: ConstructRRMRotamer(residue,rotamer_id,settings,probability,[chi1=NaN,chi2=NaN,chi3=NaN,chi4=NaN])
+
+ :param residue: Residue from which the anchor positions will be
+ extracted
+ :param rotamer_id: Type of :class:`RRMRotamer`
+ :param settings: Settings to control parametrization of the single
+ particles.
+ :param probability: Probability of occurence of this particular rotamer.
+ :param chi1: First sidechain dihedral angle
+ :param chi2: Second sidechain dihedral angle
+ :param chi3: Third sidechain dihedral angle
+ :param chi4: Fourth sidechain dihedral angle
+
+ :type residue: :class:`ost.mol.ResideHandle`
+ :type rotamer_id: :class:`RotamerID`
+ :type settings: :class:`RotamerSettings`
+ :type probability: :class:`float`
+ :type chi1: :class:`float`
+ :type chi2: :class:`float`
+ :type chi3: :class:`float`
+ :type chi4: :class:`float`
+
+ :raises: :class:`RuntimeError` if not all required chi angles
+ for this particular **id** are given or when not
+ all required anchor atoms are present in
+ **residue**.
+
+
+.. method:: ConstructFRMRotamer(n_pos,ca_pos,cb_pos,rotamer_id,settings,probability,[chi1=NaN,sig1=NaN,chi2=NaN,sig2=NaN,chi3=NaN,sig3=NaN,chi4=NaN,sig4=NaN])
+
+ :param n_pos: Position of nitrogen used as anchor for the rotamer
+ :param ca_pos: Position of alpha carbon used as anchor for the rotamer
+ :param cb_pos: Position of beta carbon used as anchor for the rotamer
+ :param rotamer_id: Type of :class:`FRMRotamer`
+ :param settings: Settings to control parametrization of the single
+ particles.
+ :param probability: Probability of occurence of this particular rotamer.
+ :param chi1: First sidechain dihedral angle
+ :param sig1: Standard deviation of first dihedral angle
+ :param chi2: Second sidechain dihedral angle
+ :param sig2: Standard deviation of second dihedral angle
+ :param chi3: Third sidechain dihedral angle
+ :param sig3: Standard deviation of third dihedral angle
+ :param chi4: Fourth sidechain dihedral angle
+ :param sig4: Standard deviation of fourth dihedral angle
+
+
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type rotamer_id: :class:`RotamerID`
+ :type settings: :class:`RotamerSettings`
+ :type probability: :class:`float`
+ :type chi1: :class:`float`
+ :type sig1: :class:`float`
+ :type chi2: :class:`float`
+ :type sig2: :class:`float`
+ :type chi3: :class:`float`
+ :type sig3: :class:`float`
+ :type chi4: :class:`float`
+ :type sig4: :class:`float`
+
+ :raises: :class:`RuntimeError` if not all required chi angles
+ for this particular **id** are given.
+
+
+.. method:: ConstructFRMRotamer(residue,rotamer_id,settings,probability,[chi1=NaN,sig1=NaN,chi2=NaN,sig2=NaN,chi3=NaN,sig3=NaN,chi4=NaN,sig4=NaN])
+
+ :param residue: Residue from which the anchor positions will be
+ extracted
+ :param rotamer_id: Type of :class:`FRMRotamer`
+ :param settings: Settings to control parametrization of the single
+ particles.
+ :param probability: Probability of occurence of this particular rotamer.
+ :param chi1: First sidechain dihedral angle
+ :param sig1: Standard deviation of first dihedral angle
+ :param chi2: Second sidechain dihedral angle
+ :param sig2: Standard deviation of second dihedral angle
+ :param chi3: Third sidechain dihedral angle
+ :param sig3: Standard deviation of third dihedral angle
+ :param chi4: Fourth sidechain dihedral angle
+ :param sig4: Standard deviation of fourth dihedral angle
+
+ :type residue: :class:`ost.mol.ResideHandle`
+ :type rotamer_id: :class:`RotamerID`
+ :type settings: :class:`RotamerSettings`
+ :type probability: :class:`float`
+ :type chi1: :class:`float`
+ :type sig1: :class:`float`
+ :type chi2: :class:`float`
+ :type sig2: :class:`float`
+ :type chi3: :class:`float`
+ :type sig3: :class:`float`
+ :type chi4: :class:`float`
+ :type sig4: :class:`float`
+
+ :raises: :class:`RuntimeError` if not all required chi angles
+ or standard deviations for this particular **id**
+ are given or when not all required anchor atoms are present in
+ **residue**.
+
+
+Convenient functions for constructing rotamer groups
+--------------------------------------------------------------------------------
+
+Instead of building single rotamers, following convenient functions query a
+rotamer library and build all possible rotamers for a particular residue
+position. If hbond scoring is enabled and sample_polar_hydrogens is true (**settings**),
+several rotamers might be constructed and added to the group per library instance:
+
+#. SER construct three rotamers with hydrogen chi angles 180,-60 and 60
+#. THR construct three rotamers with hydrogen chi angles 180,-60 and 60
+#. TYR construct two rotamers with hydrogen chi angles 180 and 0
+#. HIS construct both possible protonation states (HSE,HSD)
+
+.. _rotamer_group_construction_label:
+
+.. method:: ConstructRRMRotamerGroup(n_pos,ca_pos,cb_pos,rotamer_id,residue_index,rot_lib,settings,[phi=-1.0472,psi=-0.7854])
+
+ Constructs a full group of :class:`RRMRotamer` objects. It extracts rotamers
+ from *rot_lib* and adds them to the group until the summed probability
+ reaches the probability cutoff defined in **settings**.
+
+ :param n_pos: Position of nitrogen used as anchor for the rotamers
+ :param ca_pos: Position of alpha carbon used as anchor for the rotamers
+ :param cb_pos: Position of beta carbon used as anchor for the rotamers
+ :param rotamer_id: Type of of the constructed :class:`RRMRotamer`
+ :param residue_index: Index of :class:`RRMRotamer` objects in constructed
+ :class:`RRMRotamerGroup`. This matters for calculating
+ the frame energy. Interactions to frame residues with
+ same index get neglected.
+ :param rot_lib: Library from which the data is taken to construct the
+ rotamers.
+ :param settings: Settings to control parametrization of the single
+ particles.
+ :param phi: Phi backbone dihedral angle used as input for backbone
+ dependent rotamer library. Default value is a typical
+ alpha helical value.
+ :param psi: Psi backbone dihedral angle used as input for backbone
+ dependent rotamer library. Default value is a typical
+ alpha helical value.
+
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type rotamer_id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type rot_lib: :class:`BBDepRotamerLib`
+ :type settings: :class:`RotamerSettings`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+
+
+.. method:: ConstructRRMRotamerGroup(residue,rotamer_id,residue_index,rot_lib,settings,[phi=-1.0472,psi=-0.7854])
+
+ Constructs a full group of :class:`RRMRotamer` objects. It extracts rotamers
+ from *rot_lib* and adds them to the group until the summed probability
+ reaches the probability cutoff defined in **settings**.
+
+
+ :param residue: Residue from which the anchor positions will be
+ extracted
+ :param rotamer_id: Type of of the constructed :class:`RRMRotamer`
+ :param residue_index: Index of :class:`RRMRotamer` objects in constructed
+ :class:`RRMRotamerGroup`. This matters for calculating
+ the frame energy. Interactions to frame residues with
+ same index get neglected.
+ :param rot_lib: Library from which the data is taken to construct the
+ rotamers.
+ :param settings: Settings to control parametrization of the single
+ particles.
+ :param phi: Phi backbone dihedral angle used as input for backbone
+ dependent rotamer library. Default value is a typical
+ alpha helical value.
+ :param psi: Psi backbone dihedral angle used as input for backbone
+ dependent rotamer library. Default value is a typical
+ alpha helical value.
+
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type rotamer_id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type rot_lib: :class:`BBDepRotamerLib`
+ :type settings: :class:`RotamerSettings`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+
+ :raises: :class:`RuntimeError` if not all required anchor atoms
+ are present in **residue**.
+
+
+.. method:: ConstructFRMRotamerGroup(n_pos,ca_pos,cb_pos,rotamer_id,residue_index,rot_lib,settings,[phi=-1.0472,psi=-0.7854])
+
+ Constructs a full group of :class:`FRMRotamer` objects. It extracts rotamers
+ from *rot_lib* and adds them to the group until the summed probability
+ reaches the probability cutoff defined in **settings**.
+
+ :param n_pos: Position of nitrogen used as anchor for the rotamers
+ :param ca_pos: Position of alpha carbon used as anchor for the rotamers
+ :param cb_pos: Position of beta carbon used as anchor for the rotamers
+ :param rotamer_id: Type of of the constructed :class:`FRMRotamer`
+ :param residue_index: Index of :class:`FRMRotamer` objects in constructed
+ :class:`RRMRotamerGroup`. This matters for calculating
+ the frame energy. Interactions to frame residues with
+ same index get neglected.
+ :param rot_lib: Library from which the data is taken to construct the
+ rotamers.
+ :param settings: Settings to control parametrization of the single
+ particles.
+ :param phi: Phi backbone dihedral angle used as input for backbone
+ dependent rotamer library. Default value is a typical
+ alpha helical value.
+ :param psi: Psi backbone dihedral angle used as input for backbone
+ dependent rotamer library. Default value is a typical
+ alpha helical value.
+
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type rotamer_id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type rot_lib: :class:`BBDepRotamerLib`
+ :type settings: :class:`RotamerSettings`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+
+
+.. method:: ConstructFRMRotamerGroup(residue,rotamer_id,residue_index,rot_lib,settings,[phi=-1.0472,psi=-0.7854])
+
+ Constructs a full group of :class:`FRMRotamer` objects. It extracts rotamers
+ from *rot_lib* and adds them to the group until the summed probability
+ reaches the probability cutoff defined in **settings**.
+
+ :param residue: Residue from which the anchor positions will be
+ extracted
+ :param rotamer_id: Type of of the constructed :class:`FRMRotamer`
+ :param residue_index: Index of :class:`FRMRotamer` objects in constructed
+ :class:`RRMRotamerGroup`. This matters for calculating
+ the frame energy. Interactions to frame residues with
+ same index get neglected.
+ :param rot_lib: Library from which the data is taken to construct the
+ rotamers.
+ :param settings: Settings to control parametrization of the single
+ particles.
+ :param phi: Phi backbone dihedral angle used as input for backbone
+ dependent rotamer library. Default value is a typical
+ alpha helical value.
+ :param psi: Psi backbone dihedral angle used as input for backbone
+ dependent rotamer library. Default value is a typical
+ alpha helical value.
+
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type rotamer_id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type rot_lib: :class:`BBDepRotamerLib`
+ :type settings: :class:`RotamerSettings`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+
+ :raises: :class:`RuntimeError` if not all required anchor atoms
+ are present in **residue**.
+
+
+
+.. method:: ConstructRRMRotamerGroup(n_pos,ca_pos,cb_pos,rotamer_id,residue_index,rot_lib,settings)
+
+ Constructs a full group of :class:`RRMRotamer` objects. It extracts rotamers
+ from *rot_lib* and adds them to the group until the summed probability
+ reaches the probability cutoff defined in **settings**.
+
+ :param n_pos: Position of nitrogen used as anchor for the rotamers
+ :param ca_pos: Position of alpha carbon used as anchor for the rotamers
+ :param cb_pos: Position of beta carbon used as anchor for the rotamers
+ :param rotamer_id: Type of of the constructed :class:`RRMRotamer`
+ :param residue_index: Index of :class:`RRMRotamer` objects in constructed
+ :class:`RRMRotamerGroup`. This matters for calculating
+ the frame energy. Interactions to frame residues with
+ same index get neglected.
+ :param rot_lib: Library from which the data is taken to construct the
+ rotamers.
+ :param settings: Settings to control parametrization of the single
+ particles.
+
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type rotamer_id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type rot_lib: :class:`RotamerLib`
+ :type settings: :class:`RotamerSettings`
+
+
+.. method:: ConstructRRMRotamerGroup(residue,rotamer_id,residue_index,rot_lib,settings)
+
+ Constructs a full group of :class:`RRMRotamer` objects. It extracts rotamers
+ from *rot_lib* and adds them to the group until the summed probability
+ reaches the probability cutoff defined in **settings**.
+
+
+ :param residue: Residue from which the anchor positions will be
+ extracted
+ :param rotamer_id: Type of of the constructed :class:`RRMRotamer`
+ :param residue_index: Index of :class:`RRMRotamer` objects in constructed
+ :class:`RRMRotamerGroup`. This matters for calculating
+ the frame energy. Interactions to frame residues with
+ same index get neglected.
+ :param rot_lib: Library from which the data is taken to construct the
+ rotamers.
+ :param settings: Settings to control parametrization of the single
+ particles.
+
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type rotamer_id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type rot_lib: :class:`RotamerLib`
+ :type settings: :class:`RotamerSettings`
+
+ :raises: :class:`RuntimeError` if not all required anchor atoms
+ are present in **residue**.
+
+
+.. method:: ConstructFRMRotamerGroup(n_pos,ca_pos,cb_pos,rotamer_id,residue_index,rot_lib,settings)
+
+ Constructs a full group of :class:`FRMRotamer` objects. It extracts rotamers
+ from *rot_lib* and adds them to the group until the summed probability
+ reaches the probability cutoff defined in **settings**.
+
+ :param n_pos: Position of nitrogen used as anchor for the rotamers
+ :param ca_pos: Position of alpha carbon used as anchor for the rotamers
+ :param cb_pos: Position of beta carbon used as anchor for the rotamers
+ :param rotamer_id: Type of of the constructed :class:`FRMRotamer`
+ :param residue_index: Index of :class:`FRMRotamer` objects in constructed
+ :class:`RRMRotamerGroup`. This matters for calculating
+ the frame energy. Interactions to frame residues with
+ same index get neglected.
+ :param rot_lib: Library from which the data is taken to construct the
+ rotamers.
+ :param settings: Settings to control parametrization of the single
+ particles.
+
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type rotamer_id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type rot_lib: :class:`RotamerLib`
+ :type settings: :class:`RotamerSettings`
+
+
+.. method:: ConstructFRMRotamerGroup(residue,rotamer_id,residue_index,rot_lib,settings)
+
+ Constructs a full group of :class:`FRMRotamer` objects. It extracts rotamers
+ from *rot_lib* and adds them to the group until the summed probability
+ reaches the probability cutoff defined in **settings**.
+
+ :param residue: Residue from which the anchor positions will be
+ extracted
+ :param rotamer_id: Type of of the constructed :class:`FRMRotamer`
+ :param residue_index: Index of :class:`FRMRotamer` objects in constructed
+ :class:`RRMRotamerGroup`. This matters for calculating
+ the frame energy. Interactions to frame residues with
+ same index get neglected.
+ :param rot_lib: Library from which the data is taken to construct the
+ rotamers.
+ :param settings: Settings to control parametrization of the single
+ particles.
+
+ :type n_pos: :class:`ost.geom.Vec3`
+ :type ca_pos: :class:`ost.geom.Vec3`
+ :type cb_pos: :class:`ost.geom.Vec3`
+ :type rotamer_id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type rot_lib: :class:`BBDepRotamerLib`
+ :type settings: :class:`RotamerSettings`
+
+ :raises: :class:`RuntimeError` if not all required anchor atoms
+ are present in **residue**.
+
\ No newline at end of file
diff --git a/doc/html/_sources/sidechain/rotamer_id.txt b/doc/html/_sources/sidechain/rotamer_id.txt
index 5cb57818f11ec4cb08dc01a78c7b2a84eb1263ea..d85dcb158f9192e4ade9c560d8bb35b18a780bd7 100644
--- a/doc/html/_sources/sidechain/rotamer_id.txt
+++ b/doc/html/_sources/sidechain/rotamer_id.txt
@@ -12,39 +12,46 @@ that affect the hbond term or different versions of proline/cysteine.
The RotamerID
--------------------------------------------------------------------------------
-* ARG - Arginine
-* ASN - Asparagine
-* ASP - Aspartate
-* GLN - Glutamine
-* GLU - Glutamate
-* LYS - Lysine
-* SER - Serine
-* CYS - Cystein
-* CYH - "free" Cystein
-* CYD - disulfid bonded Cystein
-* MET - Methionine
-* TRP - Tryptophane
-* TYR - Tyrosine
-* THR - Threonine
-* VAL - Valine
-* ILE - Isoleucine
-* LEU - Leucine
-* PRO - Proline
-* CPR - cis-Proline
-* TPR - trans-Proline
-* HIS - Histidine
-* HSD - d-protonated Histidine
-* HSE - e-protonated Histidine
-* PHE - Phenylalanine
-* GLY - Glycine
-* ALA - Alanine
-* XXX - Invalid
+.. class:: RotamerID
+
+ Enumerates the amino acids. Possible values:
+
+ * ARG - Arginine
+ * ASN - Asparagine
+ * ASP - Aspartate
+ * GLN - Glutamine
+ * GLU - Glutamate
+ * LYS - Lysine
+ * SER - Serine
+ * CYS - Cystein
+ * CYH - "free" Cystein
+ * CYD - disulfid bonded Cystein
+ * MET - Methionine
+ * TRP - Tryptophane
+ * TYR - Tyrosine
+ * THR - Threonine
+ * VAL - Valine
+ * ILE - Isoleucine
+ * LEU - Leucine
+ * PRO - Proline
+ * CPR - cis-Proline
+ * TPR - trans-Proline
+ * HIS - Histidine
+ * HSD - d-protonated Histidine
+ * HSE - e-protonated Histidine
+ * PHE - Phenylalanine
+ * GLY - Glycine
+ * ALA - Alanine
+ * XXX - Invalid
+
+ The RotamerID enum can be accessed either directly as ``promod3.sidechain.ARG``
+ or as ``promod3.sidechain.RotamerID.ARG``.
How can I get an ID?
--------------------------------------------------------------------------------
The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the ost.conop.AminoAcid enum
+functions exist to get RotamerIDs from the :class:`ost.conop.AminoAcid` enum
or from amino acid three letter codes.
.. method:: TLCToRotID(tlc)
diff --git a/doc/html/_sources/sidechain/rotamer_lib.txt b/doc/html/_sources/sidechain/rotamer_lib.txt
index 0b1ca5356f552a260f44e73f44c9cde776a4d10f..2e716e2240c38a6eefcbc8e947441718ae1cf880 100644
--- a/doc/html/_sources/sidechain/rotamer_lib.txt
+++ b/doc/html/_sources/sidechain/rotamer_lib.txt
@@ -11,18 +11,82 @@ can be gathered in rotamer libraries. Different libraries exist in the field
and their main difference is, whether the provided sidechain conformations
are dependent on their backbone or not. PROMOD3 provides you with a
:class:`BBDepRotamerLib` organizing rotamers for the different aminoacids
-in equidistant phi/psi bins.
+in equidistant phi/psi bins, as well as a simple :class:`RotamerLib`.
+Both libraries are containers for :class:`RotamerLibEntry` and are optimized
+for fast writing/loading from/to disk. Once initialized, the library is in a
+dynamic mode where rotamers can be added.
+No rotamers can be read at this stage. As soon as
+all required rotamers are added, the library can be made static. This is the
+mode you can get the rotamers out of it or dump it to disk.
-The Backbone Dependent Rotamer Library
+The Non Backbone Dependent Rotamer Library
--------------------------------------------------------------------------------
-The PROMOD3 :class:`BBDepRotamerLib` is a container for :class:`RotamerLibEntry`
-and is optimized for fast writing/loading from/to disk.
-Once initialized, the library is in a dynamic mode where
-rotamers can be added. No rotamers can be read at this stage. As soon as
-all required rotamers are added, the library can be made static. This is the
-mode you can get the rotamers out of it or dump it to disk.
+
+.. class:: RotamerLib()
+
+ Non backbone dependent rotamer library
+
+ .. method:: Save(filename)
+
+ :param filename: Name of file, the library will be dumped into
+
+ :type filename: :class:`str`
+
+ .. method:: Load(filename)
+
+ :param filename: Name of file, the library will be loaded from
+
+ :type filename: :class:`str`
+
+ :raises: :class:`RuntimeError` if file doesn't exist
+
+ .. method:: AddRotamer(id, rotamer)
+
+ :param id: Identity of rotamer to be added
+ :param rotamer: the rotamer to be added
+
+ :type id: :class:`RotamerID`
+ :type rotamer: :class:`RotamerLibEntry`
+
+ :raises: :class:`RuntimeError` if the library is already static
+
+ .. method:: QueryLib(id)
+
+ The query function follows following strategies in case of
+ special *id* requests.
+
+ * if id = HSD (d-protonated HIS) try to find HSD, fallback to HIS in case of failure
+
+ * if id = HSE (e-protonated HIS) try to find HSE, fallback to HIS in case of failure
+
+ * if id = CYH ("free" CYS) try to find CYH, fallback to CYS in case of failure
+
+ * if id = CYD ("disulfid" CYS) try to find CYD, fallback to CYS in case of failure
+
+ * if id = CPR (cis-PRO) try to find CPR, fallback to PRO in case of failure
+
+ * if id = TPR (trans-PRO) try to find TPR, fallback to PRO in case of failure
+
+ :param id: Identity of rotamer of interest
+
+ :type id: :class:`RotamerID`
+
+ :returns: :class:`list` of :class:`RotamerLibEntry` of nonzero
+ probability sorted by their probability
+
+ :raises: :class:`RuntimeError` if no entries for *id* can be
+ found
+
+ .. method:: MakeStatic()
+
+ Once all rotamers are added, the library can be made static to become readable
+ and ready for io.
+
+
+The Backbone Dependent Rotamer Library
+--------------------------------------------------------------------------------
.. class:: BBDepRotamerLib(phi_bins,psi_bins)
@@ -106,7 +170,7 @@ mode you can get the rotamers out of it or dump it to disk.
:type psi: :class:`float`
:returns: :class:`list` of :class:`RotamerLibEntry` of nonzero
- probability for given phi/psi pair
+ probability for given phi/psi pair sorted by their probability
:raises: :class:`RuntimeError` if no entries for *id* can be
found
@@ -248,10 +312,10 @@ functionalities.
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/ambiguous rotamers
- (TYR,VAL,PHE,ASP,GLU)
-
+ 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.
+
:param other: The Entry you want to compare with
:param thresh: The max difference between two dihedrals to be
considered similar
@@ -268,9 +332,9 @@ functionalities.
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 (TYR,VAL,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.
+ 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.
:param other: The Entry you want to compare with
:param thresh: The max difference between two dihedrals to be
@@ -289,8 +353,8 @@ functionalities.
Compares a specific dihedral angle.
The function doesn't know the identity of the entries and can therefore
- not specifically treat symmetric/ambiguous rotamers
- (TYR,VAL,PHE,ASP,GLU)
+ not specifically treat symmetric rotamers
+ (TYR,PHE,ASP,GLU) or rotamers with ambiguous naming in general.
:param other: The Entry you want to compare with
:param dihedral_idx: Index of the dihedral to be checked
@@ -309,7 +373,7 @@ functionalities.
.. method:: SimilarDihedral(other, dihedral_idx, thresh, id)
Compares a specific dihedral angle.
- Sidechains with ambigous naming (TYR,VAL,PHE,ASP,GLU)
+ 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.
diff --git a/doc/html/_sources/sidechain/sidechain_settings.txt b/doc/html/_sources/sidechain/sidechain_settings.txt
index 5fe161afdbe7fa04d99a9c7f41d5e8d278042036..5652f945b9b321b969605f019e29bfd94bd8159d 100644
--- a/doc/html/_sources/sidechain/sidechain_settings.txt
+++ b/doc/html/_sources/sidechain/sidechain_settings.txt
@@ -21,7 +21,7 @@ Ser,Thr and Tyr when using the convenient functions for constructing full
rotamer groups of them (see :ref:`here <rotamer_group_construction_label>`).
Constructing the rotamer groups can further be controlled by assigning a max
summed probability resulting in less very unlikely rotamers added to the
-rotamer group(see :ref:`here <rotamer_group_construction_label>`).
+rotamer group (see :ref:`here <rotamer_group_construction_label>`).
.. class:: RotamerSettings
@@ -187,25 +187,6 @@ rotamer group(see :ref:`here <rotamer_group_construction_label>`).
.. attribute:: sample_polar_hydrogens default: True
- .. attribute:: H_radius default: 0.49
-
- .. attribute:: C_radius default: 1.68
-
- .. attribute:: S_radius default: 1.71
-
- .. attribute:: N_radius default: 1.28
-
- .. attribute:: O_radius default: 1.29
-
- .. attribute:: H_max_radius default: 1.0300
-
- .. attribute:: C_max_radius default: 2.2400
-
- .. attribute:: S_max_radius default: 2.2800
-
- .. attribute:: N_max_radius default: 1.7067
-
- .. attribute:: O_max_radius default: 1.7200
diff --git a/doc/html/_static/alabaster.css b/doc/html/_static/alabaster.css
index 0857c04b30f3125e7c405fe149e2abeff21577bd..07a9e2a42ae0c0d42495b844723754f80d111911 100644
--- a/doc/html/_static/alabaster.css
+++ b/doc/html/_static/alabaster.css
@@ -15,9 +15,6 @@
-
-
-
@import url("basic.css");
/* -- page layout ----------------------------------------------------------- */
@@ -71,10 +68,12 @@ div.footer a {
color: #888;
}
-div.related {
+
+div.relations {
display: none;
}
+
div.sphinxsidebar a {
color: #444;
text-decoration: none;
@@ -287,6 +286,13 @@ pre, tt, code {
font-size: 0.9em;
}
+.hll {
+ background-color: #FFC;
+ margin: 0 -12px;
+ padding: 0 12px;
+ display: block;
+}
+
img.screenshot {
}
@@ -380,8 +386,8 @@ pre {
}
dl pre, blockquote pre, li pre {
- margin-left: -60px;
- padding-left: 60px;
+ margin-left: 0;
+ padding-left: 30px;
}
dl dl pre {
@@ -520,18 +526,6 @@ a:hover tt, a:hover code {
margin: 0;
}
- div.related {
- display: block;
- margin: 0;
- padding: 10px 0 20px 0;
- }
-
- div.related ul,
- div.related ul li {
- margin: 0;
- padding: 0;
- }
-
div.footer {
display: none;
}
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index e46d68283dd5eb2831485e88ca7cee77e3619dda..f7100ea7f67424bd657f882f311242944d513826 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Developes" href="../developers.html" />
+ <link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="Building ProMod3" href="../buildsystem.html" />
<link rel="prev" title="Disulfid Bond Evaluation" href="../sidechain/disulfid.html" />
@@ -32,26 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="../buildsystem.html" title="Building ProMod3"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="../sidechain/disulfid.html" title="Disulfid Bond Evaluation"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" accesskey="U">Documentation For Developes</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -193,7 +174,7 @@ is derived from the <a class="reference external" href="https://docs.python.org/
<h3>Must Have Tests<a class="headerlink" href="#must-have-tests" title="Permalink to this headline">¶</a></h3>
<p>What needs testing without exclusion are the exit codes of actions. Those
states will be placed in the userlevel documentation. This topic is already
-covered in <a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a> by <code class="xref py py-meth docutils literal"><span class="pre">RunExitStatusTest()</span></code>.
+covered in <a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a> by <a class="reference internal" href="#test_actions.ActionTestCase.RunExitStatusTest" title="test_actions.ActionTestCase.RunExitStatusTest"><code class="xref py py-meth docutils literal"><span class="pre">RunExitStatusTest()</span></code></a>.
As an example, testing for <code class="docutils literal"><span class="pre">$?=0</span></code> could work like this:</p>
<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
12</pre></div></td><td class="code"><div class="highlight"><pre><span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
@@ -208,7 +189,7 @@ happens if a user throws dirty input data in.</p>
</div>
<div class="section" id="making-the-script-executable">
<h3>Making the Script Executable<a class="headerlink" href="#making-the-script-executable" title="Permalink to this headline">¶</a></h3>
-<p>In ProMod3, unit tests are run via <a class="reference external" href="http://www.OpenStructure.org">OST</a> and Python‘s
+<p>In ProMod3, unit tests are run via <a class="reference external" href="http://www.OpenStructure.org">OST</a>‘s <a class="reference external" href="http://www.openstructure.org/docs/1.3/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.3.3)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python‘s
<a class="reference external" href="https://docs.python.org/2.7/library/unittest.html#unittest.TestCase" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed
as a script:</p>
<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
@@ -283,9 +264,7 @@ Otherwise the whole idea does not work.</p>
<dl class="attribute">
<dt id="test_actions.ActionTestCase.pm_bin">
<code class="descname">pm_bin</code><a class="headerlink" href="#test_actions.ActionTestCase.pm_bin" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<p>This is the path of the <code class="docutils literal"><span class="pre">pm</span></code> binary. Automatically set by calling
+<dd><p>This is the path of the <code class="docutils literal"><span class="pre">pm</span></code> binary. Automatically set by calling
<code class="xref py py-meth docutils literal"><span class="pre">__init__()</span></code> inside the initialisation of your class.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -295,12 +274,12 @@ Otherwise the whole idea does not work.</p>
</tr>
</tbody>
</table>
+</dd></dl>
+
<dl class="attribute">
<dt id="test_actions.ActionTestCase.pm_action">
<code class="descname">pm_action</code><a class="headerlink" href="#test_actions.ActionTestCase.pm_action" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<p>The action to be tested. Needs to be set by your initialisation routine,
+<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"><span class="pre">__init__()</span></code> from here. Skip the
“pm-” in front of the action name.</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -311,6 +290,8 @@ Otherwise the whole idea does not work.</p>
</tr>
</tbody>
</table>
+</dd></dl>
+
<dl class="method">
<dt id="test_actions.ActionTestCase.RunAction">
<code class="descname">RunAction</code><span class="sig-paren">(</span><em>arguments</em>, <em>verbose=False</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/test_actions.html#ActionTestCase.RunAction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#test_actions.ActionTestCase.RunAction" title="Permalink to this definition">¶</a></dt>
@@ -391,13 +372,17 @@ file (also complains if a directory is found instead).</p>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="../sidechain/disulfid.html"
- title="previous chapter">Disulfid Bond Evaluation</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="../buildsystem.html"
- title="next chapter">Building ProMod3</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li>Previous: <a href="../sidechain/disulfid.html" title="previous chapter">Disulfid Bond Evaluation</a></li>
+ <li>Next: <a href="../buildsystem.html" title="next chapter">Building ProMod3</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -427,11 +412,11 @@ file (also complains if a directory is found instead).</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/actions/index_dev.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index 155465772278177421b99295f62e4bd216135415..567594d728c2eceb250a275fef02b8cc9d2daff2 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="index.html" />
- <link rel="up" title="Documentation For Developes" href="developers.html" />
+ <link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="Contributing" href="contributing.html" />
<link rel="prev" title="test_actions.ActionTestCase - Testing Actions" href="actions/index_dev.html" />
@@ -32,26 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="contributing.html" title="Contributing"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="actions/index_dev.html" title="test_actions.ActionTestCase - Testing Actions"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="developers.html" accesskey="U">Documentation For Developes</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -59,24 +40,26 @@
<div class="body" role="main">
<div class="section" id="building-project">
-<h1>Building ProMod3<a class="headerlink" href="#building-project" title="Permalink to this headline">¶</a></h1>
+<span id="building-promod"></span><h1>Building ProMod3<a class="headerlink" href="#building-project" title="Permalink to this headline">¶</a></h1>
<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="http://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
-1.4, and <a class="reference external" href="http://swissmodel.expasy.org/qmean/cgi/index.cgi?">QMEAN</a>. To create the build system, <a class="reference external" href="http://www.cmake.org/">CMake</a> is required in version
+1.4. OST must be configured and compiled with <code class="docutils literal"><span class="pre">ENABLE_MM=1</span></code> to use <a class="reference external" href="https://simtk.org/home/openmm">OpenMM</a>.
+To create the build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required in version
2.8.7 or higher. <a class="reference external" href="https://www.python.org/">Python</a> works well from version 2.7. For OST and the
C++ bit of ProMod3, <a class="reference external" href="http://www.boost.org/">Boost</a> is required in version 1.47.0 (the same as
used for OST). Also <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> and <a class="reference external" href="http://www.netlib.org/lapack/">LAPACK</a> are needed. To build
documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.2b1 is used.</p>
+<p>The currently (Nov. 2015) preferred versions are:</p>
<ul class="simple">
<li><a class="reference external" href="http://www.OpenStructure.org">OST</a> 1.4</li>
-<li><a class="reference external" href="http://swissmodel.expasy.org/qmean/cgi/index.cgi?">QMEAN</a></li>
-<li><a class="reference external" href="http://www.cmake.org/">CMake</a> 2.8.7</li>
-<li><a class="reference external" href="https://www.python.org/">Python</a> 2.7</li>
-<li><a class="reference external" href="http://www.boost.org/">Boost</a> 1.47.0</li>
-<li><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.3.1</li>
+<li><a class="reference external" href="https://simtk.org/home/openmm">OpenMM</a> 6.1</li>
+<li><a class="reference external" href="https://cmake.org/">CMake</a> 2.8.12</li>
+<li><a class="reference external" href="https://www.python.org/">Python</a> 2.7.5</li>
+<li><a class="reference external" href="http://www.boost.org/">Boost</a> 1.53.0</li>
<li><a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> 3.2.1</li>
-<li><a class="reference external" href="http://www.netlib.org/lapack/">LAPACK</a> 3.0</li>
+<li><a class="reference external" href="http://www.netlib.org/lapack/">LAPACK</a> 3.4.2</li>
+<li><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.3.1</li>
</ul>
</div>
<div class="section" id="using-cmake">
@@ -84,18 +67,22 @@ documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphin
<p>CMake is used to configure the build system and in the end produces makefiles
and certain directories needed for building ProMod3. Basically it is called
right from a shell with the directory containing the top-level
-<code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> as an argument:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> cmake . -DOST_ROOT<span class="o">=</span><PATH TO OST> -DQMEAN_ROOT<span class="o">=</span><PATH TO QMEAN>
+<code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> as an argument. The preferred approach is to generate a
+build folder and configure and compile in there:</p>
+<div class="highlight-console"><div class="highlight"><pre><span class="gp">#</span> execute this in the ProMod3 root folder
+<span class="gp">$</span> mkdir build
+<span class="gp">$</span> <span class="nb">cd </span>build
+<span class="gp">$</span> cmake .. -DOST_ROOT<span class="o">=</span><PATH TO OST>
</pre></div>
</div>
-<p>For us, at least pointers to the OST and QMEAN installation directories
-are needed, handed over to CMake by <code class="docutils literal"><span class="pre">-D</span></code> into the variables <code class="docutils literal"><span class="pre">OST_ROOT</span></code>
-and <code class="docutils literal"><span class="pre">QMEAN_ROOT</span></code>. Other important variables would be <code class="docutils literal"><span class="pre">BOOST_ROOT</span></code>, set to
-the same path as for OST and probably <code class="docutils literal"><span class="pre">PYTHON_ROOT</span></code> if you want to use a
-certain Python. Also Eigen 3 can be pulled in like this, e.g. if you have to
-download it by yourself because its not installed on your system. Just point
-<code class="docutils literal"><span class="pre">EIGEN3_INCLUDE_DIR</span></code> to the path which provides the <code class="file docutils literal"><span class="pre">Eigen</span></code> header
-directory. Don’t forget to put a <code class="docutils literal"><span class="pre">-D</span></code> in front of options.</p>
+<p>For us, at least pointer to the OST installation directory is needed,
+handed over to CMake by <code class="docutils literal"><span class="pre">-D</span></code> into the variable <code class="docutils literal"><span class="pre">OST_ROOT</span></code> (e.g. OST
+headers would be located in <code class="docutils literal"><span class="pre">OST_ROOT/include/ost</span></code>).</p>
+<p>Similarly, one can specify folders for Boost, Python, Eigen 3 and LAPACK
+if multiple versions exist and/or they are not installed in a default location.
+These are set with the <code class="docutils literal"><span class="pre">BOOST_ROOT</span></code> (make sure that’s the same as for OST),
+<code class="docutils literal"><span class="pre">PYTHON_ROOT</span></code>, <code class="docutils literal"><span class="pre">EIGEN3_INCLUDE_DIR</span></code>, <code class="docutils literal"><span class="pre">BLAS_blas_LIBRARY</span></code> (BLAS library used
+by LAPACK) and <code class="docutils literal"><span class="pre">LAPACK_lapack_LIBRARY</span></code>.</p>
<p>Here is a list of more options used within ProMod3:</p>
<ul class="simple">
<li><code class="docutils literal"><span class="pre">DISABLE_DOCUMENTATION</span></code> Don’t build documentation, don’t search for Sphinx</li>
@@ -115,14 +102,13 @@ in the <code class="file docutils literal"><span class="pre">CMakeCache.txt</spa
</ul>
<p>Instead of calling CMake by yourself, there is the <code class="file docutils literal"><span class="pre">conf-scripts</span></code>
directory, providing smallish scripts to invoke CMake the right way for
-various systems. Usually those scripts just need the OST and QMEAN paths
+various systems. Usually those scripts just need the OST path
and the location of the top-level <code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code>.</p>
-<p>What we highly recommend is going for out-of-source builds. This means creating
-a dedicated directory for building ProMod3 and calling CMake or a
-configuration script from there. This way, you can have several builds with
-different configurations. Also if anything goes wrong, just remove the build
-directory to get to a clean state again. No searching for CMake cache files or
-checking if certain files really got rebuild and similar things required.</p>
+<p>As mentioned earlier, we highly recommend to use out-of-source builds.
+This way, you can have several builds with different configurations. Also if
+anything goes wrong, just remove the build directory to get to a clean state
+again. No searching for CMake cache files or checking if certain files
+really got rebuild and similar things required.</p>
<div class="section" id="running-make">
<h3>Running Make<a class="headerlink" href="#running-make" title="Permalink to this headline">¶</a></h3>
<p>After configuring, you want to build ProMod3 by</p>
@@ -166,13 +152,17 @@ builder</li>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="actions/index_dev.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">test_actions.ActionTestCase</span></code> - Testing Actions</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="contributing.html"
- title="next chapter">Contributing</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<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="docutils literal"><span class="pre">test_actions.ActionTestCase</span></code> - Testing Actions</a></li>
+ <li>Next: <a href="contributing.html" title="next chapter">Contributing</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -202,11 +192,11 @@ builder</li>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="_sources/buildsystem.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 8611701ec36c4833374e9d30e056ad31f3887971..657d2efb1521cddc2692ba4d96df600a99cd732e 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -30,22 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="cmake/index.html" title="ProMod3‘s Share Of CMake"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="index.html">ProMod3 0 documentation</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -98,10 +83,14 @@
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="cmake/index.html"
- title="previous chapter">ProMod3‘s Share Of CMake</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
+ <li>Previous: <a href="cmake/index.html" title="previous chapter">ProMod3‘s Share Of CMake</a></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -131,11 +120,11 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="_sources/changelog.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index e599bea80f88eebb4bf9d05ab5ff1f5483ce08e6..54039a58990d77ebdbc6a72c17d9b11bf7712117 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Developes" href="../developers.html" />
+ <link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="Changelog" href="../changelog.html" />
<link rel="prev" title="Contributing" href="../contributing.html" />
@@ -32,26 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="../changelog.html" title="Changelog"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="../contributing.html" title="Contributing"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" accesskey="U">Documentation For Developes</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -234,13 +215,17 @@ target has to be created <strong>before</strong> any action may be attached to i
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="../contributing.html"
- title="previous chapter">Contributing</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="../changelog.html"
- title="next chapter">Changelog</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li>Previous: <a href="../contributing.html" title="previous chapter">Contributing</a></li>
+ <li>Next: <a href="../changelog.html" title="next chapter">Changelog</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -270,11 +255,11 @@ target has to be created <strong>before</strong> any action may be attached to i
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/cmake/index.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 2ebb7b5993849c76ca4647ae9f8d2d076e39b82d..3dbbfa782340ffd20b5e699b56f9dec2e408883a 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="index.html" />
- <link rel="up" title="Documentation For Developes" href="developers.html" />
+ <link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="ProMod3‘s Share Of CMake" href="cmake/index.html" />
<link rel="prev" title="Building ProMod3" href="buildsystem.html" />
@@ -32,26 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="cmake/index.html" title="ProMod3‘s Share Of CMake"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="buildsystem.html" title="Building ProMod3"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="developers.html" accesskey="U">Documentation For Developes</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -61,7 +42,7 @@
<div class="section" id="contributing">
<h1>Contributing<a class="headerlink" href="#contributing" title="Permalink to this headline">¶</a></h1>
<p>The following should explain, in a coarse grain manner, how to add new
-features/ your project to ProMod3. Important topics are Git branches, the
+features or your project to ProMod3. Important topics are Git branches, the
directory structure and tightly linked with this also CMake. The most general
advice would be to use existing bits and pieces as examples and to be
consistent with what you already find here. As an example, documentation
@@ -73,7 +54,7 @@ one is a bit special and provides core functionality to everybody else.</p>
<p>In the end of this chapter you will find a little walk-through on how to get
started.</p>
<div class="section" id="git-branches">
-<h2>Git Branches<a class="headerlink" href="#git-branches" title="Permalink to this headline">¶</a></h2>
+<span id="id1"></span><h2>Git Branches<a class="headerlink" href="#git-branches" title="Permalink to this headline">¶</a></h2>
<p>Basically we have two, sometimes three major branches. <code class="docutils literal"><span class="pre">master</span></code>, <code class="docutils literal"><span class="pre">develop</span></code>
and in front of a new release a dedicated release branch. For bugs, hotfix
branches of a rather short life are used.</p>
@@ -293,7 +274,7 @@ documentation, here is a helpful list of standard formatters:
the Changelog. It will be automatically pulled into the documentation.</p>
</div>
<div class="section" id="how-to-start-your-own-module">
-<span id="id1"></span><h2>How To Start Your Own Module<a class="headerlink" href="#how-to-start-your-own-module" title="Permalink to this headline">¶</a></h2>
+<span id="id2"></span><h2>How To Start Your Own Module<a class="headerlink" href="#how-to-start-your-own-module" title="Permalink to this headline">¶</a></h2>
<p>This is just a walk-through how the topics from above work together when you
start your own module. For the entry point, lets assume that you already cloned
the repository into a directory and just changed into it.</p>
@@ -914,13 +895,17 @@ contributions to web pages using ProMod3.</p>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="buildsystem.html"
- title="previous chapter">Building ProMod3</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="cmake/index.html"
- title="next chapter">ProMod3‘s Share Of CMake</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
+ <li><a href="developers.html">Documentation For Developers</a><ul>
+ <li>Previous: <a href="buildsystem.html" title="previous chapter">Building ProMod3</a></li>
+ <li>Next: <a href="cmake/index.html" title="next chapter">ProMod3‘s Share Of CMake</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -950,11 +935,11 @@ contributions to web pages using ProMod3.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="_sources/contributing.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 422dd95c123f64a5e89ac34af1ab8984bfc937ee..30dbc497fe7655932f526096f1d8028a241952fa 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="../pipeline/index.html" title="pipeline - ProMod3 Modelling Pipeline"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="pm3argparse.html" title="pm3argparse - Parsing Command Lines"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -226,13 +206,19 @@ script will terminate if a gzip file is found.</li>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="pm3argparse.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="../pipeline/index.html"
- title="next chapter"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li>Previous: <a href="pm3argparse.html" title="previous chapter"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
+ <li>Next: <a href="../pipeline/index.html" title="next chapter"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -262,11 +248,11 @@ script will terminate if a gzip file is found.</li>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/core/helper.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index a916e4415a772584ca5361a705167a96560a03da..e559518c243945e994ed6ff0b4527c6127a79964 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Developes" href="../developers.html" />
+ <link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
<link rel="prev" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" />
@@ -32,26 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="pm3argparse.html" title="pm3argparse - Parsing Command Lines"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="setcompoundschemlib.html" title="SetCompoundsChemlib()"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" accesskey="U">Documentation For Developes</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -84,13 +65,17 @@ modeling per se but cover standard programming issues.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="setcompoundschemlib.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="pm3argparse.html"
- title="next chapter"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></p>
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li>Previous: <a href="setcompoundschemlib.html" title="previous chapter"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+ <li>Next: <a href="pm3argparse.html" title="next chapter"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -120,11 +105,11 @@ modeling per se but cover standard programming issues.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/core/index.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index 5315053e80e4c5d87db2adc5d893c451b277feb6..78a102afe49f4e4aa9ae4fa7bade9a945b2831be 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="helper.html" title="helper - Shared Functionality For the Everything"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="index.html" title="core - ProMod3 Core Functionality"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -72,13 +52,17 @@ There <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentP
simplification. It provides a set of standard arguments you just need to
activate for your action plus it comes with some verification functionality for
input.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="sd">'''\</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="sd">'''</span>
<span class="sd">Place the description of your script right in the file and import</span>
-<span class="sd">it via '__doc__' as description to the parser ('-h', '--help').\</span>
+<span class="sd">it via '__doc__' as description to the parser ('-h', '--help').</span>
<span class="sd">'''</span>
<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">pm3argparse</span>
+<span class="c"># make sure we see output when passing '-h'</span>
+<span class="kn">import</span> <span class="nn">ost</span>
+<span class="n">ost</span><span class="o">.</span><span class="n">PushVerbosityLevel</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
+
<span class="n">parser</span> <span class="o">=</span> <span class="n">pm3argparse</span><span class="o">.</span><span class="n">PM3ArgumentParser</span><span class="p">(</span><span class="n">__doc__</span><span class="p">)</span>
<span class="n">parser</span><span class="o">.</span><span class="n">AddAlignment</span><span class="p">()</span>
<span class="n">parser</span><span class="o">.</span><span class="n">AssembleParser</span><span class="p">()</span>
@@ -105,9 +89,7 @@ called on unrecognised arguments, the script exits with a code 2 by
<dl class="attribute">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.action">
<code class="descname">action</code><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.action" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-<p>Indicates if the calling script is a ProMod3 action.</p>
+<dd><p>Indicates if the calling script is a ProMod3 action.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -116,6 +98,8 @@ called on unrecognised arguments, the script exits with a code 2 by
</tr>
</tbody>
</table>
+</dd></dl>
+
<dl class="method">
<dt id="promod3.core.pm3argparse.PM3ArgumentParser.__init__">
<code class="descname">__init__</code><span class="sig-paren">(</span><em>description</em>, <em>action=True</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.__init__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.__init__" title="Permalink to this definition">¶</a></dt>
@@ -292,13 +276,19 @@ and with the right constraints.</p>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="index.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="helper.html"
- title="next chapter"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+ <li>Next: <a href="helper.html" title="next chapter"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -328,11 +318,11 @@ and with the right constraints.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/core/pm3argparse.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index d80077365c77731ef1efd4b99da149fc20e10773..57a724568d4d01cb9fe312efb31db03fa4fc6127 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -24,34 +24,15 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Developes" href="../developers.html" />
+ <link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="core - ProMod3 Core Functionality" href="index.html" />
- <link rel="prev" title="Documentation For Developes" href="../developers.html" />
+ <link rel="prev" title="Documentation For Developers" href="../developers.html" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="index.html" title="core - ProMod3 Core Functionality"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="../developers.html" title="Documentation For Developes"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" accesskey="U">Documentation For Developes</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -89,13 +70,17 @@ enabled globally.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="../developers.html"
- title="previous chapter">Documentation For Developes</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="index.html"
- title="next chapter"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></p>
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li>Previous: <a href="../developers.html" title="previous chapter">Documentation For Developers</a></li>
+ <li>Next: <a href="index.html" title="next chapter"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -125,11 +110,11 @@ enabled globally.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/core/setcompoundschemlib.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index 7fa8a012229c42873f68649572f07bf5a7a6dda2..4174ce715e8cce8095da3260c7c68f2f7d72587b 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Documentation For Developes — ProMod3 0 documentation</title>
+ <title>Documentation For Developers — ProMod3 0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -24,43 +24,30 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="index.html" />
- <link rel="next" title="SetCompoundsChemlib()" href="core/setcompoundschemlib.html" />
+ <link rel="next" title="Getting Started" href="gettingstarted.html" />
<link rel="prev" title="Documentation For Users" href="users.html" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="core/setcompoundschemlib.html" title="SetCompoundsChemlib()"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="users.html" title="Documentation For Users"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="index.html">ProMod3 0 documentation</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
- <div class="section" id="documentation-for-developes">
-<h1>Documentation For Developes<a class="headerlink" href="#documentation-for-developes" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="documentation-for-developers">
+<h1>Documentation For Developers<a class="headerlink" href="#documentation-for-developers" title="Permalink to this headline">¶</a></h1>
<p>Contents:</p>
<div class="toctree-wrapper compound">
<ul>
+<li class="toctree-l1"><a class="reference internal" href="gettingstarted.html">Getting Started</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html#get-and-run-project">Get and Run ProMod3</a></li>
+<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html#modelling-pipeline">Modelling pipeline</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l1"><a class="reference internal" href="core/index.html"><code class="docutils literal"><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"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
@@ -71,8 +58,8 @@
<li class="toctree-l2"><a class="reference internal" href="pipeline/run_engine.html"><code class="docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="rawmodel/index.html"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modeling</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="rawmodel/index.html#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
+<li class="toctree-l1"><a class="reference internal" href="rawmodel/index.html"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modelling</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="rawmodel/index.html#raw-coordinate-modelling-api">Raw Coordinate Modelling API</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="loop/index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a><ul>
@@ -87,13 +74,8 @@
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_id.html">RotamerID</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer.html">Rotamers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/frame.html">Frame</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_lib.html">Rotamer Library</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/graph.html">Graph</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/sidechain_settings.html">The Settings - Control Things...</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/disulfid.html">Disulfid Bond Evaluation</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html#reconstruct-function">Reconstruct Function</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html#sidechain-module-functionality">Sidechain Module Functionality</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="actions/index_dev.html"><code class="docutils literal"><span class="pre">test_actions.ActionTestCase</span></code> - Testing Actions</a><ul>
@@ -133,13 +115,15 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="users.html"
- title="previous chapter">Documentation For Users</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="core/setcompoundschemlib.html"
- title="next chapter"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></p>
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
+ <li>Previous: <a href="users.html" title="previous chapter">Documentation For Users</a></li>
+ <li>Next: <a href="gettingstarted.html" title="next chapter">Getting Started</a></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -169,11 +153,11 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="_sources/developers.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 1265ed7cb9530bd179ea49df6cee7339d80ab60d..1e85ebb707a55b10223eb04aa23663862d3d076f 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -30,19 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="#" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="index.html">ProMod3 0 documentation</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -198,11 +186,9 @@
</dt>
- <dt><a href="sidechain/frame.html#promod3.sidechain.Frame.AddFrameEnergy">AddFrameEnergy() (promod3.sidechain.Frame method)</a>, <a href="sidechain/frame.html#promod3.sidechain.Frame.AddFrameEnergy">[1]</a>
+ <dt><a href="sidechain/frame.html#promod3.sidechain.Frame.AddFrameEnergy">AddFrameEnergy() (promod3.sidechain.Frame method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.AddLonePair">AddLonePair() (promod3.sidechain.Particle method)</a>
</dt>
@@ -211,6 +197,34 @@
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.AddRotamer">AddRotamer() (promod3.sidechain.BBDepRotamerLib method)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.AddRotamer">(promod3.sidechain.RotamerLib method)</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddSeqIDParameters">AddSeqIDParameters() (promod3.loop.Fragger method)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddSeqSimParameters">AddSeqSimParameters() (promod3.loop.Fragger method)</a>
+ </dt>
+
+
+ <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddSequenceProfileParameters">AddSequenceProfileParameters() (promod3.loop.Fragger method)</a>
+ </dt>
+
+
+ <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddSSAgreeParameters">AddSSAgreeParameters() (promod3.loop.Fragger method)</a>
+ </dt>
+
+
+ <dt><a href="loop/structure_db.html#promod3.loop.Fragger.AddStructureProfileParameters">AddStructureProfileParameters() (promod3.loop.Fragger method)</a>
+ </dt>
+
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.append">append() (promod3.loop.BackboneList method)</a>
</dt>
@@ -247,6 +261,12 @@
<dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThres">ApplySelfEnergyThres() (promod3.sidechain.FRMRotamerGroup method)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThres">(promod3.sidechain.RRMRotamerGroup method)</a>
+ </dt>
+
+ </dl></dd>
<dt><a href="loop/backbone.html#promod3.loop.Backbone.ApplyTransform">ApplyTransform() (promod3.loop.Backbone method)</a>
</dt>
@@ -367,6 +387,12 @@
<dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.CalculateInternalEnergies">CalculateInternalEnergies() (promod3.sidechain.FRMRotamerGroup method)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamerGroup.CalculateInternalEnergies">(promod3.sidechain.RRMRotamerGroup method)</a>
+ </dt>
+
+ </dl></dd>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.CalculateInternalEnergy">CalculateInternalEnergy() (promod3.sidechain.FRMRotamer method)</a>
</dt>
@@ -412,16 +438,20 @@
</dt>
- <dt><a href="loop/loop_closing.html#promod3.loop.CCD">CCD() (in module promod3.loop)</a>, <a href="loop/loop_closing.html#promod3.loop.CCD">[1]</a>, <a href="loop/loop_closing.html#promod3.loop.CCD">[2]</a>, <a href="loop/loop_closing.html#promod3.loop.CCD">[3]</a>, <a href="loop/loop_closing.html#promod3.loop.CCD">[4]</a>, <a href="loop/loop_closing.html#promod3.loop.CCD">[5]</a>
+ <dt><a href="loop/loop_closing.html#promod3.loop.CCD">CCD (class in promod3.loop)</a>
</dt>
- <dt><a href="loop/monte_carlo.html#promod3.loop.CCDCloser">CCDCloser (class in promod3.loop)</a>
+ <dt><a href="loop/loop_closing.html#promod3.loop.CCD.CCD">CCD() (promod3.loop.CCD method)</a>, <a href="loop/loop_closing.html#promod3.loop.CCD.CCD">[1]</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
+ <dt><a href="loop/monte_carlo.html#promod3.loop.CCDCloser">CCDCloser (class in promod3.loop)</a>
+ </dt>
+
+
<dt><a href="loop/structure_db.html#promod3.loop.FragmentInfo.chain_index">chain_index (promod3.loop.FragmentInfo attribute)</a>
</dt>
@@ -446,15 +476,23 @@
</dt>
- <dt><a href="loop/monte_carlo.html#promod3.loop.CCDCloser.Close">Close() (promod3.loop.CCDCloser method)</a>
+ <dt><a href="loop/loop_closing.html#promod3.loop.CCD.Close">Close() (promod3.loop.CCD method)</a>
</dt>
<dd><dl>
+ <dt><a href="loop/monte_carlo.html#promod3.loop.CCDCloser.Close">(promod3.loop.CCDCloser method)</a>
+ </dt>
+
+
<dt><a href="loop/monte_carlo.html#promod3.loop.DirtyCCDCloser.Close">(promod3.loop.DirtyCCDCloser method)</a>
</dt>
+ <dt><a href="loop/loop_closing.html#promod3.loop.KIC.Close">(promod3.loop.KIC method)</a>
+ </dt>
+
+
<dt><a href="loop/monte_carlo.html#promod3.loop.KICCloser.Close">(promod3.loop.KICCloser method)</a>
</dt>
@@ -503,7 +541,7 @@
</dt>
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.ConstructFRMRotamerGroup">ConstructFRMRotamerGroup() (in module promod3.sidechain)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.ConstructFRMRotamerGroup">[1]</a>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.ConstructFRMRotamerGroup">ConstructFRMRotamerGroup() (in module promod3.sidechain)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.ConstructFRMRotamerGroup">[1]</a>, <a href="sidechain/rotamer.html#promod3.sidechain.ConstructFRMRotamerGroup">[2]</a>, <a href="sidechain/rotamer.html#promod3.sidechain.ConstructFRMRotamerGroup">[3]</a>
</dt>
@@ -511,7 +549,7 @@
</dt>
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.ConstructRRMRotamerGroup">ConstructRRMRotamerGroup() (in module promod3.sidechain)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.ConstructRRMRotamerGroup">[1]</a>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.ConstructRRMRotamerGroup">ConstructRRMRotamerGroup() (in module promod3.sidechain)</a>, <a href="sidechain/rotamer.html#promod3.sidechain.ConstructRRMRotamerGroup">[1]</a>, <a href="sidechain/rotamer.html#promod3.sidechain.ConstructRRMRotamerGroup">[2]</a>, <a href="sidechain/rotamer.html#promod3.sidechain.ConstructRRMRotamerGroup">[3]</a>
</dt>
@@ -523,11 +561,11 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.Graph.CreateFromFRMList">CreateFromFRMList() (promod3.sidechain.Graph method)</a>
+ <dt><a href="sidechain/graph.html#promod3.sidechain.Graph.CreateFromFRMList">CreateFromFRMList() (promod3.sidechain.Graph static method)</a>
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.Graph.CreateFromRRMList">CreateFromRRMList() (promod3.sidechain.Graph method)</a>
+ <dt><a href="sidechain/graph.html#promod3.sidechain.Graph.CreateFromRRMList">CreateFromRRMList() (promod3.sidechain.Graph static method)</a>
</dt>
@@ -541,27 +579,19 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="loop/backbone.html#promod3.loop.DihedralPair">DihedralPair (class in promod3.loop)</a>
- </dt>
-
-
- <dt><a href="loop/backbone.html#promod3.loop.DihedralPair.DihedralPair">DihedralPair() (promod3.loop.DihedralPair method)</a>
- </dt>
-
-
<dt><a href="loop/monte_carlo.html#promod3.loop.DirtyCCDCloser">DirtyCCDCloser (class in promod3.loop)</a>
</dt>
- <dt><a href="sidechain/disulfid.html#promod3.sidechain.DisulfidScore">DisulfidScore() (in module promod3.sidechain)</a>, <a href="sidechain/disulfid.html#promod3.sidechain.DisulfidScore">[1]</a>
+ <dt><a href="sidechain/disulfid.html#promod3.sidechain.DisulfidScore">DisulfidScore() (in module promod3.sidechain)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Draw">Draw() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Draw">[1]</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.DrawPhiGivenPsi">DrawPhiGivenPsi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.DrawPhiGivenPsi">[1]</a>
</dt>
@@ -613,10 +643,6 @@
</dt>
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.FillBackbone">FillBackbone() (promod3.loop.StructureDB method)</a>, <a href="loop/structure_db.html#promod3.loop.StructureDB.FillBackbone">[1]</a>
- </dt>
-
-
<dt><a href="loop/loop_candidate.html#promod3.loop.LoopCandidates.FillFromDatabase">FillFromDatabase() (promod3.loop.LoopCandidates method)</a>
</dt>
@@ -635,15 +661,15 @@
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="loop/structure_db.html#promod3.loop.FraggerScoreParameters">FraggerScoreParameters (class in promod3.loop)</a>
+ <dt><a href="loop/structure_db.html#promod3.loop.Fragger.Fragger">Fragger() (promod3.loop.Fragger method)</a>
</dt>
- <dt><a href="loop/structure_db.html#promod3.loop.FraggerScoreParameters.FraggerScoreParameters">FraggerScoreParameters() (promod3.loop.FraggerScoreParameters method)</a>, <a href="loop/structure_db.html#promod3.loop.FraggerScoreParameters.FraggerScoreParameters">[1]</a>, <a href="loop/structure_db.html#promod3.loop.FraggerScoreParameters.FraggerScoreParameters">[2]</a>, <a href="loop/structure_db.html#promod3.loop.FraggerScoreParameters.FraggerScoreParameters">[3]</a>, <a href="loop/structure_db.html#promod3.loop.FraggerScoreParameters.FraggerScoreParameters">[4]</a>
+ <dt><a href="loop/structure_db.html#promod3.loop.FragmentInfo">FragmentInfo (class in promod3.loop)</a>
</dt>
- <dt><a href="loop/structure_db.html#promod3.loop.FragmentInfo">FragmentInfo (class in promod3.loop)</a>
+ <dt><a href="loop/monte_carlo.html#promod3.loop.FragmentSampler">FragmentSampler (class in promod3.loop)</a>
</dt>
@@ -677,6 +703,10 @@
</dt>
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GenerateStructureProfile">GenerateStructureProfile() (promod3.loop.StructureDB method)</a>
+ </dt>
+
+
<dt><a href="loop/structure_db.html#promod3.loop.FragDB.GetAngularBinSize">GetAngularBinSize() (promod3.loop.FragDB method)</a>
</dt>
@@ -709,6 +739,10 @@
</dt>
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetBackboneList">GetBackboneList() (promod3.loop.StructureDB method)</a>, <a href="loop/structure_db.html#promod3.loop.StructureDB.GetBackboneList">[1]</a>
+ </dt>
+
+
<dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetBinSize">GetBinSize() (promod3.loop.TorsionSampler method)</a>
</dt>
@@ -745,10 +779,6 @@
</dt>
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetEMin">GetEMin() (promod3.sidechain.Particle method)</a>
- </dt>
-
-
<dt><a href="loop/structure_db.html#promod3.loop.Fragger.GetFragmentInfo">GetFragmentInfo() (promod3.loop.Fragger method)</a>
</dt>
@@ -806,12 +836,12 @@
<dt><a href="sidechain/graph.html#promod3.sidechain.Graph.GetNumActiveNodes">GetNumActiveNodes() (promod3.sidechain.Graph method)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetNumCoords">GetNumCoords() (promod3.loop.StructureDB method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="sidechain/graph.html#promod3.sidechain.Graph.GetNumEdges">GetNumEdges() (promod3.sidechain.Graph method)</a>
</dt>
@@ -845,6 +875,10 @@
</dt>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetParticleType">GetParticleType() (promod3.sidechain.Particle method)</a>
+ </dt>
+
+
<dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi">GetPhiProbabilityGivenPsi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPhiProbabilityGivenPsi">[1]</a>
</dt>
@@ -871,10 +905,6 @@
</dl></dd>
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetProfileScore">GetProfileScore() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
<dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi">GetPsiProbabilityGivenPhi() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.GetPsiProbabilityGivenPhi">[1]</a>
</dt>
@@ -883,31 +913,29 @@
</dt>
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetRadius">GetRadius() (promod3.sidechain.Particle method)</a>
- </dt>
-
-
- <dt><a href="loop/monte_carlo.html#promod3.loop.LinearScorer.GetScore">GetScore() (promod3.loop.LinearScorer method)</a>
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetResidueDepths">GetResidueDepths() (promod3.loop.StructureDB method)</a>
</dt>
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetSelfEnergy">GetSelfEnergy() (promod3.sidechain.FRMRotamer method)</a>
+ <dt><a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">GetScore() (promod3.loop.Fragger method)</a>, <a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">[1]</a>
</dt>
<dd><dl>
- <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetSelfEnergy">(promod3.sidechain.RRMRotamer method)</a>
+ <dt><a href="loop/monte_carlo.html#promod3.loop.LinearScorer.GetScore">(promod3.loop.LinearScorer method)</a>
</dt>
</dl></dd>
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSeqID">GetSeqID() (promod3.loop.StructureDB method)</a>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetSelfEnergy">GetSelfEnergy() (promod3.sidechain.FRMRotamer method)</a>
</dt>
-
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSeqSim">GetSeqSim() (promod3.loop.StructureDB method)</a>
+ <dd><dl>
+
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.RRMRotamer.GetSelfEnergy">(promod3.sidechain.RRMRotamer method)</a>
</dt>
+ </dl></dd>
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetSequence">GetSequence() (promod3.loop.BackboneList method)</a>
</dt>
@@ -919,7 +947,15 @@
</dl></dd>
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSSAgreement">GetSSAgreement() (promod3.loop.StructureDB method)</a>
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSequenceProfile">GetSequenceProfile() (promod3.loop.StructureDB method)</a>
+ </dt>
+
+
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetSolventAccessibilitites">GetSolventAccessibilitites() (promod3.loop.StructureDB method)</a>
+ </dt>
+
+
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetStructureProfile">GetStructureProfile() (promod3.loop.StructureDB method)</a>
</dt>
@@ -941,10 +977,6 @@
</dl></dd>
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetTorsionProbability">GetTorsionProbability() (promod3.loop.StructureDB method)</a>
- </dt>
-
-
<dt><a href="loop/backbone.html#promod3.loop.Backbone.GetTransform">GetTransform() (promod3.loop.Backbone method)</a>
</dt>
@@ -984,6 +1016,10 @@
<dd><dl>
+ <dt><a href="loop/monte_carlo.html#promod3.loop.FragmentSampler.Initialize">(promod3.loop.FragmentSampler method)</a>
+ </dt>
+
+
<dt><a href="loop/monte_carlo.html#promod3.loop.PhiPsiSampler.Initialize">(promod3.loop.PhiPsiSampler method)</a>
</dt>
@@ -993,10 +1029,6 @@
</dl></dd>
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.insert">insert() (promod3.loop.BackboneList method)</a>
- </dt>
-
-
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.InsertInto">InsertInto() (promod3.loop.BackboneList method)</a>
</dt>
@@ -1006,12 +1038,12 @@
</dt>
</dl></dd>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.IsHBondAcceptor">IsHBondAcceptor() (promod3.sidechain.Particle method)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.IsHBondDonor">IsHBondDonor() (promod3.sidechain.Particle method)</a>
</dt>
@@ -1027,7 +1059,11 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="loop/loop_closing.html#promod3.loop.KIC">KIC() (in module promod3.loop)</a>, <a href="loop/loop_closing.html#promod3.loop.KIC">[1]</a>
+ <dt><a href="loop/loop_closing.html#promod3.loop.KIC">KIC (class in promod3.loop)</a>
+ </dt>
+
+
+ <dt><a href="loop/loop_closing.html#promod3.loop.KIC.KIC">KIC() (promod3.loop.KIC method)</a>
</dt>
</dl></td>
@@ -1071,6 +1107,10 @@
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.Load">(promod3.sidechain.BBDepRotamerLib method)</a>
</dt>
+
+ <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.Load">(promod3.sidechain.RotamerLib method)</a>
+ </dt>
+
</dl></dd>
<dt><a href="loop/load_loop_objects.html#promod3.loop.LoadBackboneLoopScorer">LoadBackboneLoopScorer() (in module promod3.loop)</a>
@@ -1146,6 +1186,12 @@
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.MakeStatic">MakeStatic() (promod3.sidechain.BBDepRotamerLib method)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.MakeStatic">(promod3.sidechain.RotamerLib method)</a>
+ </dt>
+
+ </dl></dd>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamerGroup.Merge">Merge() (promod3.sidechain.FRMRotamerGroup method)</a>
</dt>
@@ -1268,15 +1314,17 @@
</dt>
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.PrindStatistics">PrindStatistics() (promod3.loop.StructureDB method)</a>
+ <dt><a href="loop/structure_db.html#promod3.loop.FragDB.PrintStatistics">PrintStatistics() (promod3.loop.FragDB method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
-
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.PrintStatistics">PrintStatistics() (promod3.loop.FragDB method)</a>
+ <dd><dl>
+
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.PrintStatistics">(promod3.loop.StructureDB method)</a>
</dt>
+ </dl></dd>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.probability">probability (promod3.sidechain.RotamerLibEntry attribute)</a>
</dt>
@@ -1317,11 +1365,15 @@
</dl></dd>
- <dt><a href="loop/monte_carlo.html#promod3.loop.PhiPsiSampler.ProposeStep">ProposeStep() (promod3.loop.PhiPsiSampler method)</a>
+ <dt><a href="loop/monte_carlo.html#promod3.loop.FragmentSampler.ProposeStep">ProposeStep() (promod3.loop.FragmentSampler method)</a>
</dt>
<dd><dl>
+ <dt><a href="loop/monte_carlo.html#promod3.loop.PhiPsiSampler.ProposeStep">(promod3.loop.PhiPsiSampler method)</a>
+ </dt>
+
+
<dt><a href="loop/monte_carlo.html#promod3.loop.SoftSampler.ProposeStep">(promod3.loop.SoftSampler method)</a>
</dt>
@@ -1340,6 +1392,12 @@
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.QueryLib">QueryLib() (promod3.sidechain.BBDepRotamerLib method)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.QueryLib">(promod3.sidechain.RotamerLib method)</a>
+ </dt>
+
+ </dl></dd>
</dl></td>
</tr></table>
@@ -1355,6 +1413,14 @@
</dt>
+ <dt><a href="loop/backbone.html#promod3.loop.BackboneList.ReconstructCBetaPositions">ReconstructCBetaPositions() (promod3.loop.BackboneList method)</a>
+ </dt>
+
+
+ <dt><a href="loop/backbone.html#promod3.loop.BackboneList.ReconstructOxygenPositions">ReconstructOxygenPositions() (promod3.loop.BackboneList method)</a>
+ </dt>
+
+
<dt><a href="loop/loop_candidate.html#promod3.loop.LoopCandidates.Remove">Remove() (promod3.loop.LoopCandidates method)</a>
</dt>
@@ -1377,20 +1443,32 @@
</dl></dd>
- <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry">RotamerLibEntry (class in promod3.sidechain)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry">[1]</a>
+ <dt><a href="sidechain/rotamer_id.html#promod3.sidechain.RotamerID">RotamerID (class in promod3.sidechain)</a>
</dt>
- <dt><a href="sidechain/sidechain_settings.html#promod3.sidechain.RotamerSettings">RotamerSettings (class in promod3.sidechain)</a>
+ <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib">RotamerLib (class in promod3.sidechain)</a>
+ </dt>
+
+
+ <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry">RotamerLibEntry (class in promod3.sidechain)</a>, <a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry">[1]</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
+ <dt><a href="sidechain/sidechain_settings.html#promod3.sidechain.RotamerSettings">RotamerSettings (class in promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundOmegaTorsion">RotateAroundOmegaTorsion() (promod3.loop.BackboneList method)</a>
</dt>
+ <dt><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundPhiPsiTorsion">RotateAroundPhiPsiTorsion() (promod3.loop.BackboneList method)</a>
+ </dt>
+
+
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.RotateAroundPhiTorsion">RotateAroundPhiTorsion() (promod3.loop.BackboneList method)</a>
</dt>
@@ -1445,6 +1523,10 @@
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.Save">(promod3.sidechain.BBDepRotamerLib method)</a>
</dt>
+
+ <dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLib.Save">(promod3.sidechain.RotamerLib method)</a>
+ </dt>
+
</dl></dd>
<dt><a href="loop/structure_db.html#promod3.loop.FragDB.SearchDB">SearchDB() (promod3.loop.FragDB method)</a>
@@ -1475,7 +1557,7 @@
</dt>
- <dt><a href="sidechain/frame.html#promod3.sidechain.Frame.SetFrameEnergy">SetFrameEnergy() (promod3.sidechain.Frame method)</a>, <a href="sidechain/frame.html#promod3.sidechain.Frame.SetFrameEnergy">[1]</a>
+ <dt><a href="sidechain/frame.html#promod3.sidechain.Frame.SetFrameEnergy">SetFrameEnergy() (promod3.sidechain.Frame method)</a>
</dt>
<dd><dl>
@@ -1525,6 +1607,10 @@
</dt>
+ <dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetPhiPsiTorsion">SetPhiPsiTorsion() (promod3.loop.BackboneList method)</a>
+ </dt>
+
+
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetPhiTorsion">SetPhiTorsion() (promod3.loop.BackboneList method)</a>
</dt>
@@ -1532,8 +1618,6 @@
<dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.SetPolarDirection">SetPolarDirection() (promod3.sidechain.Particle method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetProbability">SetProbability() (promod3.sidechain.FRMRotamer method)</a>
</dt>
@@ -1544,11 +1628,17 @@
</dt>
</dl></dd>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetPsiTorsion">SetPsiTorsion() (promod3.loop.BackboneList method)</a>
</dt>
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.SetStructureProfile">SetStructureProfile() (promod3.loop.StructureDB method)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.SetTemperature">SetTemperature() (promod3.sidechain.FRMRotamer method)</a>
</dt>
@@ -1565,6 +1655,10 @@
</dt>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.SidechainParticle">SidechainParticle (class in promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.RotamerLibEntry.sig1">sig1 (promod3.sidechain.RotamerLibEntry attribute)</a>
</dt>
@@ -1671,7 +1765,13 @@
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
-
+ <div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
+ </ul></li>
+</ul>
+</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
@@ -1695,7 +1795,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
new file mode 100644
index 0000000000000000000000000000000000000000..6e9dc618e74fdf5544ca0fd605dff1d534455f15
--- /dev/null
+++ b/doc/html/gettingstarted.html
@@ -0,0 +1,159 @@
+<!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 http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Getting Started — ProMod3 0 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">
+ var DOCUMENTATION_OPTIONS = {
+ URL_ROOT: './',
+ VERSION: '0',
+ COLLAPSE_INDEX: false,
+ FILE_SUFFIX: '.html',
+ HAS_SOURCE: true
+ };
+ </script>
+ <script type="text/javascript" src="_static/jquery.js"></script>
+ <script type="text/javascript" src="_static/underscore.js"></script>
+ <script type="text/javascript" src="_static/doctools.js"></script>
+ <link rel="top" title="ProMod3 0 documentation" href="index.html" />
+ <link rel="up" title="Documentation For Developers" href="developers.html" />
+ <link rel="next" title="SetCompoundsChemlib()" href="core/setcompoundschemlib.html" />
+ <link rel="prev" title="Documentation For Developers" href="developers.html" />
+
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+
+ </head>
+ <body role="document">
+
+ <div class="document">
+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <div class="section" id="getting-started">
+<h1>Getting Started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="get-and-run-project">
+<h2>Get and Run ProMod3<a class="headerlink" href="#get-and-run-project" title="Permalink to this headline">¶</a></h2>
+<p>First steps to get ProMod3 up and running:</p>
+<ol class="arabic simple">
+<li>Get <a class="reference external" href="http://www.OpenStructure.org">OST</a>.</li>
+<li>Get ProMod3 from the <code class="docutils literal"><span class="pre">git</span></code> repository (see <a class="reference internal" href="contributing.html#git-branches"><span>here</span></a>).</li>
+<li>Compile ProMod3 with <code class="docutils literal"><span class="pre">cmake</span></code> and <code class="docutils literal"><span class="pre">make</span></code> (see <a class="reference internal" href="buildsystem.html#building-promod"><span>here</span></a>).</li>
+<li>Ensure that you have a <code class="docutils literal"><span class="pre">stage/bin</span></code> folder which includes a <code class="docutils literal"><span class="pre">pm</span></code> executable.
+For convenience, add the folder to your <code class="docutils literal"><span class="pre">PATH</span></code> env. variable.</li>
+<li>You can now execute ProMod3 by running the following in your terminal:</li>
+</ol>
+<blockquote>
+<div><div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> pm <COMMAND>
+</pre></div>
+</div>
+<p>Here <code class="docutils literal"><span class="pre"><COMMAND></span></code> can be:</p>
+<ul>
+<li><p class="first">a predefined “action” (execute <code class="docutils literal"><span class="pre">pm</span> <span class="pre">help</span></code> for a list of possible actions)</p>
+</li>
+<li><p class="first">the path to a python script, such as the following example:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+
+<span class="c"># generate backbone with dihedrals of a helix and store it</span>
+<span class="n">sequence</span> <span class="o">=</span> <span class="s">"HELLYEAH"</span>
+<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s">"test.pdb"</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>The execution of this script should generate a <code class="docutils literal"><span class="pre">test.pdb</span></code> file, which you
+can visualize with any pdb reader (e.g. <code class="docutils literal"><span class="pre">dng</span></code> from OST).</p>
+</li>
+</ul>
+</div></blockquote>
+</div>
+<div class="section" id="modelling-pipeline">
+<h2>Modelling pipeline<a class="headerlink" href="#modelling-pipeline" title="Permalink to this headline">¶</a></h2>
+<p>ProMod3 is meant to help you perform operations for protein homology modelling.
+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>Build a raw model from the template (see <a class="reference internal" href="rawmodel/index.html#module-promod3.rawmodel" title="promod3.rawmodel: Raw Coordinate Model"><code class="xref py py-mod docutils literal"><span class="pre">rawmodel</span></code></a> module)</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 Modelling"><code class="xref py py-mod docutils literal"><span class="pre">loop</span></code></a> module)</li>
+<li>Reconstruct sidechains (see <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal"><span class="pre">sidechain</span></code></a> module)</li>
+<li>Minimize energy of final model using molecular mechanics
+(using <code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code> from OST)</li>
+</ul>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+ <h3><a href="index.html">Table Of Contents</a></h3>
+ <ul>
+<li><a class="reference internal" href="#">Getting Started</a><ul>
+<li><a class="reference internal" href="#get-and-run-project">Get and Run ProMod3</a></li>
+<li><a class="reference internal" href="#modelling-pipeline">Modelling pipeline</a></li>
+</ul>
+</li>
+</ul>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
+ <li><a href="developers.html">Documentation For Developers</a><ul>
+ <li>Previous: <a href="developers.html" title="previous chapter">Documentation For Developers</a></li>
+ <li>Next: <a href="core/setcompoundschemlib.html" title="next chapter"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
+ <div role="note" aria-label="source link">
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="_sources/gettingstarted.txt"
+ rel="nofollow">Show Source</a></li>
+ </ul>
+ </div>
+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
+ <form class="search" action="search.html" method="get">
+ <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>
+ <p class="searchtip" style="font-size: 90%">
+ Enter search terms or a module, class or function name.
+ </p>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="footer">
+ ©2015, Bienchen.
+
+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+
+ |
+ <a href="_sources/gettingstarted.txt"
+ rel="nofollow">Page source</a>
+ </div>
+
+
+
+
+ </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/index.html b/doc/html/index.html
index d5591f4553da35bcc5680a7834460a1451fc7df6..a197ab7499c793a1b6f15d92af3daa69607a3d0a 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -30,22 +30,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="users.html" title="Documentation For Users"
- accesskey="N">next</a> |</li>
- <li class="nav-item nav-item-0"><a href="#">ProMod3 0 documentation</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -59,10 +44,11 @@
<ul>
<li class="toctree-l1"><a class="reference internal" href="users.html">Users</a></li>
<li class="toctree-l1"><a class="reference internal" href="developers.html">Developers</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="gettingstarted.html">Getting Started</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="core/index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></li>
<li class="toctree-l2"><a class="reference internal" href="pipeline/index.html"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a></li>
-<li class="toctree-l2"><a class="reference internal" href="rawmodel/index.html"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modeling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rawmodel/index.html"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modelling</a></li>
<li class="toctree-l2"><a class="reference internal" href="loop/index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
<li class="toctree-l2"><a class="reference internal" href="actions/index_dev.html"><code class="docutils literal"><span class="pre">test_actions.ActionTestCase</span></code> - Testing Actions</a></li>
@@ -100,10 +86,14 @@
<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>
-
- <h4>Next topic</h4>
- <p class="topless"><a href="users.html"
- title="next chapter">Documentation For Users</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="#">Documentation overview</a><ul>
+ <li>Next: <a href="users.html" title="next chapter">Documentation For Users</a></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -133,11 +123,11 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="_sources/index.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index 1d95887a4d2db82334c1dccf8f2752a1a7858fd1..83e6ac93982689d65fc7eff679a183cb9609c005 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="torsion_sampler.html" title="Torsion Sampler"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="index.html" title="loop - Loop Modelling"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -66,7 +46,8 @@
a residue. For simple structural manipulations they can be gathered to a
<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> that can be inserted into or converted to a
<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a> at any time.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
<span class="n">sequence</span> <span class="o">=</span> <span class="s">"AAAAAAAA"</span>
@@ -99,30 +80,6 @@ a residue. For simple structural manipulations they can be gathered to a
</div>
<div class="section" id="the-basic-building-blocks">
<h2>The Basic Building Blocks<a class="headerlink" href="#the-basic-building-blocks" title="Permalink to this headline">¶</a></h2>
-<dl class="class">
-<dt id="promod3.loop.DihedralPair">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">DihedralPair</code><a class="headerlink" href="#promod3.loop.DihedralPair" title="Permalink to this definition">¶</a></dt>
-<dd><p>The DihedralPair class only serves as a helper to initialize a
-<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> given consecutive dihedral angles.</p>
-<dl class="method">
-<dt id="promod3.loop.DihedralPair.DihedralPair">
-<code class="descname">DihedralPair</code><span class="sig-paren">(</span><em>phi</em>, <em>psi</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.DihedralPair.DihedralPair" title="Permalink to this definition">¶</a></dt>
-<dd></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"><ul class="first last simple">
-<li><strong>phi</strong> – Phi dihedral angle</li>
-<li><strong>psi</strong> – Psi dihedral angle</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
<dl class="class">
<dt id="promod3.loop.Backbone">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">Backbone</code><a class="headerlink" href="#promod3.loop.Backbone" title="Permalink to this definition">¶</a></dt>
@@ -298,8 +255,12 @@ torsion angles.</p>
<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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of <code class="xref py py-class docutils literal"><span class="pre">DihedralAngle</span></code> objects defining the phi/psi
-angles of created BackboneList</li>
+<li><strong>dihedral_angles</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of <code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> objects defining the backbone dihedral
+angles of created BackboneList. Every <code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> 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.</li>
</ul>
</td>
</tr>
@@ -339,21 +300,19 @@ providing all necessary positions.</p>
<dl class="method">
<dt id="promod3.loop.BackboneList.ToEntity">
<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></dd></dl>
-
-<p>Transforms the backbone list into an <a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
-<blockquote>
-<div><table class="docutils field-list" frame="void" rules="none">
+<dd><p>Transforms the backbone list into an <a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></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">return:</th><td class="field-body">The entity</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The entity</td>
</tr>
-<tr class="field-even field"><th class="field-name">rtype:</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)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return 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)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
-</div></blockquote>
+</dd></dl>
+
<dl class="method">
<dt id="promod3.loop.BackboneList.GetSequence">
<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>
@@ -369,7 +328,7 @@ providing all necessary positions.</p>
<dl class="method">
<dt id="promod3.loop.BackboneList.InsertInto">
-<code class="descname">InsertInto</code><span class="sig-paren">(</span><em>chain</em>, <em>n_stem</em>, <em>c_stem</em><span class="optional">[</span>, <em>reset_stem_positions=True</em><span class="optional">]</span><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>n_stem</em>, <em>c_stem</em><span class="optional">[</span>, <em>remodel_cterminal_o = True</em><span class="optional">]</span><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 <strong>chain</strong>. 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"><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>
@@ -379,9 +338,13 @@ be replaced, otherwise they will be added to the entity.</p>
<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> – The chain</li>
-<li><strong>n_stem</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code>) – The residue number of the n_stem</li>
-<li><strong>c_stem</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code>) – The residue number of the c_stem</li>
-<li><strong>reset_stem_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">Bool</span></code>) – Whether <em>n_stem</em> and <em>c_stem</em> residues’positions whould be set to the positions of the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a></li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The residue number of the n_stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The residue number of the c_stem</li>
+<li><strong>remodel_cterminal_o</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – The position of the cterminal o is dependent
+on the residue after the c_stem. If this flag
+is set and the residue after the cterminus is
+present in <strong>chain</strong>, the according oxygen
+position gets recalculated.</li>
</ul>
</td>
</tr>
@@ -389,6 +352,30 @@ be replaced, otherwise they will be added to the entity.</p>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.loop.BackboneList.ReconstructCBetaPositions">
+<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 CBeta positions based on the actual
+n, ca, and c positions.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.loop.BackboneList.ReconstructOxygenPositions">
+<code class="descname">ReconstructOxygenPositions</code><span class="sig-paren">(</span><span class="optional">[</span><em>last_psi = -0.78540</em><span class="optional">]</span><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>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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.ApplyTransform">
<code class="descname">ApplyTransform</code><span class="sig-paren">(</span><em>transformation_matrix</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.ApplyTransform" title="Permalink to this definition">¶</a></dt>
@@ -426,7 +413,7 @@ be replaced, otherwise they will be added to the entity.</p>
<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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle shout be set.</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle should be set.</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The angle</li>
<li><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all residues after the one with <strong>index</strong>. Otherwise it will be propagated in the direction where it will affect the least number of residues.</li>
</ul>
@@ -445,7 +432,7 @@ be replaced, otherwise they will be added to the entity.</p>
<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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle shout be set.</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle should be set.</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The angle</li>
<li><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all residues after the one with <strong>index</strong>. Otherwise it will be propagated in the direction where it will affect the least number of residues.</li>
</ul>
@@ -464,7 +451,7 @@ be replaced, otherwise they will be added to the entity.</p>
<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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle shout be set.</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle should be set.</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The angle</li>
<li><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all residues after the one with <strong>index</strong>. Otherwise it will be propagated in the direction where it will affect the least number of residues.</li>
</ul>
@@ -474,6 +461,26 @@ be replaced, otherwise they will be added to the entity.</p>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.loop.BackboneList.SetPhiPsiTorsion">
+<code class="descname">SetPhiPsiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>psi</em><span class="optional">[</span>, <em>sequential=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.SetPhiPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets the <em>phi</em> and <em>psi</em> torsion angle of the backbone at position <strong>index</strong> in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></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 last simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle should be set.</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The phi angle</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The psi angle</li>
+<li><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all residues after the one with <strong>index</strong>. Otherwise it will be propagated in the direction where it will affect the least number of residues.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
<dl class="method">
<dt id="promod3.loop.BackboneList.RotateAroundPhiTorsion">
<code class="descname">RotateAroundPhiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>angle</em><span class="optional">[</span>, <em>sequential=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPhiTorsion" title="Permalink to this definition">¶</a></dt>
@@ -483,7 +490,7 @@ be replaced, otherwise they will be added to the entity.</p>
<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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle shout be set.</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle should be set.</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The angle</li>
<li><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all residues after the one with <strong>index</strong>. Otherwise it will be propagated in the direction where it will affect the least number of residues.</li>
</ul>
@@ -502,7 +509,7 @@ be replaced, otherwise they will be added to the entity.</p>
<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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle shout be set.</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle should be set.</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The angle</li>
<li><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all residues after the one with <strong>index</strong>. Otherwise it will be propagated in the direction where it will affect the least number of residues.</li>
</ul>
@@ -521,7 +528,7 @@ be replaced, otherwise they will be added to the entity.</p>
<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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle shout be set.</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle should be set.</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The angle</li>
<li><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all residues after the one with <strong>index</strong>. Otherwise it will be propagated in the direction where it will affect the least number of residues.</li>
</ul>
@@ -531,6 +538,26 @@ be replaced, otherwise they will be added to the entity.</p>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.loop.BackboneList.RotateAroundPhiPsiTorsion">
+<code class="descname">RotateAroundPhiPsiTorsion</code><span class="sig-paren">(</span><em>index</em>, <em>phi</em>, <em>psi</em><span class="optional">[</span>, <em>sequential=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.RotateAroundPhiPsiTorsion" title="Permalink to this definition">¶</a></dt>
+<dd><p>Rotates the <em>phi</em> and <em>psi</em> torsion angle of the backbone at position <strong>index</strong> in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> by <strong>phi</strong> and <strong>psi</strong>.</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 last simple">
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the residue in the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> for which the angle should be set.</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The phi angle</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The psi angle</li>
+<li><strong>sequential</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If <em>True</em>, the rotation will be propagated to all residues after the one with <strong>index</strong>. Otherwise it will be propagated in the direction where it will affect the least number of residues.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
<dl class="method">
<dt id="promod3.loop.BackboneList.GetPhiTorsion">
<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>
@@ -575,18 +602,30 @@ be replaced, otherwise they will be added to the entity.</p>
<dl class="method">
<dt id="promod3.loop.BackboneList.ReplaceFragment">
-<code class="descname">ReplaceFragment</code><span class="sig-paren">(</span><em>sub_fragment</em>, <em>index</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"><span class="pre">BackboneList</span></code></a> starting at position <strong>index</strong> by the <strong>sub_fragment</strong>.</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 last simple">
+<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"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The position at which the fragment replacement will begin</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to false, the function will simply
+replace the according
+<a class="reference internal" href="#promod3.loop.Backbone" title="promod3.loop.Backbone"><code class="xref py py-class docutils literal"><span class="pre">Backbone</span></code></a> objects. If set to true,
+the n-terminal and c-terminal tails are superposed onto the <strong>sub_fragment</strong>
+stems using the positions at <strong>index</strong> and
+<strong>index</strong> + len( <strong>sub_fragment</strong> )-1.</li>
</ul>
</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"><span class="pre">RuntimeError</span></code> If <strong>sub_fragment</strong>
+does not fully fit into actual fragment at
+specified <strong>index</strong></p>
+</td>
+</tr>
</tbody>
</table>
</dd></dl>
@@ -641,24 +680,6 @@ be replaced, otherwise they will be added to the entity.</p>
</table>
</dd></dl>
-<dl class="method">
-<dt id="promod3.loop.BackboneList.insert">
-<code class="descname">insert</code><span class="sig-paren">(</span><em>index</em>, <em>bb</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.insert" title="Permalink to this definition">¶</a></dt>
-<dd><p>Insert the backbone <strong>bb</strong> into the <a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> at position <strong>index</strong>.</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 last simple">
-<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index</li>
-<li><strong>bb</strong> (<a class="reference internal" href="#promod3.loop.Backbone" title="promod3.loop.Backbone"><code class="xref py py-class docutils literal"><span class="pre">Backbone</span></code></a>) – The backbone</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
<dl class="method">
<dt id="promod3.loop.BackboneList.append">
<code class="descname">append</code><span class="sig-paren">(</span><em>bb</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.BackboneList.append" title="Permalink to this definition">¶</a></dt>
@@ -692,13 +713,19 @@ be replaced, otherwise they will be added to the entity.</p>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="index.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="torsion_sampler.html"
- title="next chapter">Torsion Sampler</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a></li>
+ <li>Next: <a href="torsion_sampler.html" title="next chapter">Torsion Sampler</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -728,11 +755,11 @@ be replaced, otherwise they will be added to the entity.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/loop/backbone.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/backbone_loop_score.html b/doc/html/loop/backbone_loop_score.html
index cd9b56214e274f0e22dd27a07533528ed30400b8..4c60335a54e6e2cba5fe9fe61c5e38d65a319d13 100644
--- a/doc/html/loop/backbone_loop_score.html
+++ b/doc/html/loop/backbone_loop_score.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="monte_carlo.html" title="Monte Carlo Sampling"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="loop_closing.html" title="Loop Closing"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -664,13 +644,19 @@ smaller than 3.</p>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="loop_closing.html"
- title="previous chapter">Loop Closing</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="monte_carlo.html"
- title="next chapter">Monte Carlo Sampling</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a><ul>
+ <li>Previous: <a href="loop_closing.html" title="previous chapter">Loop Closing</a></li>
+ <li>Next: <a href="monte_carlo.html" title="next chapter">Monte Carlo Sampling</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -700,11 +686,11 @@ smaller than 3.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/loop/backbone_loop_score.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index d9fd10519c577a0a5750b8f8d324eef841ce56be..be37732a5b334e4d42146cff4502f66e478e8a3f 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -24,34 +24,15 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Developes" href="../developers.html" />
+ <link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="Backbone" href="backbone.html" />
- <link rel="prev" title="rawmodel - Coordinate Modeling" href="../rawmodel/index.html" />
+ <link rel="prev" title="rawmodel - Coordinate Modelling" href="../rawmodel/index.html" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="backbone.html" title="Backbone"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="../rawmodel/index.html" title="rawmodel - Coordinate Modeling"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" accesskey="U">Documentation For Developes</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -60,7 +41,74 @@
<div class="section" id="module-promod3.loop">
<span id="loop-loop-modelling"></span><h1><a class="reference internal" href="#module-promod3.loop" title="promod3.loop: Loop Modelling"><code class="xref py py-mod docutils literal"><span class="pre">loop</span></code></a> - Loop Modelling<a class="headerlink" href="#module-promod3.loop" title="Permalink to this headline">¶</a></h1>
-<p>Tools and algorithms to for loop modelling.</p>
+<p>Tools and algorithms for loop modelling.
+This module provides ways for representation and manipulation of peptides and
+finally connect them to larger structures. The following example should give
+you a starting point to get an idea of what can be done.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+
+<span class="c">#let's load a crambin structure from the pdb</span>
+<span class="n">crambin</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">"1crn"</span><span class="p">,</span><span class="n">remote</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+<span class="n">SEQRES</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">crambin</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+
+<span class="c">#this is the sequence we want to remodel</span>
+<span class="n">loop_seq</span> <span class="o">=</span> <span class="n">SEQRES</span><span class="p">[</span><span class="mi">23</span><span class="p">:</span><span class="mi">31</span><span class="p">]</span>
+
+<span class="c">#let's define the stem residues</span>
+<span class="n">n_stem</span> <span class="o">=</span> <span class="n">crambin</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">23</span><span class="p">]</span>
+<span class="n">c_stem</span> <span class="o">=</span> <span class="n">crambin</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">30</span><span class="p">]</span>
+
+<span class="c">#we use the StructureDB as source for structural information</span>
+<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
+
+<span class="c">#the FragDB allows to access the StructureDB based on geometric</span>
+<span class="c">#features of the loop stem residue</span>
+<span class="n">frag_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
+
+<span class="c">#the LoopCandidates allow to handle several loops at once</span>
+<span class="c">#we directly want to find potential loop candidates from the</span>
+<span class="c">#previously loaded databases</span>
+<span class="n">loop_candidates</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoopCandidates</span><span class="o">.</span><span class="n">FillFromDatabase</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span>
+ <span class="n">c_stem</span><span class="p">,</span>
+ <span class="n">loop_seq</span><span class="p">,</span>
+ <span class="n">frag_db</span><span class="p">,</span>
+ <span class="n">structure_db</span><span class="p">)</span>
+
+<span class="c">#The candidates usually don't match exactly the required stem coordinates</span>
+<span class="c">#CCD (Cyclic Coordinate Descent) is one way to enforce this match.</span>
+<span class="n">loop_candidates</span><span class="o">.</span><span class="n">ApplyCCD</span><span class="p">()</span>
+
+<span class="c">#now it's time to select one candidate, we load a scorer object to do that</span>
+<span class="n">scorer</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadBackboneLoopScorer</span><span class="p">()</span>
+
+<span class="c">#initialize scorer with the environment given by the crambin structure</span>
+<span class="n">scorer</span><span class="o">.</span><span class="n">Initialize</span><span class="p">(</span><span class="n">SEQRES</span><span class="p">)</span>
+<span class="n">scorer</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span><span class="n">crambin</span><span class="p">)</span>
+
+<span class="c">#the scorer can then be attached to the LoopCandidates object</span>
+<span class="c">#to calculate several different scores, we go for a distance dependent</span>
+<span class="c">#statistical potential considering the CBeta positions of each residue</span>
+<span class="c">#and a clash score</span>
+<span class="n">loop_candidates</span><span class="o">.</span><span class="n">AttachScorer</span><span class="p">(</span><span class="n">scorer</span><span class="p">)</span>
+<span class="n">loop_candidates</span><span class="o">.</span><span class="n">CalculateCBetaScores</span><span class="p">()</span>
+<span class="n">loop_candidates</span><span class="o">.</span><span class="n">CalculateClashScores</span><span class="p">()</span>
+
+<span class="c">#we simply sum up the previously calculated scores and search for the</span>
+<span class="c">#loop with minimal score</span>
+<span class="n">min_score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s">"inf"</span><span class="p">)</span>
+<span class="n">min_candidate</span> <span class="o">=</span> <span class="mi">0</span>
+<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">lc</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">loop_candidates</span><span class="p">):</span>
+ <span class="n">score</span> <span class="o">=</span> <span class="n">lc</span><span class="o">.</span><span class="n">cbeta_score</span> <span class="o">+</span> <span class="n">lc</span><span class="o">.</span><span class="n">clash_score</span>
+ <span class="k">if</span> <span class="n">score</span> <span class="o"><</span> <span class="n">min_score</span><span class="p">:</span>
+ <span class="n">min_score</span> <span class="o">=</span> <span class="n">score</span>
+ <span class="n">min_candidate</span> <span class="o">=</span> <span class="n">i</span>
+
+<span class="c">#let's insert that loop and save the structure down to disk</span>
+<span class="n">loop_candidates</span><span class="o">.</span><span class="n">InsertInto</span><span class="p">(</span><span class="n">crambin</span><span class="p">,</span><span class="n">min_candidate</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">crambin</span><span class="p">,</span><span class="s">"remodeled_crambin.pdb"</span><span class="p">)</span>
+</pre></div>
+</div>
<p>Contents:</p>
<div class="toctree-wrapper compound">
<ul>
@@ -92,10 +140,10 @@
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="monte_carlo.html">Generating Loops DeNovo</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="monte_carlo.html#sampler-objects">Sampler Objects</a></li>
-<li class="toctree-l2"><a class="reference internal" href="monte_carlo.html#closer-objects">Closer Objects</a></li>
-<li class="toctree-l2"><a class="reference internal" href="monte_carlo.html#scorer-objects">Scorer Objects</a></li>
-<li class="toctree-l2"><a class="reference internal" href="monte_carlo.html#cooler-objects">Cooler Objects</a></li>
+<li class="toctree-l2"><a class="reference internal" href="monte_carlo.html#sampler-object">Sampler Object</a></li>
+<li class="toctree-l2"><a class="reference internal" href="monte_carlo.html#closer-object">Closer Object</a></li>
+<li class="toctree-l2"><a class="reference internal" href="monte_carlo.html#scorer-object">Scorer Object</a></li>
+<li class="toctree-l2"><a class="reference internal" href="monte_carlo.html#cooler-object">Cooler Object</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="loop_candidate.html">Handle several loop candidates at once</a></li>
@@ -109,13 +157,17 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="../rawmodel/index.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modeling</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="backbone.html"
- title="next chapter">Backbone</a></p>
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li>Previous: <a href="../rawmodel/index.html" title="previous chapter"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modelling</a></li>
+ <li>Next: <a href="backbone.html" title="next chapter">Backbone</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -145,11 +197,11 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/loop/index.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index ff96687abf44f55831af0063b1627aac1e0a4a36..225202d240ab8fb10a358ab5990f9d3aca27394f 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="../sidechain/index.html" title="sidechain - Sidechain Modelling"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="loop_candidate.html" title="Loop Candidates"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
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@@ -212,13 +192,19 @@ Proteins, 62(4):892–908, Mar 2006.</dd>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="loop_candidate.html"
- title="previous chapter">Loop Candidates</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="../sidechain/index.html"
- title="next chapter"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></p>
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a><ul>
+ <li>Previous: <a href="loop_candidate.html" title="previous chapter">Loop Candidates</a></li>
+ <li>Next: <a href="../sidechain/index.html" title="next chapter"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -248,11 +234,11 @@ Proteins, 62(4):892–908, Mar 2006.</dd>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/loop/load_loop_objects.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
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diff --git a/doc/html/loop/loop_candidate.html b/doc/html/loop/loop_candidate.html
index e196c126eaeed2549d5c1ff93b64ab3d3ca4df03..591d3e9cad6318ed109ac8548c31535dd916b55a 100644
--- a/doc/html/loop/loop_candidate.html
+++ b/doc/html/loop/loop_candidate.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="load_loop_objects.html" title="Load Loop Objects"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="monte_carlo.html" title="Monte Carlo Sampling"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -250,7 +230,7 @@
<dl class="class">
<dt id="promod3.loop.LoopCandidates">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">LoopCandidates</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoopCandidates" title="Permalink to this definition">¶</a></dt>
-<dd><p>The <em>LoopCandidates</em> is the basic object used for loop modelling. It contains the positions of the two anchor residues, the <em>n_stem</em> and <em>c_stem</em> residues, and thes sequence of the residues to be modelled in between these anchor residues.
+<dd><p>The <em>LoopCandidates</em> is the basic object used for loop modelling. It contains the positions of the two anchor residues, the <em>n_stem</em> and <em>c_stem</em> residues, and the sequence of the residues to be modelled in between these anchor residues.
It also contains a list of <a class="reference internal" href="#promod3.loop.LoopCandidate" title="promod3.loop.LoopCandidate"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidate</span></code></a>, which are possible conformations of the backbone between the stem residues.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -307,11 +287,11 @@ It also contains a list of <a class="reference internal" href="#promod3.loop.Loo
<li><strong>initial_bb</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence of residues to be added between the <em>n_stem</em> and <em>c_stem</em></li>
<li><strong>num_loops</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate generated.</li>
-<li><strong>cooler</strong> (<code class="xref py py-class docutils literal"><span class="pre">MonteCarloCooler</span></code>) – Controls the temperature profile of the simulated annealing</li>
-<li><strong>scorer</strong> (<code class="xref py py-class docutils literal"><span class="pre">MonteCarloScorer</span></code>) – Used to score the generated configurations at each MC step.</li>
-<li><strong>sampler</strong> (<a class="reference internal" href="monte_carlo.html#promod3.loop.MonteCarloSampler" title="promod3.loop.MonteCarloSampler"><code class="xref py py-class docutils literal"><span class="pre">MonteCarloSampler</span></code></a>) – Used to generate a new configuration at each MC step.</li>
-<li><strong>closer</strong> (<code class="xref py py-class docutils literal"><span class="pre">MonteCarloCloser</span></code>) – Used to close the loop (make it match the <em>n_stem</em> and <em>c_stem</em> geometry) after each MC step.</li>
+<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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>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>Closer Object</span></a>) – Used to close the loop (make it match the <em>n_stem</em> and <em>c_stem</em> geometry) after each MC step</li>
+<li><strong>scorer</strong> (<a class="reference internal" href="monte_carlo.html#mc-scorer-object"><span>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>Cooler Object</span></a>) – Controls the temperature profile of the simulated annealing</li>
</ul>
</td>
</tr>
@@ -338,11 +318,11 @@ It also contains a list of <a class="reference internal" href="#promod3.loop.Loo
<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence of residues to be added between the <em>n_stem</em> and <em>c_stem</em></li>
<li><strong>num_loops</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate generated.</li>
-<li><strong>cooler</strong> (<code class="xref py py-class docutils literal"><span class="pre">MonteCarloCooler</span></code>) – Controls the temperature profile of the simulated annealing</li>
-<li><strong>scorer</strong> (<code class="xref py py-class docutils literal"><span class="pre">MonteCarloScorer</span></code>) – Used to score the generated configurations at each MC step.</li>
-<li><strong>sampler</strong> (<a class="reference internal" href="monte_carlo.html#promod3.loop.MonteCarloSampler" title="promod3.loop.MonteCarloSampler"><code class="xref py py-class docutils literal"><span class="pre">MonteCarloSampler</span></code></a>) – Used to generate a new configuration at each MC step.</li>
-<li><strong>closer</strong> (<code class="xref py py-class docutils literal"><span class="pre">MonteCarloCloser</span></code>) – Used to close the loop (make it match the <em>n_stem</em> and <em>c_stem</em> geometry) after each MC step.</li>
+<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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>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>Closer Object</span></a>) – Used to close the loop (make it match the <em>n_stem</em> and <em>c_stem</em> geometry) after each MC step</li>
+<li><strong>scorer</strong> (<a class="reference internal" href="monte_carlo.html#mc-scorer-object"><span>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>Cooler Object</span></a>) – Controls the temperature profile of the simulated annealing</li>
</ul>
</td>
</tr>
@@ -438,7 +418,7 @@ It also contains a list of <a class="reference internal" href="#promod3.loop.Loo
<dl class="method">
<dt id="promod3.loop.LoopCandidates.ApplyKIC">
<code class="descname">ApplyKIC</code><span class="sig-paren">(</span><em>pivot_one</em>, <em>pivot_two</em>, <em>pivot_three</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LoopCandidates.ApplyKIC" title="Permalink to this definition">¶</a></dt>
-<dd><p>Closes all <a class="reference internal" href="#promod3.loop.LoopCandidate" title="promod3.loop.LoopCandidate"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidate</span></code></a> in <a class="reference internal" href="#promod3.loop.LoopCandidates" title="promod3.loop.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a> (i.e. modifies the <a class="reference internal" href="#promod3.loop.LoopCandidate" title="promod3.loop.LoopCandidate"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidate</span></code></a> so that its stem residues match those of the <a class="reference internal" href="#promod3.loop.LoopCandidates" title="promod3.loop.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a>, which are the stem residues of the loop being modelled), using the KIC algorithm. This algorithm finds analytical solutions for closing the loop by modifying the torsion angles of just three pivot residues.</p>
+<dd><p>Closes all <a class="reference internal" href="#promod3.loop.LoopCandidate" title="promod3.loop.LoopCandidate"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidate</span></code></a> in <a class="reference internal" href="#promod3.loop.LoopCandidates" title="promod3.loop.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a> (i.e. modifies the <a class="reference internal" href="#promod3.loop.LoopCandidate" title="promod3.loop.LoopCandidate"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidate</span></code></a> so that its stem residues match those of the <a class="reference internal" href="#promod3.loop.LoopCandidates" title="promod3.loop.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a>, which are the stem residues of the loop being modelled), using the KIC algorithm. This 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>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -783,13 +763,19 @@ This score measures the energy of H-bonds as defined by DSSP.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="monte_carlo.html"
- title="previous chapter">Monte Carlo Sampling</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="load_loop_objects.html"
- title="next chapter">Load Loop Objects</a></p>
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a><ul>
+ <li>Previous: <a href="monte_carlo.html" title="previous chapter">Monte Carlo Sampling</a></li>
+ <li>Next: <a href="load_loop_objects.html" title="next chapter">Load Loop Objects</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
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@@ -819,11 +805,11 @@ This score measures the energy of H-bonds as defined by DSSP.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/loop/loop_candidate.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
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diff --git a/doc/html/loop/loop_closing.html b/doc/html/loop/loop_closing.html
index 4b8643e7c3908886d6ffbb0e4e59dd533b6dbf90..90f5e900276ce229005f916b963d899657ed9e51 100644
--- a/doc/html/loop/loop_closing.html
+++ b/doc/html/loop/loop_closing.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="backbone_loop_score.html" title="Loop Scoring"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="structure_db.html" title="Structural Database"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -64,10 +44,12 @@
<p>Loops, represented as <a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> objects, often need to undergo
conformational changes to fit into gaps defined by stem residues.
ProMod3 implements two algorithms performing this task.</p>
-<p>There is cyclic coordinate descent (CCD):
-Adrian A. Canutescu and Roland L. Dunbrack Jr. “Cyclic coordinate descent: A robotics algorithm for protein loop closure.” Protein Sci. 12(5):963–972. (2003)</p>
-<p>and kinematic closure (KIC):
-Mandell DJ, Coutsias EA and Kortemme T. “Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling.” Nat Methods. 6(8):551-2. (2009)</p>
+<blockquote>
+<div><ul class="simple">
+<li>There is cyclic coordinate descent (CCD) <a class="reference internal" href="#canutescu2003" id="id1">[canutescu2003]</a></li>
+<li>and kinematic closure (KIC) <a class="reference internal" href="#mandell2009" id="id2">[mandell2009]</a></li>
+</ul>
+</div></blockquote>
<p>In case of small gaps or small issues in the <a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> you might
also consider the <a class="reference internal" href="#promod3.loop.BackboneRelaxer" title="promod3.loop.BackboneRelaxer"><code class="xref py py-class docutils literal"><span class="pre">BackboneRelaxer</span></code></a>.</p>
<div class="section" id="ccd">
@@ -89,54 +71,41 @@ pair before and after performing the phi/psi update. If the fraction
after/before is smaller than a random number in range [0;1[, the proposed
dihedral pair gets rejected and the next iteration starts. Please note, that
this increases the probability of non-convergence.</p>
-<dl class="method">
+<dl class="class">
<dt id="promod3.loop.CCD">
-<code class="descclassname">promod3.loop.</code><code class="descname">CCD</code><span class="sig-paren">(</span><em>bb_list</em>, <em>n_stem</em>, <em>c_stem</em><span class="optional">[</span>, <em>max_steps=1000</em>, <em>rmsd_cutoff=0.1</em>, <em>random_seed=0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.CCD" 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>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"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which the desired n-stem positions are
-extracted</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which the desired c-stem positions are
-extracted</li>
-<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max number of iterations</li>
-<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Iterations abort when this RMSD between the c-stem of
-the loop and the desired c-stem is reached</li>
-<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal randomness</li>
-</ul>
-</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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether the RMSD threshold has been reached</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">CCD</code><a class="headerlink" href="#promod3.loop.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>
-<code class="descclassname">promod3.loop.</code><code class="descname">CCD</code><span class="sig-paren">(</span><em>bb_list</em>, <em>n_stem_pos</em>, <em>c_stem_pos</em><span class="optional">[</span>, <em>max_steps=1000</em>, <em>rmsd_cutoff=0.1</em>, <em>random_seed=0</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
+<dt id="promod3.loop.CCD.CCD">
+<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.loop.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>
+<table class="docutils field-list" frame="void" rules="none">
<col class="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"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</li>
-<li><strong>n_stem_pos</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – 3 positions describing the desired
-N, CA and C positions of the n_stem</li>
-<li><strong>c_stem_pos</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – 3 positions describing the desired
-N, CA and C positions of the c_stem</li>
-<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max number of iterations</li>
-<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Iterations abort when this RMSD between the c-stem of
-the loop and the desired c-stem is reached</li>
-<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal randomness</li>
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</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"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – To extract probabilities for the analysis of the backbone
+dihedrals. You either pass a list with <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>
+objects for every residue of the loop to be closed or a single
+<a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>, that will be applied on all residues.</li>
+<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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 <strong>c_stem</strong></li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed of random number generator to decide whether new phi/psi pair
+should be accepted.</li>
</ul>
</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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether the RMSD threshold has been reached</p>
+<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"><span class="pre">RuntimeError</span></code> if a list of torsion samplers is given
+with inconsistent length regarding the sequence. Another
+requirement is that the residue before <strong>n_stem</strong> and
+after <strong>c_stem</strong> must be valid and all backbone atoms
+are present.</p>
</td>
</tr>
</tbody>
@@ -145,149 +114,46 @@ the loop and the desired c-stem is reached</li>
<dl class="method">
<dt>
-<code class="descclassname">promod3.loop.</code><code class="descname">CCD</code><span class="sig-paren">(</span><em>bb_list, n_stem, c_stem, torsion_sampler [max_steps=1000,rmsd_cutoff=0.1,random_seed=0]</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
+<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>
+<table class="docutils field-list" frame="void" rules="none">
<col class="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"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which the desired n-stem positions are
-extracted</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which the desired c-stem positions are
-extracted</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"><span class="pre">TorsionSampler</span></code></a>) – For extracting probabilities to decide whether a new
-dihedral pair should be accepted or not. This sampler
-gets applied to all residues of the loop.</li>
-<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max number of iterations</li>
-<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Iterations abort when this RMSD between the c-stem of
-the loop and the desired c-stem is reached</li>
-<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal randomness</li>
+<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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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 <strong>c_stem</strong></li>
</ul>
</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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether the RMSD threshold has been reached</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-class docutils literal"><span class="pre">RuntimeError</span></code> when assigining of histogram
-indices for torsion sampler fails. This is the case
-when the residue before the given n-stem or the
-residue after the given c-stem is not present.</p>
-</td>
-</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt>
-<code class="descclassname">promod3.loop.</code><code class="descname">CCD</code><span class="sig-paren">(</span><em>bb_list, n_stem, c_stem, torsion_sampler[max_steps=1000,rmsd_cutoff=0.1,random_seed=0]</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
+<dt id="promod3.loop.CCD.Close">
+<code class="descname">Close</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.CCD.Close" title="Permalink to this definition">¶</a></dt>
+<dd><p>Closes given <strong>bb_list</strong> with the settings set at initialization.</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>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"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which the desired n-stem positions are
-extracted</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which the desired c-stem positions are
-extracted</li>
-<li><strong>torsion_sampler</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> For extracting
-probabilities to decide whether a new dihedral pair
-should be accepted or not. There must be one sampler
-for every residue.</li>
-<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max number of iterations</li>
-<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Iterations abort when this RMSD between the c-stem of
-the loop and the desired c-stem is reached</li>
-<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal randomness</li>
-</ul>
-</td>
+<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"><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"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether the RMSD threshold has been
-reached</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-class docutils literal"><span class="pre">RuntimeError</span></code> when assigining of histogram
-indices for torsion sampler fails. This is the case
-when the residue before the given n-stem or the
-residue after the given c-stem is not present.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<code class="descclassname">promod3.loop.</code><code class="descname">CCD</code><span class="sig-paren">(</span><em>bb_list, n_stem_pos, c_stem_pos, torsion_sampler, dihedral_indices[max_steps=1000,rmsd_cutoff=0.1,random_seed=0]</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="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</li>
-<li><strong>n_stem_pos</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – 3 positions describing the desired
-N, CA and C positions of the n_stem</li>
-<li><strong>c_stem_pos</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – 3 positions describing the desired
-N, CA and C positions of the c_stem</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"><span class="pre">TorsionSampler</span></code></a>) – List of <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> For extracting
-probabilities to decide whether a new dihedral pair
-should be accepted or not. There must be one sampler
-for every residue.</li>
-<li><strong>dihedral_indices</strong> – If no stem residues are given, there is no
-possibility to figure out the torsion sampler indices
-for the stem residues. All indices must therefore be
-given.</li>
-<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max number of iterations</li>
-<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Iterations abort when this RMSD between the c-stem of
-the loop and the desired c-stem is reached</li>
-<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal randomness</li>
-<li><strong>dihedral_indices</strong> – <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a></li>
-</ul>
-</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> Whether <strong>rmsd_cutoff</strong> has been reached</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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether the RMSD threshold has been
-reached</p>
-</td>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if the CCD object has been initialized
+with <a class="reference internal" href="torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> support and the length of the
+<strong>bb_list</strong> is not consistent with the initial sequence.</td>
</tr>
</tbody>
</table>
</dd></dl>
-<dl class="method">
-<dt>
-<code class="descclassname">promod3.loop.</code><code class="descname">CCD</code><span class="sig-paren">(</span><em>bb_list, n_stem_pos, c_stem_pos, torsion_sampler, dihedral_indices[max_steps=1000,rmsd_cutoff=0.1,random_seed=0]</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="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</li>
-<li><strong>n_stem_pos</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – 3 positions describing the desired
-N, CA and C positions of the n_stem</li>
-<li><strong>c_stem_pos</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – 3 positions describing the desired
-N, CA and C positions of the c_stem</li>
-<li><strong>torsion_sampler</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – For extracting probabilities to decide whether a new
-dihedral pair should be accepted or not. This sampler
-gets applied to all residues of the loop.</li>
-<li><strong>dihedral_indices</strong> – If no stem residues are given, there is no
-possibility to figure out the torsion sampler indices
-for the stem residues. All indices must therefore be
-given.</li>
-<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max number of iterations</li>
-<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Iterations abort when this RMSD between the c-stem of
-the loop and the desired c-stem is reached</li>
-<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal randomness</li>
-<li><strong>dihedral_indices</strong> – <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a></li>
-</ul>
-</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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether the RMSD threshold has been
-reached</p>
-</td>
-</tr>
-</tbody>
-</table>
</dd></dl>
</div>
@@ -298,49 +164,40 @@ pivot residues. It then calculates possible relative orientations
of these fragments by considering constraints of bond length and bond angles
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="method">
+<dl class="class">
<dt id="promod3.loop.KIC">
-<code class="descclassname">promod3.loop.</code><code class="descname">KIC</code><span class="sig-paren">(</span><em>bb_list</em>, <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.loop.KIC" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">KIC</code><a class="headerlink" href="#promod3.loop.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.loop.KIC.KIC">
+<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.loop.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>
+<table class="docutils field-list" frame="void" rules="none">
<col class="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"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which the desired n-stem positions are
-extracted</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which the desired c-stem positions are
-extracted</li>
-<li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of third pivot residue</li>
+<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>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">List of <a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> objects representing
-the closed loops. There is a maximum of 16 entries.</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-class docutils literal"><span class="pre">RuntimeError</span></code> in case of invalid pivot indices.</p>
-</td>
-</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt>
-<code class="descclassname">promod3.loop.</code><code class="descname">KIC</code><span class="sig-paren">(</span><em>bb_list</em>, <em>n_stem_pos</em>, <em>c_stem_pos</em>, <em>pivot_one</em>, <em>pivot_two</em>, <em>pivot_three</em><span class="sig-paren">)</span></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
+<dt id="promod3.loop.KIC.Close">
+<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.loop.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>
+<table class="docutils field-list" frame="void" rules="none">
<col class="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"><span class="pre">BackboneList</span></code></a>) – Loop to be closed</li>
-<li><strong>n_stem_pos</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – 3 positions describing the desired
-N, CA and C positions of the n_stem</li>
-<li><strong>c_stem_pos</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – 3 positions describing the desired
-N, CA and C positions of the c_stem</li>
<li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of third pivot residue</li>
@@ -358,6 +215,8 @@ the closed loops. There is a maximum of 16 entries.</p>
</table>
</dd></dl>
+</dd></dl>
+
</div>
<div class="section" id="relaxing-backbones">
<h2>Relaxing Backbones<a class="headerlink" href="#relaxing-backbones" title="Permalink to this headline">¶</a></h2>
@@ -381,7 +240,7 @@ relaxed.</p>
<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"><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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether n-terminal backbone positions should kept
rigid during relaxation.</li>
-<li><strong>fix_cterm</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether c-termainl backbone positions should kept
+<li><strong>fix_cterm</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether c-terminal backbone positions should kept
rigid during relaxation.</li>
</ul>
</td>
@@ -408,7 +267,7 @@ relaxation aborts.</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Forcefield energy</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Forcefield energy upon relaxation</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-class docutils literal"><span class="pre">RuntimeError</span></code> if <strong>bb_list</strong> has not the same
@@ -421,6 +280,18 @@ size or sequence as the initial one.</p>
</dd></dl>
+<table class="docutils citation" frame="void" id="canutescu2003" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label"><a class="fn-backref" href="#id1">[canutescu2003]</a></td><td>Canutescu AA and Dunbrack RL Jr. (2003). Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12(5):963–972.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="mandell2009" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label"><a class="fn-backref" href="#id2">[mandell2009]</a></td><td>Mandell DJ, Coutsias EA and Kortemme T (2009). Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods. 6(8):551-2.</td></tr>
+</tbody>
+</table>
</div>
</div>
@@ -439,13 +310,19 @@ size or sequence as the initial one.</p>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="structure_db.html"
- title="previous chapter">Structural Database</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="backbone_loop_score.html"
- title="next chapter">Loop Scoring</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a><ul>
+ <li>Previous: <a href="structure_db.html" title="previous chapter">Structural Database</a></li>
+ <li>Next: <a href="backbone_loop_score.html" title="next chapter">Loop Scoring</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -475,11 +352,11 @@ size or sequence as the initial one.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/loop/loop_closing.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/monte_carlo.html b/doc/html/loop/monte_carlo.html
index 1c0f635fda7458071b923ac6a0e6bd422fdb134f..c1cda0350fa7973ef40b14c1d58a0f16e7c65edb 100644
--- a/doc/html/loop/monte_carlo.html
+++ b/doc/html/loop/monte_carlo.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="loop_candidate.html" title="Loop Candidates"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="backbone_loop_score.html" title="Loop Scoring"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -88,13 +68,13 @@ temperature given by the <strong>cooler</strong>
<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>cooler</strong> (<code class="xref py py-class docutils literal"><span class="pre">CoolerObject</span></code>) – Cooler object to control the temperature of the
-monte carlo trajectory</li>
-<li><strong>scorer</strong> (<code class="xref py py-class docutils literal"><span class="pre">ScorerObject</span></code>) – Scorer object to score new loop conformations</li>
-<li><strong>sampler</strong> (<code class="xref py py-class docutils literal"><span class="pre">SamplerObject</span></code>) – Sampler object capable of initializing and altering
+<li><strong>sampler</strong> (<a class="reference internal" href="#mc-sampler-object"><span>Sampler Object</span></a>) – Sampler object capable of initializing and altering
conformations.</li>
-<li><strong>closer</strong> (<code class="xref py py-class docutils literal"><span class="pre">CloserObject</span></code>) – Closer object to adapt a new conformation to
+<li><strong>closer</strong> (<a class="reference internal" href="#mc-closer-object"><span>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>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>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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The lowest scoring conformation of the trajectory
gets stored in here</li>
@@ -112,6 +92,7 @@ The input <strong>bb_list</strong> gets used otherwise.</li>
<div class="highlight-python"><div class="highlight"><pre><span class="c">#Example script, that applies monte-carlo sampling to the n-terminal</span>
<span class="c">#part of crambin</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
@@ -127,7 +108,7 @@ The input <strong>bb_list</strong> gets used otherwise.</li>
<span class="c">#setup mc_sampler</span>
<span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSampler</span><span class="p">()</span>
-<span class="n">mc_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">SoftSampler</span><span class="p">(</span><span class="n">terminal_sequence</span><span class="p">,</span><span class="n">torsion_sampler</span><span class="p">,</span><span class="mf">20.0</span><span class="o">/</span><span class="mi">180</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">)</span>
+<span class="n">mc_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">SoftSampler</span><span class="p">(</span><span class="n">terminal_sequence</span><span class="p">,</span><span class="n">torsion_sampler</span><span class="p">,</span><span class="mf">10.0</span><span class="o">/</span><span class="mi">180</span><span class="o">*</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">)</span>
<span class="c">#setup mc_closer</span>
<span class="n">mc_closer</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">NTerminalCloser</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">n_terminal_length</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
@@ -139,7 +120,6 @@ The input <strong>bb_list</strong> gets used otherwise.</li>
<span class="n">weights</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
<span class="n">weights</span><span class="p">[</span><span class="s">"cbeta"</span><span class="p">]</span><span class="o">=</span><span class="mf">10.0</span>
-<span class="n">weights</span><span class="p">[</span><span class="s">"cb_packing"</span><span class="p">]</span><span class="o">=</span><span class="mf">1.0</span>
<span class="n">weights</span><span class="p">[</span><span class="s">"clash"</span><span class="p">]</span><span class="o">=</span><span class="mf">0.1</span>
<span class="n">mc_scorer</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LinearScorer</span><span class="p">(</span><span class="n">scorer</span><span class="p">,</span><span class="n">start_resnum</span><span class="p">,</span><span class="n">chain_index</span><span class="p">,</span><span class="n">weights</span><span class="p">)</span>
@@ -156,8 +136,8 @@ The input <strong>bb_list</strong> gets used otherwise.</li>
<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span><span class="s">"sampled_frag.pdb"</span><span class="p">)</span>
</pre></div>
</div>
-<div class="section" id="sampler-objects">
-<h2>Sampler Objects<a class="headerlink" href="#sampler-objects" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="sampler-object">
+<span id="mc-sampler-object"></span><h2>Sampler Object<a class="headerlink" href="#sampler-object" title="Permalink to this headline">¶</a></h2>
<p>The sampler objects can be used to generate initial conformations and
propose new conformations for a sequence of interest. They build the basis
for any monte carlo sampling pipeline.</p>
@@ -331,9 +311,70 @@ efficiency reasons.</p>
</dd></dl>
+<dl class="class">
+<dt id="promod3.loop.FragmentSampler">
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FragmentSampler</code><span class="sig-paren">(</span><em>sequence</em>, <em>fraggers</em><span class="optional">[</span>, <em>init_fragments = 3</em>, <em>seed = 0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.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="structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> objects.</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 last simple">
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence that should be sampled</li>
+<li><strong>fraggers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – A list of <a class="reference internal" href="structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> objects. The first fragger
+covers the region starting at the first letter of the
+<strong>sequence</strong> and so on. All fraggers must contain fragments
+of equal size an exactly cover the full sequence to
+be sampled.</li>
+<li><strong>init_fragments</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – When calling the Initialize function, a completely helical
+conformation gets created. This is the number of fragments
+that gets randomly selected and inserted.</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for the internal random number generators</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.loop.FragmentSampler.Initialize">
+<code class="descname">Initialize</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragmentSampler.Initialize" title="Permalink to this definition">¶</a></dt>
+<dd><p>Sets up a new <a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> by creating a helix and replace n fragments
+with n = <strong>init_fragments</strong> as given at the samplers initialization</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"><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"><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.loop.FragmentSampler.ProposeStep">
+<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.loop.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>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="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="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Conformation to be changed</li>
+<li><strong>proposed_positions</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Changed conformation gets stored in here</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
</div>
-<div class="section" id="closer-objects">
-<h2>Closer Objects<a class="headerlink" href="#closer-objects" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="closer-object">
+<span id="mc-closer-object"></span><h2>Closer Object<a class="headerlink" href="#closer-object" title="Permalink to this headline">¶</a></h2>
<p>After the proposal of new conformations by the sampler objects, the
conformations typically have to undergo some structural changes, so they
fit to a given environment. This can either be structural changes, that
@@ -397,7 +438,7 @@ stems.</p>
<dl class="class">
<dt id="promod3.loop.DirtyCCDCloser">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">DirtyCCDCloser</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.loop.DirtyCCDCloser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.loop.</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.loop.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.</p>
@@ -410,7 +451,6 @@ the stems given by the closer.</p>
should adapt.</li>
<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for internal random generators.</li>
</ul>
</td>
</tr>
@@ -518,8 +558,8 @@ adapt.</td>
</dd></dl>
</div>
-<div class="section" id="scorer-objects">
-<h2>Scorer Objects<a class="headerlink" href="#scorer-objects" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="scorer-object">
+<span id="mc-scorer-object"></span><h2>Scorer Object<a class="headerlink" href="#scorer-object" title="Permalink to this headline">¶</a></h2>
<p>The scorer asses a proposed conformation and are intended to return a pseudo
energy, the lower the better.</p>
<dl class="class">
@@ -551,22 +591,14 @@ An additional possible key is: “intercept”.</li>
</table>
<dl class="method">
<dt id="promod3.loop.LinearScorer.GetScore">
-<code class="descname">GetScore</code><span class="sig-paren">(</span><em>temperature</em>, <em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.LinearScorer.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.loop.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"><ul class="first simple">
-<li><strong>temperature</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Current temperature in the monte carlo trajectory.
-This has no effect on the score of the LinearScorer
-and is only there to fulfill the requirements of the
-abstract baseclass.</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"><span class="pre">BackboneList</span></code></a>) – Current loop conformation to be scored.</li>
-</ul>
-</td>
+<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"><span class="pre">BackboneList</span></code></a>) – Current loop conformation to be scored.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A linear combination of the scores</p>
-</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A linear combination of the scores</td>
</tr>
</tbody>
</table>
@@ -575,8 +607,8 @@ abstract baseclass.</li>
</dd></dl>
</div>
-<div class="section" id="cooler-objects">
-<h2>Cooler Objects<a class="headerlink" href="#cooler-objects" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="cooler-object">
+<span id="mc-cooler-object"></span><h2>Cooler Object<a class="headerlink" href="#cooler-object" title="Permalink to this headline">¶</a></h2>
<p>The cooler objects control the temperature of the monte carlo trajectory.
They’re intended to deliver steadily decreasing temperatures with calls
to their GetTemperature function.</p>
@@ -632,20 +664,26 @@ the returned temperature gets multiplied by the <strong>cooling_factor</strong>.
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Monte Carlo Sampling</a><ul>
-<li><a class="reference internal" href="#sampler-objects">Sampler Objects</a></li>
-<li><a class="reference internal" href="#closer-objects">Closer Objects</a></li>
-<li><a class="reference internal" href="#scorer-objects">Scorer Objects</a></li>
-<li><a class="reference internal" href="#cooler-objects">Cooler Objects</a></li>
+<li><a class="reference internal" href="#sampler-object">Sampler Object</a></li>
+<li><a class="reference internal" href="#closer-object">Closer Object</a></li>
+<li><a class="reference internal" href="#scorer-object">Scorer Object</a></li>
+<li><a class="reference internal" href="#cooler-object">Cooler Object</a></li>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="backbone_loop_score.html"
- title="previous chapter">Loop Scoring</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="loop_candidate.html"
- title="next chapter">Loop Candidates</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a><ul>
+ <li>Previous: <a href="backbone_loop_score.html" title="previous chapter">Loop Scoring</a></li>
+ <li>Next: <a href="loop_candidate.html" title="next chapter">Loop Candidates</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -675,11 +713,11 @@ the returned temperature gets multiplied by the <strong>cooling_factor</strong>.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/loop/monte_carlo.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 73bc0c069f166e54e43c58d66bfb23312e7edeee..ade6c2338ca8ab7bbd5736147b28d1e660f6e4a4 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="loop_closing.html" title="Loop Closing"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="torsion_sampler.html" title="Torsion Sampler"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -63,7 +43,30 @@
<h1>Structural Database<a class="headerlink" href="#structural-database" title="Permalink to this headline">¶</a></h1>
<p>The structural database serves as a container for structural backbone
and profile data. It can be filled with chains of pdb structures with their
-corresponding profiles as they are produced by the HHSuite tools.</p>
+corresponding profiles as they are produced by the HHSuite tools <a class="reference internal" href="#soding2005" id="id1">[soding2005]</a>.
+Some of the extracted features expect the secondary structure, as well as the solvent
+accessibility to be assigned using dssp <a class="reference internal" href="#kabsch1983" id="id2">[kabsch1983]</a>.
+Following features get stored on a per residue basis:</p>
+<ul class="simple">
+<li>The amino acid one letter code</li>
+<li>The coordinates of the backbone atoms (N,CA,C,O)</li>
+<li>The phi/psi dihedral angles</li>
+<li>The secondary structure state as defined by dssp</li>
+<li>The solvent accessibility in square Angstrom as calculated by dssp</li>
+<li>The residue depth defined as the average distance from all atoms of a
+residue to the closest surface vertex as calculated by msms <a class="reference internal" href="#sanner1996" id="id3">[sanner1996]</a>
+- This is a simplified version of
+the residue depth as discussed in <a class="reference internal" href="#chakravarty1999" id="id4">[chakravarty1999]</a> and gets directly calculated
+when structural information gets added to the StructureDB</li>
+<li>The amino acid frequencies as given by an input HMM</li>
+<li>The amino acid frequency derived from structural alignments as described
+in <a class="reference internal" href="#zhou2005" id="id5">[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).</li>
+</ul>
<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">
@@ -76,20 +79,20 @@ the according chain is stored in the database.</p>
<dt id="promod3.loop.CoordInfo.pdb_id">
<code class="descname">pdb_id</code><a class="headerlink" href="#promod3.loop.CoordInfo.pdb_id" title="Permalink to this definition">¶</a></dt>
<dd><p>A character residue string containing the 4 character pdb_id and the
-1 character chain_id.</p>
+1 character chain_id. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.offset">
<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 structures are stored in a linear memory layout.
-The offset parameter tells us where it exactly starts...</p>
+The offset parameter tells us where it exactly starts. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.size">
<code class="descname">size</code><a class="headerlink" href="#promod3.loop.CoordInfo.size" title="Permalink to this definition">¶</a></dt>
-<dd><p>The length of the stretch of residues.</p>
+<dd><p>The length of the stretch of residues. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
</dd></dl>
</dd></dl>
@@ -103,10 +106,9 @@ The offset parameter tells us where it exactly starts...</p>
<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> – The index of the chain in the structure db this particle
-belongs to.</li>
-<li><strong>offset</strong> – Index of residue in <strong>chain</strong> the fragment starts.</li>
-<li><strong>length</strong> – Length of the fragment, which is limited to 255</li>
+<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"><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"><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"><span class="pre">length</span></code></a></li>
</ul>
</td>
</tr>
@@ -115,23 +117,106 @@ belongs to.</li>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.chain_index">
<code class="descname">chain_index</code><a class="headerlink" href="#promod3.loop.FragmentInfo.chain_index" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
+<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"><span class="pre">CoordInfo</span></code></a>) in the structure db this particle belongs to. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.offset">
<code class="descname">offset</code><a class="headerlink" href="#promod3.loop.FragmentInfo.offset" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
+<dd><p>Index of residue in <strong>chain</strong> the fragment starts. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.length">
<code class="descname">length</code><a class="headerlink" href="#promod3.loop.FragmentInfo.length" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
+<dd><p>Length of the fragment (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+</dd></dl>
</dd></dl>
</div>
<div class="section" id="the-database">
<h2>The Database<a class="headerlink" href="#the-database" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre><span class="c">#this code example demonstrates how to create a structural database and</span>
+<span class="c">#fill it with content</span>
+
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<span class="kn">import</span> <span class="nn">os</span>
+
+<span class="c">#we also need the external tools dssp and msms, you have to make sure</span>
+<span class="c">#that they are somewhere in your PATH</span>
+<span class="kn">from</span> <span class="nn">ost.bindings</span> <span class="kn">import</span> <span class="n">dssp</span>
+<span class="kn">from</span> <span class="nn">ost.bindings</span> <span class="kn">import</span> <span class="n">msms</span>
+
+<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">StructureDB</span><span class="p">()</span>
+
+<span class="c">#lets fill in some structures. It gets assumed, that all required data lies</span>
+<span class="c">#in following directories</span>
+<span class="n">structure_dir</span> <span class="o">=</span> <span class="s">"foo"</span>
+<span class="n">hmm_dir</span> <span class="o">=</span> <span class="s">"bar"</span>
+
+<span class="c">#the first 4 letters are suposed to be the pdb id, and the last one</span>
+<span class="c">#the corresponding chain name. The naming of the files in the</span>
+<span class="c">#directories is e.g. 1CRN.pdb for the structure and 1CRNA.hhm for the</span>
+<span class="c">#hmm. Please note, that the structure can contain several chains, whereas</span>
+<span class="c">#an hmm is considered unique for one particular sequence.</span>
+<span class="n">ids</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="n">CRNA</span><span class="p">,</span><span class="mi">1</span><span class="n">AKEA</span><span class="p">]</span>
+
+<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">:</span>
+
+ <span class="n">pdb_id</span> <span class="o">=</span> <span class="n">i</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span>
+ <span class="n">chain_id</span> <span class="o">=</span> <span class="n">i</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
+
+ <span class="c">#join together the data paths</span>
+ <span class="n">structure_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">structure_dir</span><span class="p">,</span><span class="n">pdb_id</span><span class="o">+</span><span class="s">".pdb"</span><span class="p">)</span>
+ <span class="n">hmm_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">hmm_dir</span><span class="p">,</span><span class="n">pdb_id</span><span class="o">+</span><span class="n">chain_id</span><span class="o">+</span><span class="s">".hhm"</span><span class="p">)</span>
+
+ <span class="c">#let's load the structure</span>
+ <span class="n">structure</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="n">structure_path</span><span class="p">)</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"cname="</span><span class="o">+</span><span class="n">chain_id</span><span class="o">+</span><span class="s">" and peptide=True"</span><span class="p">)</span>
+ <span class="c">#and the according HMM, that has to be in hhm format</span>
+ <span class="n">hmm</span> <span class="o">=</span> <span class="n">ost</span><span class="o">.</span><span class="n">seq</span><span class="o">.</span><span class="n">HMM</span><span class="o">.</span><span class="n">Load</span><span class="p">(</span><span class="n">hmm_path</span><span class="p">)</span>
+
+ <span class="c">#we run dssp in a way, that the secondary structure, as well as</span>
+ <span class="c">#the solvent accessibily gets assigned</span>
+ <span class="n">dssp</span><span class="o">.</span><span class="n">AssignDSSP</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span><span class="n">extract_burial_status</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+
+ <span class="c">#as a final step we need the surface as calculated by msms</span>
+ <span class="n">surf</span> <span class="o">=</span> <span class="n">msms</span><span class="o">.</span><span class="n">CalculateSurface</span><span class="p">(</span><span class="n">structure</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+
+ <span class="c">#let's add it</span>
+ <span class="n">structure_db</span><span class="o">.</span><span class="n">AddCoordinates</span><span class="p">(</span><span class="n">pdb_id</span><span class="p">,</span><span class="n">chain_id</span><span class="p">,</span><span class="n">structure</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="n">surf</span><span class="p">,</span><span class="n">hmm</span><span class="p">)</span>
+
+<span class="c">#we Now have two structures in the database... Please note, that there</span>
+<span class="c">#is no profile derived from structures assigned yet. You might consider to use</span>
+<span class="c">#the default StructureDB to derive such profiles</span>
+<span class="n">default_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
+
+<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">structure_db</span><span class="o">.</span><span class="n">GetNumCoords</span><span class="p">()):</span>
+ <span class="c">#get the CoordInfo for chain with index i</span>
+ <span class="n">coord_info</span> <span class="o">=</span> <span class="n">structure_db</span><span class="o">.</span><span class="n">GetCoordInfo</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+ <span class="c">#define a fragment, that covers the full length</span>
+ <span class="n">fragment_info</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">FragmentInfo</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="n">coord_info</span><span class="o">.</span><span class="n">size</span><span class="p">)</span>
+ <span class="c">#extract the according BackboneList and the residue depths</span>
+ <span class="n">bb_list</span> <span class="o">=</span> <span class="n">structure_db</span><span class="o">.</span><span class="n">GetBackboneList</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span><span class="n">fragment_info</span><span class="p">)</span>
+ <span class="n">depths</span> <span class="o">=</span> <span class="n">structure_db</span><span class="o">.</span><span class="n">GetResidueDepths</span><span class="p">(</span><span class="n">fragment_info</span><span class="p">)</span>
+ <span class="c">#generate a profile based on the structural data in the default_db</span>
+ <span class="n">hmm</span> <span class="o">=</span> <span class="n">default_db</span><span class="o">.</span><span class="n">GenerateStructureProfile</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span><span class="n">depths</span><span class="p">)</span>
+ <span class="c">#and add it to the previously created structure_db</span>
+ <span class="n">structure_db</span><span class="o">.</span><span class="n">SetStructureProfile</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">hmm</span><span class="p">)</span>
+
+<span class="c">#That's it! Let's save it down...</span>
+<span class="n">structure_db</span><span class="o">.</span><span class="n">Save</span><span class="p">(</span><span class="s">"my_db.dat"</span><span class="p">)</span>
+
+<span class="c">#Calculating the structural profiles is highly expensive and heavily depends</span>
+<span class="c">#on the size of the database used as source...</span>
+<span class="c">#If you want to do this for a larger database, you might consider two things:</span>
+<span class="c">#</span>
+<span class="c"># 1. Use a database of limited size as structural source (something in</span>
+<span class="c"># between 5000 and 10000 nonredundant chains is enough)</span>
+<span class="c"># 2. Use the ost.seq.HMMDB to gather hmms produced from jobs running</span>
+<span class="c"># in parallel</span>
+</pre></div>
+</div>
<dl class="class">
<dt id="promod3.loop.StructureDB">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">StructureDB</code><a class="headerlink" href="#promod3.loop.StructureDB" title="Permalink to this definition">¶</a></dt>
@@ -182,7 +267,7 @@ databases to be saved down.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.AddCoordinates">
-<code class="descname">AddCoordinates</code><span class="sig-paren">(</span><em>pdb_id</em>, <em>chain_name</em>, <em>chain</em>, <em>hmm</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>pdb_id</em>, <em>chain_name</em>, <em>chain</em>, <em>surf</em>, <em>hmm</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 a structural chain and searches the longest stretch of
connected residues containing all necessary backbone atoms. This stretch
gets then added to the database. Due to technical reasons, The maximal
@@ -192,9 +277,10 @@ extent along one of the base axis cannot exceed 650 A.</p>
<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>pdb_id</strong> (<code class="xref py py-class docutils literal"><span class="pre">String</span></code>) – 4-letter code of the structure the chain belongs to</li>
-<li><strong>chain_name</strong> (<em>:class:’String`</em>) – Name of the chain consisting of one letter</li>
+<li><strong>pdb_id</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – 4-letter code of the structure the chain belongs to</li>
+<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of the chain consisting of one letter</li>
<li><strong>chain</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ChainView" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainView</span></code></a>) – The actual chain</li>
+<li><strong>surf</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/surface/#ost.mol.SurfaceHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.SurfaceHandle</span></code></a>) – A surface describint the solvent accessible surface</li>
<li><strong>hmm</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.seq.HMM</span></code>) – An HMM containing profile information.</li>
</ul>
</td>
@@ -250,23 +336,20 @@ index <strong>idx</strong>.</td>
</dd></dl>
<dl class="method">
-<dt id="promod3.loop.StructureDB.FillBackbone">
-<code class="descname">FillBackbone</code><span class="sig-paren">(</span><em>bb_list</em>, <em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.FillBackbone" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.loop.StructureDB.GetBackboneList">
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetBackboneList" 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>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"><span class="pre">BackboneList</span></code></a>) – Structural data will be filled in here.</li>
-<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Description of the fragment from which a
-<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> should be built.</li>
-</ul>
-</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Description of the fragment from which a
+<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> should be built.</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"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
+<tr class="field-even field"><th class="field-name">Returns:</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"><span class="pre">BackboneList</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-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
the case when the fragment does not fully fit into one
-of chains in the database.</p>
-</td>
+of the chains in the database.</td>
</tr>
</tbody>
</table>
@@ -274,13 +357,12 @@ of chains in the database.</p>
<dl class="method">
<dt>
-<code class="descname">FillBackbone</code><span class="sig-paren">(</span><em>bb_list</em>, <em>n_stem</em>, <em>c_stem</em>, <em>fragment</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><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="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Structural data will be filled in here.</li>
<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the bb_list n-terminus should be
superposed onto.</li>
<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which th ebb_list c_terminus should be
@@ -290,9 +372,12 @@ superposed onto.</li>
</ul>
</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"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
+<tr class="field-even field"><th class="field-name">Returns:</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"><span class="pre">BackboneList</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-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
the case when the fragment does not fully fit into one
-of chains in the database.</p>
+of the chains in the database.</p>
</td>
</tr>
</tbody>
@@ -313,8 +398,8 @@ of chains in the database.</p>
</dd></dl>
<dl class="method">
-<dt id="promod3.loop.StructureDB.PrindStatistics">
-<code class="descname">PrindStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.PrindStatistics" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.loop.StructureDB.PrintStatistics">
+<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>
@@ -331,7 +416,7 @@ of chains in the database.</p>
</tr>
<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
the case when the fragment does not fully fit into one
-of chains in the database.</td>
+of the chains in the database.</td>
</tr>
</tbody>
</table>
@@ -350,7 +435,7 @@ of chains in the database.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
the case when the fragment does not fully fit into one
-of chains in the database.</td>
+of the chains in the database.</td>
</tr>
</tbody>
</table>
@@ -365,125 +450,129 @@ of chains in the database.</td>
<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="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the dihedrals.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A list of pairs containing the dihedral angles of every
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A list of pairs containing the phi and psi dihedral angles of every
residue of the <strong>fragment</strong>.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
the case when the fragment does not fully fit into one
-of chains in the database.</td>
+of the chains in the database.</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.loop.StructureDB.GetSeqSim">
-<code class="descname">GetSeqSim</code><span class="sig-paren">(</span><em>fragment</em>, <em>seq</em>, <em>subst_matrix</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSeqSim" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.loop.StructureDB.GetResidueDepths">
+<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>
<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>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment from the database.</li>
-<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence to which the sequence similarity should be
-calculated.</li>
-<li><strong>subst_matrix</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.seq.alg.SubstWeightMatrix</span></code>) – Source for substitution scores.</li>
-</ul>
-</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the residue
+depths</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Sequence similarity between <strong>fragment</strong> and <strong>seq</strong>
-normalized to a range [0,1]</p>
-</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> values describing
+the per residue depth</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-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
the case when the fragment does not fully fit into one
-of chains in the database.</p>
-</td>
+of the chains in the database.</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.loop.StructureDB.GetSeqID">
-<code class="descname">GetSeqID</code><span class="sig-paren">(</span><em>fragment</em>, <em>seq</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSeqID" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.loop.StructureDB.GetSolventAccessibilitites">
+<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>
<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>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment from the database.</li>
-<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence to which the sequence identity should be
-calculated.</li>
-</ul>
-</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the solvent
+accessibilities</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Sequence identity between <strong>fragment</strong> and <strong>seq</strong></p>
-</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">A <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> values describing
+the per residue solvent accessibilities in square A as
+calculated by dssp</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-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
the case when the fragment does not fully fit into one
-of chains in the database.</p>
-</td>
+of the chains in the database.</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.loop.StructureDB.GetSSAgreement">
-<code class="descname">GetSSAgreement</code><span class="sig-paren">(</span><em>fragment</em>, <em>predicted_ss</em>, <em>confidence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSSAgreement" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.loop.StructureDB.GetSequenceProfile">
+<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>
<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>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment from the database.</li>
-<li><strong>predicted_ss</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Predicted secondary structure from psipred with
-every element being in [‘H’,’E’,’C’].</li>
-<li><strong>confidence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Confidence values of psipred predictions,
-with every element being in range [0,9].</li>
-</ul>
-</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence
+profile</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Average sequence similarity with parameters also used
-in QMEAN.</p>
-</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The sequence profile for the residues defined by
+<strong>fragment</strong>, represented as a <code class="xref py py-class docutils literal"><span class="pre">ost.seq.HMM</span></code>
+with the BLOSUM62 probabilities as NULL model</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-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
the case when the fragment does not fully fit into one
-of chains in the database. It also throws an error if
-one of the psipred values is invalid.</p>
-</td>
+of the chains in the database.</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.loop.StructureDB.GetTorsionProbability">
-<code class="descname">GetTorsionProbability</code><span class="sig-paren">(</span><em>fragment</em>, <em>seq</em>, <em>torsion_sampler</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetTorsionProbability" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.loop.StructureDB.GetStructureProfile">
+<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>
<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>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the structure
+profile</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The structure profile for the residues defined by
+<strong>fragment</strong>, represented as a <code class="xref py py-class docutils literal"><span class="pre">ost.seq.HMM</span></code>
+with the BLOSUM62 probabilities as NULL model</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
+the case when the fragment does not fully fit into one
+of the chains in the database.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.loop.StructureDB.GenerateStructureProfile">
+<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>Takes the <strong>bb_list</strong> with its corresponding <strong>residue_depths</strong> to
+calculate a structure profile using the full internal structural data
+with their corresponding residue depths.</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>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment from the database</li>
-<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence the fragment is assumed to have.</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"><span class="pre">TorsionSampler</span></code></a>) – The source of the probability</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"><span class="pre">BackboneList</span></code></a>) – Structural data from which do extract structural
+profile</li>
+<li><strong>residue_depths</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> values) – Residue depth values for <strong>bb_list</strong></li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The average probablity of observing the dihedral angles
-from <strong>fragment</strong> assuming the sequence <strong>seq</strong>.
-Note, that the torsion sampler considers amino acid
-triplets, the torsion angles of the flanking residues
-are therefore neglected.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The structure profile for the input,
+represented as a <code class="xref py py-class docutils literal"><span class="pre">ost.seq.HMM</span></code>
+with the BLOSUM62 probabilities as NULL model</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-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
-the case when the fragment does not fully fit into one
-of chains in the database.</p>
+<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if <strong>bb_list</strong> and
+<strong>residue_depths</strong> differ in size or when
+their size is 0</p>
</td>
</tr>
</tbody>
@@ -491,28 +580,24 @@ of chains in the database.</p>
</dd></dl>
<dl class="method">
-<dt id="promod3.loop.StructureDB.GetProfileScore">
-<code class="descname">GetProfileScore</code><span class="sig-paren">(</span><em>fragment</em>, <em>hmm</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetProfileScore" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
+<dt id="promod3.loop.StructureDB.SetStructureProfile">
+<code class="descname">SetStructureProfile</code><span class="sig-paren">(</span><em>chain_idx</em>, <em>hmm</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 <strong>hmm</strong> and sets the corresponding StructureProfile
+frequencies in entry with <strong>chain_idx</strong></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>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment from the database</li>
-<li><strong>hmm</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.seq.HMM</span></code>) – Hmm to be aligned with fragment.</li>
+<li><strong>hmm</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.seq.HMM</span></code>) – Source of profile frequencies</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – idx of entry for which to set the frequencies</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The average column alignment score between the columns
-in the <strong>hmm</strong> and the corresponding positions in
-the database.</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-class docutils literal"><span class="pre">RuntimeError</span></code> If fragment is invalid. This is
-the case when the fragment does not fully fit into one
-of chains in the database. The function also raises
-and error if the database has been loaded with
-load_frequencies=False.</p>
+<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"><span class="pre">RuntimeError</span></code> If <strong>chain_idx</strong> does not match
+any entry in the db or when the size of the <strong>hmm</strong>
+does not exactly match the size of entry at
+<strong>chain_idx</strong></p>
</td>
</tr>
</tbody>
@@ -532,10 +617,55 @@ distance between the N-stem C atom and the C-stem N atom). It can therefore
be searched for fragments matching a certain geometry of N and C stems.
The bins are accessed through a hash table, making searching the database
ultra fast.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="c">#This example should illustrate how to create a custom FragDB</span>
+<span class="c">#based on a StructureDB</span>
+
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+
+<span class="c">#let's load the default structure_db</span>
+<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
+
+<span class="c">#and our beloved crambin...</span>
+<span class="n">structure</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'1crn'</span><span class="p">,</span><span class="n">remote</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+
+<span class="c">#we now want to connect the residue with index 17 and 21</span>
+<span class="n">n_stem</span> <span class="o">=</span> <span class="n">structure</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">17</span><span class="p">]</span>
+<span class="n">c_stem</span> <span class="o">=</span> <span class="n">structure</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">21</span><span class="p">]</span>
+
+<span class="c">#A custom FragDB can be build to identify fragments</span>
+<span class="c">#fulfilling these particular geometric constraints</span>
+<span class="n">frag_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">FragDB</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
+
+<span class="c">#At this point we add all possible fragments of length 5</span>
+<span class="c">#with an RMSD threshold of 0.5</span>
+<span class="n">frag_db</span><span class="o">.</span><span class="n">AddFragments</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span><span class="mf">0.5</span><span class="p">,</span><span class="n">structure_db</span><span class="p">)</span>
+
+<span class="c">#The FragDB can now be used to extract FragmentInfo objects to finally query</span>
+<span class="c">#the StructureDB</span>
+<span class="n">fragment_infos</span> <span class="o">=</span> <span class="n">frag_db</span><span class="o">.</span><span class="n">SearchDB</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span><span class="n">c_stem</span><span class="p">,</span><span class="mi">5</span><span class="p">)</span>
+
+<span class="c">#let's get the fragments in form of BackboneList objects and save the down</span>
+<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">f_i</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">fragment_infos</span><span class="p">):</span>
+ <span class="n">bb_list</span> <span class="o">=</span> <span class="n">structure_db</span><span class="o">.</span><span class="n">GetBackboneList</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span><span class="n">c_stem</span><span class="p">,</span><span class="n">f_i</span><span class="p">)</span>
+ <span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span><span class="o">+</span><span class="s">".pdb"</span><span class="p">)</span>
+</pre></div>
+</div>
<dl class="class">
<dt id="promod3.loop.FragDB">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FragDB</code><a class="headerlink" href="#promod3.loop.FragDB" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
+<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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Size of the angle parameter binning in degree</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
<dt id="promod3.loop.FragDB.Load">
<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>
<dd><table class="docutils field-list" frame="void" rules="none">
@@ -624,7 +754,7 @@ As the fragments are added they are organized in bins described by their length
<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 databse, notably:
1. the number of different stem groups (number of bins used to group the fragments according to the geometry of their stem residues)
-2. The total number of fragments in the databse
+2. The total number of fragments in the database
3. The minimal and maximal number of fragments found in a stem group.</p>
</dd></dl>
@@ -701,7 +831,7 @@ As the fragments are added they are organized in bins described by their length
<dl class="method">
<dt id="promod3.loop.FragDB.SearchDB">
<code class="descname">SearchDB</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>frag_size</em><span class="optional">[</span>, <em>extended_search=False</em><span class="optional">]</span><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>sequence</strong>.</p>
+<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>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -729,26 +859,35 @@ structural database with which you called the AddFragments function.</p>
<h2>Finding Fragments based on Sequence Features<a class="headerlink" href="#finding-fragments-based-on-sequence-features" title="Permalink to this headline">¶</a></h2>
<p>In some cases you might want to use the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> to search
for fragments that possibly represent the structural conformation of interest.
-The <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> allows to perform this task for several different
-features. It searches a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> for n fragments, that maximize
-a certain score and gathers a set of fragments with a guaranteed structural
-diversity based on an rmsd_threshold. The final score gets built using an
-arbitrary linear combination of the available scores as controlled by
-the <a class="reference internal" href="#promod3.loop.FraggerScoreParameters" title="promod3.loop.FraggerScoreParameters"><code class="xref py py-class docutils literal"><span class="pre">FraggerScoreParameters</span></code></a>. There are five scores available:</p>
+The <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> searches a <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> for n fragments,
+that maximize a certain score and gathers a set of fragments with a guaranteed
+structural diversity based on an rmsd_threshold. The score can be built using an
+arbitrary linear combination of following components:</p>
<ul class="simple">
-<li><strong>SequenceSimilarityScore</strong>: Takes a substitution matrix and calculates for
-every possible fragment the normalized sequence similarity in a range [0,1].</li>
-<li><strong>SequenceIdentityScore</strong>: Calculates for every possible fragment the
-sequence identity.</li>
-<li><strong>SSAgreementScore</strong>: Takes the predicted secondary structure by PSIPRED
-with its confidence and calculates an agreement score based on the
-actually observed secondary structure in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>.</li>
-<li><strong>TorsionProbabilityScore</strong>: Calculates for every possible fragment the
-average probablity of the backbone dihedral angles in the
-<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> given the input sequence.</li>
-<li><strong>ProfileScore</strong>: Calculates for every possible fragment the profile-profile
-alignment score given an input <code class="xref py py-class docutils literal"><span class="pre">ost.seq.HMM</span></code> and the amino acid
-frequencies in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>.</li>
+<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"><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"><span class="pre">StructureDB</span></code></a> and the target
+sequence</li>
+<li><strong>SSAgree</strong>:
+Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="#jones1999" id="id6">[Jones1999]</a>
+and the dssp <a class="reference internal" href="#kabsch1983" id="id7">[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"><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="#soding2005" id="id8">[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"><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"><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"><span class="pre">StructureDB</span></code></a> and a target profile assuming a gapfree alignment
+in between them. The scores are calculated as described for HHSearch <a class="reference internal" href="#soding2005" id="id9">[soding2005]</a>.</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"><span class="pre">StructureDB</span></code></a> and a target profile assuming a gapfree alignment
+in between them. The scores are calculated as described for HHSearch <a class="reference internal" href="#soding2005" id="id10">[soding2005]</a>.
+In this case, the amino acid frequencies extracted from structural alignments are used.</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
@@ -767,14 +906,15 @@ frequencies in the <a class="reference internal" href="#promod3.loop.StructureDB
<span class="n">db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
<span class="n">subst_matrix</span> <span class="o">=</span> <span class="n">ost</span><span class="o">.</span><span class="n">seq</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">BLOSUM62</span>
-<span class="c">#to fill the fragger we need a list of parameters</span>
-<span class="c">#we only add a parametrization for the sequence similarity</span>
-<span class="n">parameters</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
-<span class="n">parameters</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">loop</span><span class="o">.</span><span class="n">FraggerScoreParameters</span><span class="p">(</span><span class="n">frag_seq</span><span class="p">,</span><span class="n">subst_matrix</span><span class="p">,</span><span class="mf">1.0</span><span class="p">))</span>
+<span class="c">#the fragger object needs to be initialized with its target sequence</span>
+<span class="n">fragger</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">Fragger</span><span class="p">(</span><span class="n">frag_seq</span><span class="p">)</span>
-<span class="c">#let's finally fill the fragger</span>
-<span class="n">fragger</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">Fragger</span><span class="p">()</span>
-<span class="n">fragger</span><span class="o">.</span><span class="n">Fill</span><span class="p">(</span><span class="n">db</span><span class="p">,</span><span class="n">parameters</span><span class="p">,</span><span class="mf">1.0</span><span class="p">,</span><span class="mi">100</span><span class="p">)</span>
+<span class="c">#we could now add an arbitrary number of parameters from different features</span>
+<span class="c">#for now we only go for the sequence similarity score</span>
+<span class="n">fragger</span><span class="o">.</span><span class="n">AddSeqSimParameters</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">subst_matrix</span><span class="p">)</span>
+
+<span class="c">#the Fragger can finally be filled by providing a StructureDB</span>
+<span class="n">fragger</span><span class="o">.</span><span class="n">Fill</span><span class="p">(</span><span class="n">db</span><span class="p">,</span><span class="mf">1.0</span><span class="p">,</span><span class="mi">100</span><span class="p">)</span>
<span class="c">#let's see how good the fragments are...</span>
<span class="n">below_three</span> <span class="o">=</span> <span class="mi">0</span>
@@ -788,22 +928,38 @@ frequencies in the <a class="reference internal" href="#promod3.loop.StructureDB
</pre></div>
</div>
<dl class="class">
-<dt id="promod3.loop.FraggerScoreParameters">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FraggerScoreParameters</code><a class="headerlink" href="#promod3.loop.FraggerScoreParameters" title="Permalink to this definition">¶</a></dt>
-<dd><p>Controls the parametrization and linear weights of the available
-fragger scores.</p>
+<dt id="promod3.loop.Fragger">
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">Fragger</code><a class="headerlink" href="#promod3.loop.Fragger" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="method">
+<dt id="promod3.loop.Fragger.Fragger">
+<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.Fragger" title="Permalink to this definition">¶</a></dt>
+<dd><p>Initialize 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"><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>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of fragments to be searched</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
<dl class="method">
-<dt id="promod3.loop.FraggerScoreParameters.FraggerScoreParameters">
-<code class="descname">FraggerScoreParameters</code><span class="sig-paren">(</span><em>seq</em>, <em>matrix</em>, <em>w</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FraggerScoreParameters.FraggerScoreParameters" title="Permalink to this definition">¶</a></dt>
-<dd><p>Parametrization of sequence similarity score</p>
+<dt id="promod3.loop.Fragger.Fill">
+<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>
<table class="docutils field-list" frame="void" rules="none">
<col class="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>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of fragment</li>
-<li><strong>matrix</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.seq.alg.SubstWeightMatrix</span></code>) – Source of substitution scores</li>
-<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Linear weight for sequence similarity score</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"><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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of fragments to be extracted</li>
</ul>
</td>
</tr>
@@ -812,38 +968,30 @@ fragger scores.</p>
</dd></dl>
<dl class="method">
-<dt>
-<code class="descname">FraggerScoreParameters</code><span class="sig-paren">(</span><em>seq</em>, <em>w</em><span class="sig-paren">)</span></dt>
-<dd><p>Parametrization of sequence identity score</p>
+<dt id="promod3.loop.Fragger.AddSeqIDParameters">
+<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>
<table class="docutils field-list" frame="void" rules="none">
<col class="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>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of fragment</li>
-<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Linear weight for sequence identity score</li>
-</ul>
-</td>
+<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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt>
-<code class="descname">FraggerScoreParameters</code><span class="sig-paren">(</span><em>seq</em>, <em>psipred_prediction</em>, <em>psipred_confidence</em>, <em>w</em><span class="sig-paren">)</span></dt>
-<dd><p>Parametrization of secondary structure agreement score</p>
+<dt id="promod3.loop.Fragger.AddSeqSimParameters">
+<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>
<table class="docutils field-list" frame="void" rules="none">
<col class="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>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of fragment</li>
-<li><strong>psipred_prediction</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Per AA psipred prediction, every element
-must be in [‘H’,’E’,’C’]</li>
-<li><strong>psipred_confidence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Per AA psipred confidence values, every element
-must be in [0,9]</li>
-<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Linear weight for secondary structure agreement score</li>
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
+<li><strong>subst</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.seq.SubstWeightMatrix</span></code>) – Substitution matrix to calculate sequence similarity</li>
</ul>
</td>
</tr>
@@ -852,18 +1000,19 @@ must be in [0,9]</li>
</dd></dl>
<dl class="method">
-<dt>
-<code class="descname">FraggerScoreParameters</code><span class="sig-paren">(</span><em>seq</em>, <em>torsion_sampler</em>, <em>w</em><span class="sig-paren">)</span></dt>
-<dd><p>Parametrization of torsion angle probablity score</p>
+<dt id="promod3.loop.Fragger.AddSSAgreeParameters">
+<code class="descname">AddSSAgreeParameters</code><span class="sig-paren">(</span><em>w</em>, <em>psipred_prediction</em>, <em>psipred_confidence</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>
<table class="docutils field-list" frame="void" rules="none">
<col class="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>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of fragment</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"><span class="pre">TorsionSampler</span></code></a>) – Torsion sampler to get sequence specific backbone
-dihedral probabilities</li>
-<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Linear weight for torsion probability score</li>
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – linear weight</li>
+<li><strong>psipred_prediction</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Secondary structure state (‘H’,’E’,’C’) as predicted
+by PSIPRED for every item in the Fraggers target sequence</li>
+<li><strong>psipred_confidence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Confidence for secondary structure state ([0,9]) as predicted
+by PSIPRED for every item in the Fraggers target sequence</li>
</ul>
</td>
</tr>
@@ -872,18 +1021,16 @@ dihedral probabilities</li>
</dd></dl>
<dl class="method">
-<dt>
-<code class="descname">FraggerScoreParameters</code><span class="sig-paren">(</span><em>seq</em>, <em>hmm</em>, <em>w</em><span class="sig-paren">)</span></dt>
-<dd><p>Parametrization of profile score</p>
+<dt id="promod3.loop.Fragger.AddSequenceProfileParameters">
+<code class="descname">AddSequenceProfileParameters</code><span class="sig-paren">(</span><em>w</em>, <em>hmm</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>
<table class="docutils field-list" frame="void" rules="none">
<col class="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>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of fragment</li>
-<li><strong>hmm</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.seq.HMM</span></code>) – HMM of same size as the sequence to extract
-the according amino acid frequencies</li>
-<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Linear weight for profile score</li>
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
+<li><strong>hmm</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.seq.HMM</span></code>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -891,27 +1038,17 @@ the according amino acid frequencies</li>
</table>
</dd></dl>
-</dd></dl>
-
-<dl class="class">
-<dt id="promod3.loop.Fragger">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">Fragger</code><a class="headerlink" href="#promod3.loop.Fragger" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="promod3.loop.Fragger.Fill">
-<code class="descname">Fill</code><span class="sig-paren">(</span><em>db</em>, <em>parameters</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 as defined by the <strong>parameters</strong>.
-There will be no pair of fragments with RMSD below
-<strong>rmsd_thresh</strong>.</p>
+<dl class="method">
+<dt id="promod3.loop.Fragger.AddStructureProfileParameters">
+<code class="descname">AddStructureProfileParameters</code><span class="sig-paren">(</span><em>w</em>, <em>hmm</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>
<table class="docutils field-list" frame="void" rules="none">
<col class="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"><span class="pre">StructureDB</span></code></a>) – Source of structural data</li>
-<li><strong>parameters</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Parameters to build a per fragment score</li>
-<li><strong>rmsd_thresh</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of fragments to be extracted</li>
+<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
+<li><strong>hmm</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.seq.HMM</span></code>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -962,8 +1099,80 @@ There will be no pair of fragments with RMSD below
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.loop.Fragger.GetScore">
+<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>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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="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"><span class="pre">Fragger</span></code></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 last simple">
+<li><strong>parameter_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of score</li>
+<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of fragment</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
+<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><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id8">2</a>, <a class="fn-backref" href="#id9">3</a>, <a class="fn-backref" href="#id10">4</a>)</em> Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="sanner1996" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label"><a class="fn-backref" href="#id3">[sanner1996]</a></td><td>Sanner M, Olson AJ, Spehner JC (1996). Reduced Surface: an Efficient Way to Compute Molecular Surfaces. Biopolymers 38 (3): 305-320.</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"><a class="fn-backref" href="#id4">[chakravarty1999]</a></td><td>Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.</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"><a class="fn-backref" href="#id5">[zhou2005]</a></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 58 (2): 321–328.</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"><a class="fn-backref" href="#id6">[Jones1999]</a></td><td>Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.</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><em>(<a class="fn-backref" href="#id2">1</a>, <a class="fn-backref" href="#id7">2</a>)</em> Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 2577-2637.</td></tr>
+</tbody>
+</table>
</div>
</div>
@@ -983,13 +1192,19 @@ There will be no pair of fragments with RMSD below
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="torsion_sampler.html"
- title="previous chapter">Torsion Sampler</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="loop_closing.html"
- title="next chapter">Loop Closing</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a><ul>
+ <li>Previous: <a href="torsion_sampler.html" title="previous chapter">Torsion Sampler</a></li>
+ <li>Next: <a href="loop_closing.html" title="next chapter">Loop Closing</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
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<h3>This Page</h3>
<ul class="this-page-menu">
@@ -1019,11 +1234,11 @@ There will be no pair of fragments with RMSD below
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/loop/structure_db.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
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diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index 476550a941fdd856c0fd2d14f9e3e310bd6038d5..64ce4355b71fc0cb20e9ae406e566d7c23b5d953 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="structure_db.html" title="Structural Database"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="backbone.html" title="Backbone"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -69,15 +49,43 @@ It uses distributions specific for triplets of residues, so that when drawing
a phi/psi pair for a certain residue, the distribution from which the pair is
drawn also depends on the identity of the residues before and after the residue
in question.
-The distributions of the sampler are stored in a vector, so that
+The distributions of the sampler are internally stored in a vector, so that
most methods which need to access a specific distribution can either take 3
residue names or an index as input.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="kn">as</span> <span class="nn">plt</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
+
+<span class="c">#load a default sampler</span>
+<span class="n">t_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSampler</span><span class="p">()</span>
+
+<span class="c">#dihedral angles will be stored in here</span>
+<span class="n">phi</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+<span class="n">psi</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+
+<span class="c">#draw from a random distribution</span>
+<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1000</span><span class="p">):</span>
+ <span class="n">dihedral_pair</span> <span class="o">=</span> <span class="n">t_sampler</span><span class="o">.</span><span class="n">Draw</span><span class="p">(</span><span class="s">"ALA"</span><span class="p">,</span><span class="s">"PRO"</span><span class="p">,</span><span class="s">"ALA"</span><span class="p">)</span>
+ <span class="n">phi</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dihedral_pair</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
+ <span class="n">psi</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dihedral_pair</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+
+<span class="c">#and plot it</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">xlim</span><span class="p">((</span><span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">,</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">))</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">ylim</span><span class="p">((</span><span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">,</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">))</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">phi</span><span class="p">,</span><span class="n">psi</span><span class="p">,</span><span class="s">'.'</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s">"phi"</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="s">'large'</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s">"psi"</span><span class="p">,</span><span class="n">fontsize</span><span class="o">=</span><span class="s">'large'</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s">"ALA-PRO-ALA"</span><span class="p">)</span>
+
+<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
+</pre></div>
+</div>
<div class="section" id="defining-amino-acid-triplets">
<h2>Defining Amino Acid triplets<a class="headerlink" href="#defining-amino-acid-triplets" title="Permalink to this headline">¶</a></h2>
<p>Since the torsion sampler considers triplets of amino acids, we need to define
them. This is done with the so called torsion group definitions.
-Three strings represent the according positions of the consecu-
-tive amino acids. They are combined by “-”. It is either possible to
+Three strings represent the according positions of the consecutive
+amino acids. They are combined by “-”. It is either possible to
use the keyword “all”, or write out all allowed amino acids by their
three letter code and separate them by ”,”. An example would be: “all-
VAL,ILE-PRO”. There are cases where a tripeptide can match several
@@ -91,28 +99,25 @@ decisive.</p>
<dl class="class">
<dt id="promod3.loop.TorsionSampler">
<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>bin_size</em>, <em>seed</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler" title="Permalink to this definition">¶</a></dt>
-<dd><blockquote>
-<div><table class="docutils field-list" frame="void" rules="none">
+<dd><p>Basic object used to sample the backbone torsion angles phi and psi.</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" colspan="2">param group_definitions:</th></tr>
-<tr class="field-odd field"><td> </td><td class="field-body">List of group definitions defining
-amino acid triplets.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">param bin_size:</th><td class="field-body">Size of bins in distributions</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">param seed:</th><td class="field-body"></td>
-</tr>
-<tr class="field-even field"><th class="field-name">type bin_size:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
+<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/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – List of group definitions defining amino acid triplets</li>
+<li><strong>bin_size</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Size of bins in distributions (in degrees)</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed for random number generator</li>
+</ul>
+</td>
</tr>
-<tr class="field-odd field"><th class="field-name">raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeException</span></code> when there is a
+<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"><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.</td>
+acids not matching any of the group definitions.</p>
+</td>
</tr>
</tbody>
</table>
-</div></blockquote>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.ExtractStatistics">
<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>
@@ -332,8 +337,8 @@ standard amino acid</td>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetProbability">
-<code class="descname">GetProbability</code><span class="sig-paren">(</span><em>before</em>, <em>central</em>, <em>after</em>, <em>dihedrals</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 dihedrals for the central residue from the corresponding distribution.</p>
+<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>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -342,7 +347,8 @@ standard amino acid</td>
<li><strong>before</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue before <em>central</em></li>
<li><strong>central</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue for which the probability is calculated.</li>
<li><strong>after</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name (3 letter code) of the residue after <em>central</em></li>
-<li><strong>dihedrals</strong> ((<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>, <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)) – pair of phi/psi angles</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
</td>
</tr>
@@ -355,15 +361,16 @@ standard amino acid</td>
<dl class="method">
<dt>
-<code class="descname">GetProbability</code><span class="sig-paren">(</span><em>index</em>, <em>dihedrals</em><span class="sig-paren">)</span></dt>
-<dd><p>Returns the probability of a specific pair of phi/psi dihedrals calulated form the distribution specified by <em>index</em>.</p>
+<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 form the distribution specified by <em>index</em>.</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>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The index of the distribution.</li>
-<li><strong>dihedrals</strong> ((<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>, <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)) – pair of phi/psi angles</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
</td>
</tr>
@@ -469,7 +476,7 @@ standard amino acid</td>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetBinsPerDimension">
<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 in one dimension of the distributions.</p>
+<dd><p>Returns the number of bins per dimension of the distributions.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -483,7 +490,7 @@ standard amino acid</td>
<dl class="method">
<dt id="promod3.loop.TorsionSampler.GetBinSize">
<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 of the distributions.</p>
+<dd><p>Returns the size of the bins (in radians) of the distributions.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -513,13 +520,19 @@ standard amino acid</td>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="backbone.html"
- title="previous chapter">Backbone</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="structure_db.html"
- title="next chapter">Structural Database</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a><ul>
+ <li>Previous: <a href="backbone.html" title="previous chapter">Backbone</a></li>
+ <li>Next: <a href="structure_db.html" title="next chapter">Structural Database</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -549,11 +562,11 @@ standard amino acid</td>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/loop/torsion_sampler.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index dec261123f8786ddc611179ec18030f16d8e998f..13f56018e2c04606c20f47d65356f4dab3b9d29e 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/pipeline/index.html b/doc/html/pipeline/index.html
index a534352b622da24ce87d49051ccd947ab4624eb3..dfccc36b3444543b5aa4bd52f8dee90bd5b00075 100644
--- a/doc/html/pipeline/index.html
+++ b/doc/html/pipeline/index.html
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Developes" href="../developers.html" />
+ <link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="run_engine - Build Models From Various Starting Points" href="run_engine.html" />
<link rel="prev" title="helper - Shared Functionality For the Everything" href="../core/helper.html" />
@@ -32,26 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="run_engine.html" title="run_engine - Build Models From Various Starting Points"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="../core/helper.html" title="helper - Shared Functionality For the Everything"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" accesskey="U">Documentation For Developes</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -78,13 +59,17 @@ for external applications.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="../core/helper.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="run_engine.html"
- title="next chapter"><code class="docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points</a></p>
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li>Previous: <a href="../core/helper.html" title="previous chapter"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
+ <li>Next: <a href="run_engine.html" title="next chapter"><code class="docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -114,11 +99,11 @@ for external applications.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/pipeline/index.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/pipeline/run_engine.html b/doc/html/pipeline/run_engine.html
index a8e0caa280d199c0db09f1e310faed14708b3b18..6832504808aa8f058fe01f9cae66a0e431fce3c5 100644
--- a/doc/html/pipeline/run_engine.html
+++ b/doc/html/pipeline/run_engine.html
@@ -25,34 +25,14 @@
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
<link rel="up" title="pipeline - ProMod3 Modelling Pipeline" href="index.html" />
- <link rel="next" title="rawmodel - Coordinate Modeling" href="../rawmodel/index.html" />
+ <link rel="next" title="rawmodel - Coordinate Modelling" href="../rawmodel/index.html" />
<link rel="prev" title="pipeline - ProMod3 Modelling Pipeline" href="index.html" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="../rawmodel/index.html" title="rawmodel - Coordinate Modeling"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="index.html" title="pipeline - ProMod3 Modelling Pipeline"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -124,13 +104,19 @@ shipped with ProMod3 if omitted.</li>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="index.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="../rawmodel/index.html"
- title="next chapter"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modeling</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">pipeline</span></code> - ProMod3 Modelling Pipeline</a></li>
+ <li>Next: <a href="../rawmodel/index.html" title="next chapter"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modelling</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -160,11 +146,11 @@ shipped with ProMod3 if omitted.</li>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/pipeline/run_engine.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 4b355acda60de50d8a03c1bfce4430e7690fc706..4163ca3057d7065fafb2d639eab66cf374262977 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -32,19 +32,7 @@
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="#" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="index.html">ProMod3 0 documentation</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -114,7 +102,13 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
+ </ul></li>
+</ul>
+</div>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<form class="search" action="search.html" method="get">
@@ -137,7 +131,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/rawmodel/index.html b/doc/html/rawmodel/index.html
index 074ba58ce79f9be4739ac942f207515e412fec61..6c44ec9579499233dc5fdf8d22102ad680db3f36 100644
--- a/doc/html/rawmodel/index.html
+++ b/doc/html/rawmodel/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>rawmodel - Coordinate Modeling — ProMod3 0 documentation</title>
+ <title>rawmodel - Coordinate Modelling — ProMod3 0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Developes" href="../developers.html" />
+ <link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="loop - Loop Modelling" href="../loop/index.html" />
<link rel="prev" title="run_engine - Build Models From Various Starting Points" href="../pipeline/run_engine.html" />
@@ -32,26 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="../loop/index.html" title="loop - Loop Modelling"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="../pipeline/run_engine.html" title="run_engine - Build Models From Various Starting Points"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" accesskey="U">Documentation For Developes</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -59,7 +40,7 @@
<div class="body" role="main">
<div class="section" id="module-promod3.rawmodel">
-<span id="rawmodel-coordinate-modeling"></span><h1><a class="reference internal" href="#module-promod3.rawmodel" title="promod3.rawmodel: Raw Coordinate Model"><code class="xref py py-mod docutils literal"><span class="pre">rawmodel</span></code></a> - Coordinate Modeling<a class="headerlink" href="#module-promod3.rawmodel" title="Permalink to this headline">¶</a></h1>
+<span id="rawmodel-coordinate-modelling"></span><h1><a class="reference internal" href="#module-promod3.rawmodel" title="promod3.rawmodel: Raw Coordinate Model"><code class="xref py py-mod docutils literal"><span class="pre">rawmodel</span></code></a> - Coordinate Modelling<a class="headerlink" href="#module-promod3.rawmodel" title="Permalink to this headline">¶</a></h1>
<p>Functionality to build raw (pseudo) models based on a sequence alignment.
Here is an example of how to build a model from an alignment and a structure.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
@@ -72,8 +53,8 @@ Here is an example of how to build a model from an alignment and a structure.</p
<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="s">'model.pdb'</span><span class="p">)</span>
</pre></div>
</div>
-<div class="section" id="raw-coordinate-modeling-api">
-<h2>Raw Coordinate Modeling API<a class="headerlink" href="#raw-coordinate-modeling-api" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="raw-coordinate-modelling-api">
+<h2>Raw Coordinate Modelling API<a class="headerlink" href="#raw-coordinate-modelling-api" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="promod3.rawmodel.BuildRawModel">
<code class="descclassname">promod3.rawmodel.</code><code class="descname">BuildRawModel</code><span class="sig-paren">(</span><em>alignment</em>, <em>calpha_only=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.rawmodel.BuildRawModel" title="Permalink to this definition">¶</a></dt>
@@ -82,7 +63,7 @@ Here is an example of how to build a model from an alignment and a structure.</p
<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>
-<p>This is a basic protein core modeling algorithm that copies backbone
+<p>This is a basic protein core modelling algorithm that copies backbone
coordinates based on the sequence alignment. For matching residues, the
side chain coordinates are also copied. Gaps are ignored. Hydrogen an
deuterium atoms are not copied into the model.</p>
@@ -96,7 +77,7 @@ phosphoserine are copied as a whole with the modifications stripped off.</li>
</ul>
</div></blockquote>
<p>Residue numbers are set such that missing residue in gaps are honoured and
-subsequent loop modeling can insert new residues without having to
+subsequent loop modelling can insert new residues without having to
renumber.</p>
<p>The returned <a class="reference internal" href="#promod3.rawmodel.RawModelingResult" title="promod3.rawmodel.RawModelingResult"><code class="xref py py-class docutils literal"><span class="pre">RawModelingResult</span></code></a> stores the obtained raw model as well
as information about insertions and deletions in the gaps list.</p>
@@ -244,18 +225,22 @@ merge happens.</td>
<div class="sphinxsidebarwrapper">
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modeling</a><ul>
-<li><a class="reference internal" href="#raw-coordinate-modeling-api">Raw Coordinate Modeling API</a></li>
+<li><a class="reference internal" href="#"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modelling</a><ul>
+<li><a class="reference internal" href="#raw-coordinate-modelling-api">Raw Coordinate Modelling API</a></li>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="../pipeline/run_engine.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="../loop/index.html"
- title="next chapter"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li>Previous: <a href="../pipeline/run_engine.html" title="previous chapter"><code class="docutils literal"><span class="pre">run_engine</span></code> - Build Models From Various Starting Points</a></li>
+ <li>Next: <a href="../loop/index.html" title="next chapter"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Modelling</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -285,11 +270,11 @@ merge happens.</td>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/rawmodel/index.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/search.html b/doc/html/search.html
index 9b2f84d59d6dbbb3b7b652d55261b090015ba100..cd760235a39d67b03d322ae53cdd7c7a8d6a7586 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -37,19 +37,7 @@
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="index.html">ProMod3 0 documentation</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -84,7 +72,13 @@
</div>
</div>
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- <div class="sphinxsidebarwrapper">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
+ </ul></li>
+</ul>
+</div>
</div>
</div>
<div class="clearer"></div>
@@ -94,7 +88,7 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
</div>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index b6eb116c2bc80d1d8ca06e4286fb5a08b880a08b..30aef90488beda46f4f925544cbc493be722e4c3 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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class=\"docutils literal\"><span class=\"pre\">test_actions.ActionTestCase</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3‘s Share Of CMake","Contributing","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","Documentation For Developers","Getting Started","Welcome To ProMod3’s Documentation!","Backbone","Loop Scoring","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Modelling","Load Loop Objects","Loop Candidates","Loop Closing","Monte Carlo Sampling","Structural Database","Torsion Sampler","<code class=\"docutils literal\"><span class=\"pre\">pipeline</span></code> - ProMod3 Modelling Pipeline","<code class=\"docutils literal\"><span class=\"pre\">run_engine</span></code> - Build Models From Various Starting Points","<code class=\"docutils literal\"><span class=\"pre\">rawmodel</span></code> - Coordinate Modelling","Disulfid Bond Evaluation","Frame","Coming to a solution","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Rotamers","RotamerID","Rotamer Library","Rotamer Settings","Documentation For Users"],titleterms:{"class":20,"function":[3,5,6,25,27,28],acid:20,action:[0,3,4],actiontestcas:0,amino:20,api:[0,23],argument:7,backbon:[12,17,30],backboneloopscor:13,base:19,basic:12,block:[12,28],bond:24,branch:4,build:[1,12,22,28],can:29,candid:16,carlo:18,ccd:17,chain:19,chang:2,changelog:2,close:17,closer:18,cmake:[0,1,3,4],come:26,command:7,construct:[25,28],contribut:4,conveni:[25,28],cooler:18,coordin:23,core:6,creat:0,databas:19,defin:[19,20],depend:[1,30],develop:9,directori:4,disulfid:24,document:[3,4,9,11,32],edit:12,entri:30,evalu:24,everyth:5,execut:0,featur:19,file:5,find:19,fragment:19,frame:25,from:22,full:12,geometr:19,get:[10,29],git:4,graph:26,group:28,have:0,helper:5,hook:4,how:[4,29],indic:11,integr:0,interact:26,introduct:[3,5,7,22],issu:4,kic:17,librari:30,licens:4,line:7,load:15,loop:[13,14,15,16,17],mainten:3,make:[0,1],messag:5,model:[10,14,21,22,23,27],modul:[3,4,27],mont:18,must:0,non:30,object:[15,18,25],obtain:[],output:0,own:4,pars:7,parser:7,parti:4,particl:28,pipelin:[10,21],pm3argpars:7,point:22,promod3:[1,3,6,10,11,21],raw:23,rawmodel:23,reconstruct:27,relax:17,releas:2,residu:[12,25],rotam:[28,30,31],rotamerid:29,run:[0,1,10],run_engin:22,sampl:18,sampler:[18,20],score:13,scorer:18,script:0,sequenc:19,set:31,setcompoundschemlib:8,share:[3,5],sidechain:27,smallest:28,solut:26,stage:4,start:[4,10,22],stretch:12,structur:[4,19],subclass:0,tabl:11,test:[0,3,4,5],test_act:0,third:4,torsion:20,triplet:20,type:30,unit:[0,3,4],user:32,variou:22,welcom:11,write:4,your:4}})
\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index fa8db2c4cbb9c59df4f47861f73caba938960f08..909e1c2710e29142813b1c2cc851eaeacbe9d7c6 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="../actions/index_dev.html" title="test_actions.ActionTestCase - Testing Actions"
- accesskey="N">next</a> |</li>
- <li class="right" >
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- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -65,11 +45,8 @@
a disulfid bond, one would get an unfavourable energy due to “clashes” between
the sulfur atoms. It is possible to improve performance in sidechain
reconstruction regarding cysteins when finding and separately handle
-disulfid bonds. PROMOD3 implements a simple geometrical description of
-disulfid bonds described in:</p>
-<p>Canutescu AA, Shelenkov AA, Dunbrack RL Jr.
-A graph-theory algorithm for rapid protein side-chain prediction.
-Protein Sci (2003).</p>
+disulfid bonds. PROMOD3 implements a simple geometrical description
+<a class="reference internal" href="../loop/loop_closing.html#canutescu2003" id="id1">[canutescu2003]</a> .</p>
<p>Two methods are implemented to evaluate this disulfid score on either rigid of
flexible rotamers. The above paper proposes two rotamers to be in a disulfid
bonded state, if the resulting score is below 45.</p>
@@ -81,8 +58,8 @@ bonded state, if the resulting score is below 45.</p>
<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"><span class="pre">RRMRotamer</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"><span class="pre">RRMRotamer</span></code></a>) – Second rotamer</li>
+<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"><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"><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"><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"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</li>
<li><strong>ca_pos_one</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
@@ -94,37 +71,10 @@ bonded state, if the resulting score is below 45.</p>
exactly one particle representing the gamma sulfur.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The disulfid score based on geometric features.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<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></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>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</li>
-<li><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</li>
-<li><strong>ca_pos_one</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
-</ul>
-</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-class docutils literal"><span class="pre">RuntimeError</span></code> if given subrotamers do not contain
-exactly one particle representing the gamma sulfur.</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The disulfid score based on geometric features. Scores
-are calculated for all possible subrotamer combinations
-and the minimal score gets returned.</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The disulfid score based on geometric features. 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"><span class="pre">FRMRotamer</span></code></a> as input, the minimal score
+between all possible subrotamer combinations gets
+returned.</p>
</td>
</tr>
</tbody>
@@ -138,13 +88,19 @@ and the minimal score gets returned.</p>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="sidechain_settings.html"
- title="previous chapter">Rotamer Settings</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="../actions/index_dev.html"
- title="next chapter"><code class="docutils literal"><span class="pre">test_actions.ActionTestCase</span></code> - Testing Actions</a></p>
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li>Previous: <a href="sidechain_settings.html" title="previous chapter">Rotamer Settings</a></li>
+ <li>Next: <a href="../actions/index_dev.html" title="next chapter"><code class="docutils literal"><span class="pre">test_actions.ActionTestCase</span></code> - Testing Actions</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -174,11 +130,11 @@ and the minimal score gets returned.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/sidechain/disulfid.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index c935d1fac24e068ca8da8daffa392933cf6939c8..3e6636bb0e44040eb781af73fbba3e64c688818c 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="rotamer_lib.html" title="Rotamer Library"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="rotamer.html" title="Rotamers"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -69,6 +49,106 @@ The frame is built using single frame residues, all of them associated to
a residues index. If a rotamer associated to the same residue index
enters the frame energy calculation, all interaction with particles
belonging to the frame residue with the same residue index are neglected.</p>
+<div class="section" id="the-frame-objects">
+<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="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><p>The most simple way of constructing a frame residue is the usage
+of the convenient functions provided by PROMOD3.</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 last simple">
+<li><strong>particles</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.sidechain.FrameResidue.__len__">
+<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"><span class="pre">FrameResidue</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.FrameResidue.__getitem__">
+<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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><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"><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-class docutils literal"><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="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"><span class="pre">Frame</span></code></a> object allows to calculate frame energies for rotamers.
+Due to technical reasons, this is only possible if the rotamers are
+part of rotamer groups.</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"><strong>frame_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><span class="pre">FrameResidue</span></code></a>) – residues building the frame.</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.sidechain.Frame.SetFrameEnergy">
+<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>rotamer_group</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Frame.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculates and sets frame energies for all rotamers in the rotamer group.</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"><strong>rotamer_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><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"><span class="pre">FRMRotamerGroup</span></code></a>) – group of rotamers for energy calculation</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.Frame.AddFrameEnergy">
+<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>rotamer_group</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Frame.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculates and adds frame energies to the already existing frame
+energy values for all rotamers in the rotamer group.
+This is useful if you have several <a class="reference internal" href="#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> objects.</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"><strong>rotamer_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><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"><span class="pre">FRMRotamerGroup</span></code></a>) – group of rotamers for energy calculation</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+</div>
<div class="section" id="convenient-functions-for-constructing-frame-residues">
<h2>Convenient functions for constructing frame residues<a class="headerlink" href="#convenient-functions-for-constructing-frame-residues" title="Permalink to this headline">¶</a></h2>
<p>PROMOD3 offers some functionality to construct frame residues for standard
@@ -87,7 +167,7 @@ and sidechain frame residues.</p>
<li><strong>c_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of backbone carbon atom</li>
<li><strong>o_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of backbone oxygen atom</li>
<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of backbone c-beta carbon atom</li>
-<li><strong>id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.
Interactions to rotamers associated to the same
index are neglected.</li>
@@ -120,7 +200,7 @@ hbonds get considered.</li>
<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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which the backbone atoms are extracted.</li>
-<li><strong>id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.
Interactions to rotamers associated to the same
index are neglected.</li>
@@ -157,183 +237,47 @@ atoms are present in <strong>residue</strong></p>
<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="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which the sidechain atoms are extracted.</li>
-<li><strong>id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
particles.</li>
</ul>
</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"><span class="pre">RuntimeError</span></code> when not all required atoms
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> when not all required atoms
atoms are present in <strong>residue</strong></p>
</td>
</tr>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></p>
+</td>
+</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
<dt id="promod3.sidechain.ConstructFrameResidue">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em>, <em>settings</em><span class="optional">[</span>, <em>radius=[]</em>, <em>emin=[]</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.</code><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.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs a <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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.</p>
+there won’t be any parametrization of hbonds in this function. All
+Atoms of the residue will be represented as carbons.</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>residue</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Reside from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
-<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
-particles.</li>
-<li><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Radius for pseudo Lennard-Jones term in energy
-evaluation for every particle. If left empty,
-radius of carbon will be used for all particles.</li>
-<li><strong>emin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – Min energy for pseudo Lennard-Jones term in energy
-evaluation for every particle. If left empty,
-emin of carbon will be used for all particles.</li>
</ul>
</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"><span class="pre">RuntimeError</span></code> if size of radius and emin is not
-consistent.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</div>
-<div class="section" id="the-frame-objects">
-<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="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><p>The most simple way of constructing a frame residue is the usage
-of the convenient functions provided by PROMOD3.</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 last simple">
-<li><strong>particles</strong> – <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><span class="pre">Particle</span></code></a> objects building
-up the <a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></li>
-<li><strong>residue_index</strong> – Interaction energies between the constructed frame
-residue and any rotamer associated to the same
-residue index are neglected.</li>
-</ul>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a></p>
</td>
</tr>
</tbody>
</table>
-<dl class="method">
-<dt id="promod3.sidechain.FrameResidue.__len__">
-<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"><span class="pre">FrameResidue</span></code></a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.FrameResidue.__getitem__">
-<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 internal" href="rotamer.html#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><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"><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-class docutils literal"><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="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><table class="docutils field-list" frame="void" rules="none">
-<col class="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> – </td>
-</tr>
-</tbody>
-</table>
-<p>The <a class="reference internal" href="#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> object allows to calculate frame energies for rotamers.
-Due to technical reasons, this is only possible if the rotamers are
-part of rotamer groups.</p>
-<dl class="method">
-<dt id="promod3.sidechain.Frame.SetFrameEnergy">
-<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>rotamer_group</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Frame.SetFrameEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculates and sets frame energies</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"><strong>rotamer_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>) – group of rotamers for energy calculation</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>rotamer_group</em><span class="sig-paren">)</span></dt>
-<dd><p>Calculates and sets frame energies</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"><strong>rotamer_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – group of rotamers for energy calculation</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.Frame.AddFrameEnergy">
-<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>rotamer_group</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Frame.AddFrameEnergy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculates and adds frame energies to the already existing frame
-energy values. This might be useful if you have several <a class="reference internal" href="#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a>
-objects.</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"><strong>rotamer_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>) – group of rotamers for energy calculation</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<code class="descname">AddFrameEnergy</code><span class="sig-paren">(</span><em>rotamer_group</em><span class="sig-paren">)</span></dt>
-<dd><p>Calculates and adds frame energies to the already existing frame
-energy values. This might be useful if you have several <a class="reference internal" href="#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a>
-objects.</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"><strong>rotamer_group</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – group of rotamers for energy calculation</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
</dd></dl>
</div>
@@ -348,18 +292,24 @@ objects.</p>
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Frame</a><ul>
-<li><a class="reference internal" href="#convenient-functions-for-constructing-frame-residues">Convenient functions for constructing frame residues</a></li>
<li><a class="reference internal" href="#the-frame-objects">The Frame Objects</a></li>
+<li><a class="reference internal" href="#convenient-functions-for-constructing-frame-residues">Convenient functions for constructing frame residues</a></li>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="rotamer.html"
- title="previous chapter">Rotamers</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="rotamer_lib.html"
- title="next chapter">Rotamer Library</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li>Previous: <a href="rotamer.html" title="previous chapter">Rotamers</a></li>
+ <li>Next: <a href="rotamer_lib.html" title="next chapter">Rotamer Library</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -389,11 +339,11 @@ objects.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/sidechain/frame.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index e364e630098722b31ae499b1c8c101a9f3d06954..15dd3020f395965158601365ce7fa57066cfc06d 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="sidechain_settings.html" title="Rotamer Settings"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="rotamer_lib.html" title="Rotamer Library"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -75,9 +55,9 @@ and finally comes back with a solution.</p>
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">Graph</code><a class="headerlink" href="#promod3.sidechain.Graph" title="Permalink to this definition">¶</a></dt>
<dd><p>The Graph object has no constructor exported to python. It is meant to be
constructed using the static create functions.</p>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.sidechain.Graph.CreateFromRRMList">
-<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.Graph.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.Graph.CreateFromRRMList" 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" />
@@ -90,9 +70,9 @@ acid position.</td>
</table>
</dd></dl>
-<dl class="method">
+<dl class="staticmethod">
<dt id="promod3.sidechain.Graph.CreateFromFRMList">
-<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.Graph.CreateFromFRMList" title="Permalink to this definition">¶</a></dt>
+<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.Graph.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" />
@@ -112,7 +92,8 @@ acid position.</td>
and edge decomposition until the number of possible permutations, that
have to be enumerated in the resulting tree, fall below
<strong>max_complecity</strong>. In every iteration the epsilon value gets doubled to
-enforce more edges to be approximated by edge decomposition.</p>
+enforce more edges to be approximated by edge decomposition. This function
+assumes all self energies of the rotamers to be calculated and properly set!</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -196,7 +177,7 @@ nonzero interaction</td>
<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 number of nodes havind at least one edge, even
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The number of nodes having at least one edge, even
after performing pruning operations</td>
</tr>
</tbody>
@@ -235,13 +216,19 @@ even after performing pruning operations</td>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="rotamer_lib.html"
- title="previous chapter">Rotamer Library</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="sidechain_settings.html"
- title="next chapter">Rotamer Settings</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><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="sidechain_settings.html" title="next chapter">Rotamer Settings</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -271,11 +258,11 @@ even after performing pruning operations</td>
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Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/sidechain/graph.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
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diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index 9e7769fefc2b134aed00339937e448a230ba6304..fe5f41669c14a9c8a71fd6537d548019f1fe7104 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
- <link rel="up" title="Documentation For Developes" href="../developers.html" />
+ <link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="RotamerID" href="rotamer_id.html" />
<link rel="prev" title="Load Loop Objects" href="../loop/load_loop_objects.html" />
@@ -32,26 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="rotamer_id.html" title="RotamerID"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="../loop/load_loop_objects.html" title="Load Loop Objects"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" accesskey="U">Documentation For Developes</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
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@@ -61,17 +42,29 @@
<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"><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:</p>
-<p>G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr.
-Improved prediction of protein side-chain conformations with SCWRL4.
-Proteins (2009).</p>
-<p>The 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>
-<p>The most simple way though is the usage of following function:</p>
+The full module is heavily based on SCWRL4 <a class="reference internal" href="#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>
+<div class="section" id="reconstruct-function">
+<h2>Reconstruct Function<a class="headerlink" href="#reconstruct-function" title="Permalink to this headline">¶</a></h2>
+<p>The simplest usage of the module is provided by the <a class="reference internal" href="#promod3.sidechain.reconstruct_sidechains.Reconstruct" title="promod3.sidechain.reconstruct_sidechains.Reconstruct"><code class="xref py py-func docutils literal"><span class="pre">Reconstruct()</span></code></a> function:</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3.sidechain</span> <span class="kn">import</span> <span class="n">reconstruct_sidechains</span>
+
+<span class="c">#load a protein</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'1eye'</span><span class="p">,</span><span class="n">remote</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+<span class="c">#get only amino acids</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"peptide=true"</span><span class="p">),</span><span class="bp">True</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span><span class="s">"sidechain_test_orig.pdb"</span><span class="p">)</span>
+<span class="c">#reconstruct sidechains</span>
+<span class="n">reconstruct_sidechains</span><span class="o">.</span><span class="n">Reconstruct</span><span class="p">(</span><span class="n">prot</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span><span class="s">"sidechain_test_rec.pdb"</span><span class="p">)</span>
+</pre></div>
+</div>
<dl class="method">
<dt id="promod3.sidechain.reconstruct_sidechains.Reconstruct">
-<code class="descclassname">promod3.sidechain.reconstruct_sidechains.</code><code class="descname">Reconstruct</code><span class="sig-paren">(</span><em>prot</em><span class="optional">[</span>, <em>keep_sidechains=False</em>, <em>build_disulfids</em>, <em>rotamer_model="frm"</em>, <em>consider_hbonds=True</em>, <em>rotamer_library=None</em><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/sidechain/reconstruct_sidechains.html#Reconstruct"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.sidechain.reconstruct_sidechains.Reconstruct" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.sidechain.reconstruct_sidechains.</code><code class="descname">Reconstruct</code><span class="sig-paren">(</span><em>prot</em><span class="optional">[</span>, <em>keep_sidechains=False</em>, <em>build_disulfids</em>, <em>rotamer_model="frm"</em>, <em>consider_hbonds=True</em>, <em>rotamer_library=None</em>, <em>add_polar_hydrogens=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/sidechain/reconstruct_sidechains.html#Reconstruct"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.sidechain.reconstruct_sidechains.Reconstruct" title="Permalink to this definition">¶</a></dt>
<dd><p>The function takes a structure and reconstructs its sidechains given the input
parameters.</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -92,9 +85,14 @@ the frame.</li>
<li><strong>rotamer_model</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Rotamer model to be used, can either be “frm” or “rrm”</li>
<li><strong>consider_hbonds</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether hbonds should be evaluated in the energy
function. If set to False, no hydrogens will be built
-when building rotamers and frame.</li>
-<li><strong>rotamer_library</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – A backbone dependent rotamer library to extract the
+when building rotamers and frame and the <strong>add_polar_hydrogens</strong>
+flag won’t have any consequences.</li>
+<li><strong>rotamer_library</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a> / <a class="reference internal" href="rotamer_lib.html#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a>) – A rotamer library to extract the
rotamers from.</li>
+<li><strong>add_polar_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – All polar hydrogens will be constructed if
+<strong>consider_hbonds</strong> is True.
+If this flag is activated, they’ll be added to the
+structure.</li>
</ul>
</td>
</tr>
@@ -102,20 +100,23 @@ rotamers from.</li>
</table>
</dd></dl>
-<p>Following code fragment shows an example of a basic sidechain reconstruction
+</div>
+<div class="section" id="sidechain-module-functionality">
+<h2>Sidechain Module Functionality<a class="headerlink" href="#sidechain-module-functionality" title="Permalink to this headline">¶</a></h2>
+<p>The following code fragment shows an example of a basic sidechain reconstruction
algorithm using the functionality in the module. Note, that this code will
crash as soon as you have structures containing all the weirdness the PDB throws
-at us. In this case you should use the Reconstruct function above. An overview
-of the full provided functionality can be found at the bottom of this page.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">sidechain</span>
+at us. In this case, you should use the <a class="reference internal" href="#promod3.sidechain.reconstruct_sidechains.Reconstruct" title="promod3.sidechain.reconstruct_sidechains.Reconstruct"><code class="xref py py-func docutils literal"><span class="pre">Reconstruct()</span></code></a> function above. An overview of the full provided functionality can be found at the bottom of this page.</p>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">sidechain</span>
<span class="c">#load a protein, the rotamer library and the settings with default values</span>
-<span class="n">prot</span><span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'1eye'</span><span class="p">,</span><span class="n">remote</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'1eye'</span><span class="p">,</span><span class="n">remote</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
<span class="n">settings</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">RotamerSettings</span><span class="p">()</span>
<span class="n">library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadDunbrackLib</span><span class="p">()</span>
<span class="c">#let's create a new entity from the protein only containing the amino acids</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">ost</span><span class="o">.</span><span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"peptide=true"</span><span class="p">),</span><span class="bp">True</span><span class="p">)</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"peptide=true"</span><span class="p">),</span><span class="bp">True</span><span class="p">)</span>
<span class="c">#gather some data, the rotamer ids and backbone torsion angles</span>
<span class="n">torsion_angles</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
@@ -145,10 +146,8 @@ of the full provided functionality can be found at the bottom of this page.</p>
<span class="n">torsion_angles</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span>
<span class="n">i</span> <span class="o">==</span> <span class="mi">1</span><span class="p">,</span>
<span class="n">i</span> <span class="o">==</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">rotamer_ids</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
-
<span class="n">frame_residues</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">frame_residue</span><span class="p">)</span>
-
<span class="n">frame</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">Frame</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">)</span>
@@ -168,7 +167,7 @@ of the full provided functionality can be found at the bottom of this page.</p>
<span class="c">#internal and frame energy have to be calculated directly</span>
<span class="n">rot_group</span><span class="o">.</span><span class="n">CalculateInternalEnergies</span><span class="p">()</span>
<span class="n">frame</span><span class="o">.</span><span class="n">SetFrameEnergy</span><span class="p">(</span><span class="n">rot_group</span><span class="p">)</span>
- <span class="c">#remove supper unlikely rotamer in rotamer group</span>
+ <span class="c">#remove super unlikely rotamer in rotamer group</span>
<span class="c">#e.g. those who clash with the frame</span>
<span class="n">rot_group</span><span class="o">.</span><span class="n">ApplySelfEnergyThresh</span><span class="p">()</span>
<span class="c">#finally add it and keep track of the indices</span>
@@ -198,19 +197,20 @@ of the full provided functionality can be found at the bottom of this page.</p>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="rotamer.html">Rotamers</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="rotamer.html#convenient-functions-for-constructing-rotamers">Convenient functions for constructing rotamers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="rotamer.html#convenient-functions-for-constructing-rotamer-groups">Convenient functions for constructing rotamer groups</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer.html#the-smallest-building-block-the-particle">The Smallest Building Block - The Particle</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer.html#id1">Rotamers</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer.html#rotamer-groups">Rotamer Groups</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rotamer.html#convenient-functions-for-constructing-rotamers">Convenient functions for constructing rotamers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rotamer.html#convenient-functions-for-constructing-rotamer-groups">Convenient functions for constructing rotamer groups</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="frame.html">Frame</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="frame.html#convenient-functions-for-constructing-frame-residues">Convenient functions for constructing frame residues</a></li>
<li class="toctree-l2"><a class="reference internal" href="frame.html#the-frame-objects">The Frame Objects</a></li>
+<li class="toctree-l2"><a class="reference internal" href="frame.html#convenient-functions-for-constructing-frame-residues">Convenient functions for constructing frame residues</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="rotamer_lib.html">Rotamer Library</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-non-backbone-dependent-rotamer-library">The Non Backbone Dependent Rotamer Library</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-backbone-dependent-rotamer-library">The Backbone Dependent Rotamer Library</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-library-entry-type">The Library Entry Type</a></li>
</ul>
@@ -223,6 +223,13 @@ of the full provided functionality can be found at the bottom of this page.</p>
<li class="toctree-l1"><a class="reference internal" href="disulfid.html">Disulfid Bond Evaluation</a></li>
</ul>
</div>
+<table class="docutils citation" frame="void" id="krivov2009" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label"><a class="fn-backref" href="#id1">[krivov2009]</a></td><td>Krivov GG, Shapovalov MV and Dunbrack RL Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins.</td></tr>
+</tbody>
+</table>
+</div>
</div>
@@ -231,12 +238,25 @@ of the full provided functionality can be found at the bottom of this page.</p>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="../loop/load_loop_objects.html"
- title="previous chapter">Load Loop Objects</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="rotamer_id.html"
- title="next chapter">RotamerID</a></p>
+ <h3><a href="../index.html">Table Of Contents</a></h3>
+ <ul>
+<li><a class="reference internal" href="#"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+<li><a class="reference internal" href="#reconstruct-function">Reconstruct Function</a></li>
+<li><a class="reference internal" href="#sidechain-module-functionality">Sidechain Module Functionality</a></li>
+</ul>
+</li>
+</ul>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li>Previous: <a href="../loop/load_loop_objects.html" title="previous chapter">Load Loop Objects</a></li>
+ <li>Next: <a href="rotamer_id.html" title="next chapter">RotamerID</a></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -266,11 +286,11 @@ of the full provided functionality can be found at the bottom of this page.</p>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/sidechain/index.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index 860bde8174fa0076c852dd329547b82c54b19cb7..e5358184905bbf807601896556a77b8d1f891b59 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="frame.html" title="Frame"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="rotamer_id.html" title="RotamerID"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -70,323 +50,40 @@ PROMOD3 has the <a class="reference internal" href="#promod3.sidechain.RRMRotame
Rotamers are not intended to be built from scratch.
PROMOD3 offers a built-in construction function, directly accessing a
<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>.</p>
-<div class="section" id="convenient-functions-for-constructing-rotamers">
-<h2>Convenient functions for constructing rotamers<a class="headerlink" href="#convenient-functions-for-constructing-rotamers" title="Permalink to this headline">¶</a></h2>
-<p>PROMOD3 offers some functionality to directly access a
-<code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLibrary</span></code> and build single rotamers as well as
-rotamer groups.</p>
-<dl class="method">
-<dt id="promod3.sidechain.ConstructRRMRotamer">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructRRMRotamer</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>rotamer_id</em>, <em>settings</em>, <em>probability</em><span class="optional">[</span>, <em>chi1=NaN</em>, <em>chi2=NaN</em>, <em>chi3=NaN</em>, <em>chi4=NaN</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ConstructRRMRotamer" 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>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of nitrogen used as anchor for the rotamer</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of alpha carbon used as anchor for the rotamer</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of beta carbon used as anchor for the rotamer</li>
-<li><strong>rotamer_id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></li>
-<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
-particles.</li>
-<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of occurence of this particular rotamer.</li>
-<li><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – First sidechain dihedral angle</li>
-<li><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Second sidechain dihedral angle</li>
-<li><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Third sidechain dihedral angle</li>
-<li><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Fourth sidechain dihedral angle</li>
-</ul>
-</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"><span class="pre">RuntimeError</span></code> if not all required chi angles
-for this particular <strong>id</strong> are given.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructRRMRotamer</code><span class="sig-paren">(</span><em>residue</em>, <em>rotamer_id</em>, <em>settings</em>, <em>probability</em><span class="optional">[</span>, <em>chi1=NaN</em>, <em>chi2=NaN</em>, <em>chi3=NaN</em>, <em>chi4=NaN</em><span class="optional">]</span><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>residue</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResideHandle</span></code>) – Residue from which the anchor positions will be
-extracted</li>
-<li><strong>rotamer_id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></li>
-<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
-particles.</li>
-<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of occurence of this particular rotamer.</li>
-<li><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – First sidechain dihedral angle</li>
-<li><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Second sidechain dihedral angle</li>
-<li><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Third sidechain dihedral angle</li>
-<li><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Fourth sidechain dihedral angle</li>
-</ul>
-</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"><span class="pre">RuntimeError</span></code> if not all required chi angles
-for this particular <strong>id</strong> are given or when not
-all required anchor atoms are present in
-<strong>residue</strong>.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.ConstructFRMRotamer">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFRMRotamer</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>rotamer_id</em>, <em>settings</em>, <em>probability</em><span class="optional">[</span>, <em>chi1=NaN</em>, <em>sig1=NaN</em>, <em>chi2=NaN</em>, <em>sig2=NaN</em>, <em>chi3=NaN</em>, <em>sig3=NaN</em>, <em>chi4=NaN</em>, <em>sig4=NaN</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ConstructFRMRotamer" 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>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of nitrogen used as anchor for the rotamer</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of alpha carbon used as anchor for the rotamer</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of beta carbon used as anchor for the rotamer</li>
-<li><strong>rotamer_id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></li>
-<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
-particles.</li>
-<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of occurence of this particular rotamer.</li>
-<li><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – First sidechain dihedral angle</li>
-<li><strong>sig1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of first dihedral angle</li>
-<li><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Second sidechain dihedral angle</li>
-<li><strong>sig2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of second dihedral angle</li>
-<li><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Third sidechain dihedral angle</li>
-<li><strong>sig3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of third dihedral angle</li>
-<li><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Fourth sidechain dihedral angle</li>
-<li><strong>sig4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of fourth dihedral angle</li>
-</ul>
-</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"><span class="pre">RuntimeError</span></code> if not all required chi angles
-for this particular <strong>id</strong> are given.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFRMRotamer</code><span class="sig-paren">(</span><em>residue</em>, <em>rotamer_id</em>, <em>settings</em>, <em>probability</em><span class="optional">[</span>, <em>chi1=NaN</em>, <em>sig1=NaN</em>, <em>chi2=NaN</em>, <em>sig2=NaN</em>, <em>chi3=NaN</em>, <em>sig3=NaN</em>, <em>chi4=NaN</em>, <em>sig4=NaN</em><span class="optional">]</span><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>residue</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResideHandle</span></code>) – Residue from which the anchor positions will be
-extracted</li>
-<li><strong>rotamer_id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></li>
-<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
-particles.</li>
-<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of occurence of this particular rotamer.</li>
-<li><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – First sidechain dihedral angle</li>
-<li><strong>sig1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of first dihedral angle</li>
-<li><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Second sidechain dihedral angle</li>
-<li><strong>sig2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of second dihedral angle</li>
-<li><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Third sidechain dihedral angle</li>
-<li><strong>sig3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of third dihedral angle</li>
-<li><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Fourth sidechain dihedral angle</li>
-<li><strong>sig4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of fourth dihedral angle</li>
-</ul>
-</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"><span class="pre">RuntimeError</span></code> if not all required chi angles
-or standard deviations for this particular <strong>id</strong>
-are given or when not all required anchor atoms are present in
-<strong>residue</strong>.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</div>
-<div class="section" id="convenient-functions-for-constructing-rotamer-groups">
-<h2>Convenient functions for constructing rotamer groups<a class="headerlink" href="#convenient-functions-for-constructing-rotamer-groups" title="Permalink to this headline">¶</a></h2>
-<p>Instead of building single rotamers, following convenient functions query a
-rotamer library and build all possible rotamers for a particular residue
-position. If hbond scoring is enabled (<strong>settings</strong>) several rotamers might be
-constructed and added to the group per library instance:</p>
-<ol class="arabic simple">
-<li>SER construct three rotamers with hydrogen chi angles 180,-60 and 60</li>
-<li>THR construct three rotamers with hydrogen chi angles 180,-60 and 60</li>
-<li>TYR construct two rotamers with hydrogen chi angles 180 and 0</li>
-<li>HIS construct both possible protonation states (HSE,HSD)</li>
-</ol>
-<span class="target" id="rotamer-group-construction-label"></span><dl class="method">
-<dt id="promod3.sidechain.ConstructRRMRotamerGroup">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="optional">[</span>, <em>phi=-1.0472</em>, <em>psi=1.0472</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ConstructRRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects. It extracts rotamers
-from <em>rot_lib</em> and adds them to the group until the summed probability
-reaches the probability cutoff defined in <strong>settings</strong>.</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 last simple">
-<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of nitrogen used as anchor for the rotamers</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of alpha carbon used as anchor for the rotamers</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of beta carbon used as anchor for the rotamers</li>
-<li><strong>rotamer_id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects in constructed
-<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
-the frame energy. Interactions to frame residues with
-same index get neglected.</li>
-<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Library from which the data is taken to construct the
-rotamers.</li>
-<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
-particles.</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle used as input for backbone
-dependent rotamer library. Default value is a typical
-alpha helical value.</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle used as input for backbone
-dependent rotamer library. Default value is a typical
-alpha helical value.</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>residue</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="optional">[</span>, <em>phi=-1.0472</em>, <em>psi=1.0472</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
-<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects. It extracts rotamers
-from <em>rot_lib</em> and adds them to the group until the summed probability
-reaches the probability cutoff defined in <strong>settings</strong>.</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>residue</strong> – Residue from which the anchor positions will be
-extracted</li>
-<li><strong>rotamer_id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects in constructed
-<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
-the frame energy. Interactions to frame residues with
-same index get neglected.</li>
-<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Library from which the data is taken to construct the
-rotamers.</li>
-<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
-particles.</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle used as input for backbone
-dependent rotamer library. Default value is a typical
-alpha helical value.</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle used as input for backbone
-dependent rotamer library. Default value is a typical
-alpha helical value.</li>
-</ul>
-</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"><span class="pre">RuntimeError</span></code> if not all required anchor atoms
-are present in <strong>residue</strong>.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.ConstructFRMRotamerGroup">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFRMRotamerGroup</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="optional">[</span>, <em>phi=-1.0472</em>, <em>psi=1.0472</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ConstructFRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects. It extracts rotamers
-from <em>rot_lib</em> and adds them to the group until the summed probability
-reaches the probability cutoff defined in <strong>settings</strong>.</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 last simple">
-<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of nitrogen used as anchor for the rotamers</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of alpha carbon used as anchor for the rotamers</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of beta carbon used as anchor for the rotamers</li>
-<li><strong>rotamer_id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects in constructed
-<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
-the frame energy. Interactions to frame residues with
-same index get neglected.</li>
-<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Library from which the data is taken to construct the
-rotamers.</li>
-<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
-particles.</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle used as input for backbone
-dependent rotamer library. Default value is a typical
-alpha helical value.</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle used as input for backbone
-dependent rotamer library. Default value is a typical
-alpha helical value.</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt>
-<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFRMRotamerGroup</code><span class="sig-paren">(</span><em>residue</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="optional">[</span>, <em>phi=-1.0472</em>, <em>psi=1.0472</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
-<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects. It extracts rotamers
-from <em>rot_lib</em> and adds them to the group until the summed probability
-reaches the probability cutoff defined in <strong>settings</strong>.</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>residue</strong> – Residue from which the anchor positions will be
-extracted</li>
-<li><strong>rotamer_id</strong> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></li>
-<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects in constructed
-<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
-the frame energy. Interactions to frame residues with
-same index get neglected.</li>
-<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Library from which the data is taken to construct the
-rotamers.</li>
-<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
-particles.</li>
-<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle used as input for backbone
-dependent rotamer library. Default value is a typical
-alpha helical value.</li>
-<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle used as input for backbone
-dependent rotamer library. Default value is a typical
-alpha helical value.</li>
+<div class="section" id="the-smallest-building-block-the-particle">
+<h2>The Smallest Building Block - The Particle<a class="headerlink" href="#the-smallest-building-block-the-particle" title="Permalink to this headline">¶</a></h2>
+<p>Particles give raise to more complex objects such as rotamers and frame residues.
+They are the basis for calculating interaction energies based on a Lennard-Jones
+like term and an approximation of an hbond energy term.
+The Lennard-Jones term gets mainly controlled by the type of the particle, that
+has to be defined at initialization.</p>
+<dl class="class">
+<dt id="promod3.sidechain.SidechainParticle">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SidechainParticle</code><a class="headerlink" href="#promod3.sidechain.SidechainParticle" title="Permalink to this definition">¶</a></dt>
+<dd><p>Enumerates the types of particle. Possible values:</p>
+<ul class="simple">
+<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>
-</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"><span class="pre">RuntimeError</span></code> if not all required anchor atoms
-are present in <strong>residue</strong>.</p>
-</td>
-</tr>
-</tbody>
-</table>
</dd></dl>
-</div>
-<div class="section" id="the-smallest-building-block-the-particle">
-<h2>The Smallest Building Block - The Particle<a class="headerlink" href="#the-smallest-building-block-the-particle" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.Particle">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">Particle</code><span class="sig-paren">(</span><em>pos</em>, <em>radius</em>, <em>r</em>, <em>emin</em>, <em>charge</em>, <em>name</em><span class="sig-paren">)</span><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><span class="sig-paren">(</span><em>type</em>, <em>pos</em>, <em>charge</em>, <em>name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle" 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>type</strong> (<a class="reference internal" href="#promod3.sidechain.SidechainParticle" title="promod3.sidechain.SidechainParticle"><code class="xref py py-class docutils literal"><span class="pre">SidechainParticle</span></code></a>) – Type of particle</li>
<li><strong>pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Positions of particle</li>
-<li><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Expected distance, this particle gives
-raise to nonzero interactions. This parameter is used
-for the internal collision detection algorithm.
-If two particles have a nonzero interaction energy up to
-3 Angstrom, their radius should be at least 1.5.</li>
-<li><strong>r</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Distance for pseudo Lennard-Jones interaction term</li>
-<li><strong>emin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Emin for pseudo Lennard-Jones interaction term</li>
<li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Charge of particle, will be used in case H-Bonds</li>
<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of particle. This name will be given to an actual
<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> if a rotamer gets applied
@@ -426,39 +123,26 @@ to a <a class="reference external" href="http://www.openstructure.org/docs/1.3/m
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.Particle.GetRadius">
-<code class="descname">GetRadius</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetRadius" 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 distance of pseudo Lennard-Jones Term</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.Particle.GetEMin">
-<code class="descname">GetEMin</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetEMin" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.sidechain.Particle.GetCharge">
+<code class="descname">GetCharge</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetCharge" 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">EMin of pseudo Lennart-Jones Term</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Charge of particle used for HBond term</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.Particle.GetCharge">
-<code class="descname">GetCharge</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetCharge" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.sidechain.Particle.GetParticleType">
+<code class="descname">GetParticleType</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.Particle.GetParticleType" 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">Charge of particle used for HBond term</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Internal type of particle</td>
</tr>
</tbody>
</table>
@@ -942,214 +626,566 @@ energy has to be calculated using a <a class="reference internal" href="frame.ht
</dd></dl>
<dl class="method">
-<dt>
-<code class="descname">GetFrameEnergy</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span></dt>
-<dd><p>Returns previously calculated frame energy of the subrotamer specified by
-<strong>index</strong>, this energy has to be 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"><span class="pre">Frame</span></code></a>.</p>
+<dt>
+<code class="descname">GetFrameEnergy</code><span class="sig-paren">(</span><em>index</em><span class="sig-paren">)</span></dt>
+<dd><p>Returns previously calculated frame energy of the subrotamer specified by
+<strong>index</strong>, this energy has to be 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"><span class="pre">Frame</span></code></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"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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-class docutils literal"><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="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="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="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.SetInternalEnergy">
+<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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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.SetInternalEnergyPrefactor">
+<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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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.SetFrameEnergy">
+<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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Frame energy for full rotamer to be set to be set</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt>
+<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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Frame energy for single subrotamer to be set to be set</li>
+<li><strong>index</strong> – Index of subrotamer</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.FRMRotamer.SetTemperature">
+<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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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="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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal probability to be set</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="rotamer-groups">
+<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="descclassname">promod3.sidechain.</code><code class="descname">RRMRotamerGroup</code><span class="sig-paren">(</span><em>rotamers</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"><span class="pre">RRMRotamer</span></code></a> objects for the same
+residue position. It can either be constructed by providing a list of
+<a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects or by convenience functions provided by PROMOD3.</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"><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><span class="pre">RRMRotamer</span></code></a> objects</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if provided <strong>rotamers</strong> is empty</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.sidechain.RRMRotamerGroup.__len__">
+<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="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"><span class="pre">RRMRotamer</span></code></a> at given <strong>index</strong></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is invalid</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.RRMRotamerGroup.ApplyOneResidue">
+<code class="descname">ApplyOneResidue</code><span class="sig-paren">(</span><em>index</em>, <em>res</em><span class="optional">[</span>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplyOneResidue" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calls ApplyOnResidue function on rotamer at position <strong>index</strong></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"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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 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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
+<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
+default value (“”)</li>
+</ul>
+</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if index is invalid</td>
+<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"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
+are present in <strong>res</strong> or when <strong>index</strong> is invalid</p>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.FRMRotamer.GetSelfEnergy">
-<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">
+<dt id="promod3.sidechain.RRMRotamerGroup.Merge">
+<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 <strong>other</strong> to current <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></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">Returns:</th><td class="field-body">Self energy consisting of internal plus frame energy</td>
+<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"><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.FRMRotamer.GetTemperature">
-<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">
+<dt id="promod3.sidechain.RRMRotamerGroup.CalculateInternalEnergies">
+<code class="descname">CalculateInternalEnergies</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.CalculateInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculates internal energies of all rotamers in group</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThres">
+<code class="descname">ApplySelfEnergyThres</code><span class="sig-paren">(</span><span class="optional">[</span><em>thresh=30</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplySelfEnergyThres" title="Permalink to this definition">¶</a></dt>
+<dd><p>Searches rotamer with lowest self energy <strong>l_e</strong> and deletes all
+rotamers with <strong>self_energy</strong> > <strong>l_e</strong> + <strong>thresh</strong></p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.sidechain.FRMRotamerGroup">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">FRMRotamerGroup</code><span class="sig-paren">(</span><em>rotamers</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"><span class="pre">FRMRotamer</span></code></a> objects for the same
+residue position. It can either be constructed by providing a list of
+<a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects or by convenience functions provided by PROMOD3.</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">Returns:</th><td class="field-body">The temperature factor for this rotamer</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><span class="pre">FRMRotamer</span></code></a> objects</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if provided <strong>rotamers</strong> is empty</td>
</tr>
</tbody>
</table>
-</dd></dl>
-
<dl class="method">
-<dt id="promod3.sidechain.FRMRotamer.GetProbability">
-<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>
+<dt id="promod3.sidechain.FRMRotamerGroup.__len__">
+<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">Probability of this rotamer</td>
+<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.FRMRotamer.SetInternalEnergy">
-<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>
+<dt id="promod3.sidechain.FRMRotamerGroup.__getitem__">
+<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">Parameters:</th><td class="field-body"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal energy to be set</td>
+<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"><span class="pre">FRMRotamer</span></code></a> at given <strong>index</strong></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is invalid</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.FRMRotamer.SetInternalEnergyPrefactor">
-<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">
+<dt id="promod3.sidechain.FRMRotamerGroup.ApplyOneResidue">
+<code class="descname">ApplyOneResidue</code><span class="sig-paren">(</span><em>index</em>, <em>res</em><span class="optional">[</span>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplyOneResidue" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calls ApplyOnResidue function on rotamer at position <strong>index</strong></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"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal energy prefactor to be set</td>
+<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/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
+<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
+default value (“”)</li>
+</ul>
+</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"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
+are present in <strong>res</strong> or when <strong>index</strong> is invalid</p>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.FRMRotamer.SetFrameEnergy">
-<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">
+<dt id="promod3.sidechain.FRMRotamerGroup.Merge">
+<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 <strong>other</strong> to current <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></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"><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Frame energy for full rotamer to be set to be set</td>
+<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"><span class="pre">FRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt>
-<code class="descname">SetFrameEnergy</code><span class="sig-paren">(</span><em>energy</em>, <em>index</em><span class="sig-paren">)</span></dt>
+<dt id="promod3.sidechain.FRMRotamerGroup.CalculateInternalEnergies">
+<code class="descname">CalculateInternalEnergies</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.CalculateInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculates internal energies of all rotamers in group</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThres">
+<code class="descname">ApplySelfEnergyThres</code><span class="sig-paren">(</span><span class="optional">[</span><em>thresh=30</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThres" title="Permalink to this definition">¶</a></dt>
+<dd><p>Searches rotamer with lowest self energy <strong>l_e</strong> and deletes all
+rotamers with <strong>self_energy</strong> > <strong>l_e</strong> + <strong>thresh</strong></p>
+</dd></dl>
+
+</dd></dl>
+
+</div>
+<div class="section" id="convenient-functions-for-constructing-rotamers">
+<h2>Convenient functions for constructing rotamers<a class="headerlink" href="#convenient-functions-for-constructing-rotamers" title="Permalink to this headline">¶</a></h2>
+<p>PROMOD3 offers some functionality to directly access a
+<code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLibrary</span></code> and build single rotamers as well as
+rotamer groups.</p>
+<dl class="method">
+<dt id="promod3.sidechain.ConstructRRMRotamer">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructRRMRotamer</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>rotamer_id</em>, <em>settings</em>, <em>probability</em><span class="optional">[</span>, <em>chi1=NaN</em>, <em>chi2=NaN</em>, <em>chi3=NaN</em>, <em>chi4=NaN</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ConstructRRMRotamer" 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>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Frame energy for single subrotamer to be set to be set</li>
-<li><strong>index</strong> – Index of subrotamer</li>
+<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="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of nitrogen used as anchor for the rotamer</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of alpha carbon used as anchor for the rotamer</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of beta carbon used as anchor for the rotamer</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of occurence of this particular rotamer.</li>
+<li><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – First sidechain dihedral angle</li>
+<li><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Second sidechain dihedral angle</li>
+<li><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Third sidechain dihedral angle</li>
+<li><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Fourth sidechain dihedral angle</li>
</ul>
</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"><span class="pre">RuntimeError</span></code> if not all required chi angles
+for this particular <strong>id</strong> are given.</p>
+</td>
+</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.FRMRotamer.SetTemperature">
-<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>
+<dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructRRMRotamer</code><span class="sig-paren">(</span><em>residue</em>, <em>rotamer_id</em>, <em>settings</em>, <em>probability</em><span class="optional">[</span>, <em>chi1=NaN</em>, <em>chi2=NaN</em>, <em>chi3=NaN</em>, <em>chi4=NaN</em><span class="optional">]</span><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"><strong>temperature</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Temperature factor for this rotamer</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>residue</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResideHandle</span></code>) – Residue from which the anchor positions will be
+extracted</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of occurence of this particular rotamer.</li>
+<li><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – First sidechain dihedral angle</li>
+<li><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Second sidechain dihedral angle</li>
+<li><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Third sidechain dihedral angle</li>
+<li><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Fourth sidechain dihedral angle</li>
+</ul>
+</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"><span class="pre">RuntimeError</span></code> if not all required chi angles
+for this particular <strong>id</strong> are given or when not
+all required anchor atoms are present in
+<strong>residue</strong>.</p>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.FRMRotamer.SetProbability">
-<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>
+<dt id="promod3.sidechain.ConstructFRMRotamer">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFRMRotamer</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>rotamer_id</em>, <em>settings</em>, <em>probability</em><span class="optional">[</span>, <em>chi1=NaN</em>, <em>sig1=NaN</em>, <em>chi2=NaN</em>, <em>sig2=NaN</em>, <em>chi3=NaN</em>, <em>sig3=NaN</em>, <em>chi4=NaN</em>, <em>sig4=NaN</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ConstructFRMRotamer" 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/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Internal probability to be set</td>
+<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="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of nitrogen used as anchor for the rotamer</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of alpha carbon used as anchor for the rotamer</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of beta carbon used as anchor for the rotamer</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of occurence of this particular rotamer.</li>
+<li><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – First sidechain dihedral angle</li>
+<li><strong>sig1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of first dihedral angle</li>
+<li><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Second sidechain dihedral angle</li>
+<li><strong>sig2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of second dihedral angle</li>
+<li><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Third sidechain dihedral angle</li>
+<li><strong>sig3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of third dihedral angle</li>
+<li><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Fourth sidechain dihedral angle</li>
+<li><strong>sig4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of fourth dihedral angle</li>
+</ul>
+</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"><span class="pre">RuntimeError</span></code> if not all required chi angles
+for this particular <strong>id</strong> are given.</p>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
-</dd></dl>
-
-</div>
-<div class="section" id="rotamer-groups">
-<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="descclassname">promod3.sidechain.</code><code class="descname">RRMRotamerGroup</code><span class="sig-paren">(</span><em>rotamers</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"><span class="pre">RRMRotamer</span></code></a> objects for the same
-residue position. It can either be constructed by providing a list of
-<a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects or by convenience functions provided by PROMOD3.</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"><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><span class="pre">RRMRotamer</span></code></a> objects</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if provided <strong>rotamers</strong> is empty</td>
-</tr>
-</tbody>
-</table>
<dl class="method">
-<dt id="promod3.sidechain.RRMRotamerGroup.__len__">
-<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>
+<dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFRMRotamer</code><span class="sig-paren">(</span><em>residue</em>, <em>rotamer_id</em>, <em>settings</em>, <em>probability</em><span class="optional">[</span>, <em>chi1=NaN</em>, <em>sig1=NaN</em>, <em>chi2=NaN</em>, <em>sig2=NaN</em>, <em>chi3=NaN</em>, <em>sig3=NaN</em>, <em>chi4=NaN</em>, <em>sig4=NaN</em><span class="optional">]</span><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">Number of rotamers in group</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>residue</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResideHandle</span></code>) – Residue from which the anchor positions will be
+extracted</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+<li><strong>probability</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Probability of occurence of this particular rotamer.</li>
+<li><strong>chi1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – First sidechain dihedral angle</li>
+<li><strong>sig1</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of first dihedral angle</li>
+<li><strong>chi2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Second sidechain dihedral angle</li>
+<li><strong>sig2</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of second dihedral angle</li>
+<li><strong>chi3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Third sidechain dihedral angle</li>
+<li><strong>sig3</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of third dihedral angle</li>
+<li><strong>chi4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Fourth sidechain dihedral angle</li>
+<li><strong>sig4</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Standard deviation of fourth dihedral angle</li>
+</ul>
+</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"><span class="pre">RuntimeError</span></code> if not all required chi angles
+or standard deviations for this particular <strong>id</strong>
+are given or when not all required anchor atoms are present in
+<strong>residue</strong>.</p>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
-<dl class="method">
-<dt id="promod3.sidechain.RRMRotamerGroup.__getitem__">
-<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">
+</div>
+<div class="section" id="convenient-functions-for-constructing-rotamer-groups">
+<h2>Convenient functions for constructing rotamer groups<a class="headerlink" href="#convenient-functions-for-constructing-rotamer-groups" title="Permalink to this headline">¶</a></h2>
+<p>Instead of building single rotamers, following convenient functions query a
+rotamer library and build all possible rotamers for a particular residue
+position. If hbond scoring is enabled and sample_polar_hydrogens is true (<strong>settings</strong>),
+several rotamers might be constructed and added to the group per library instance:</p>
+<ol class="arabic simple">
+<li>SER construct three rotamers with hydrogen chi angles 180,-60 and 60</li>
+<li>THR construct three rotamers with hydrogen chi angles 180,-60 and 60</li>
+<li>TYR construct two rotamers with hydrogen chi angles 180 and 0</li>
+<li>HIS construct both possible protonation states (HSE,HSD)</li>
+</ol>
+<span class="target" id="rotamer-group-construction-label"></span><dl class="method">
+<dt id="promod3.sidechain.ConstructRRMRotamerGroup">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="optional">[</span>, <em>phi=-1.0472</em>, <em>psi=-0.7854</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ConstructRRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
+<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects. It extracts rotamers
+from <em>rot_lib</em> and adds them to the group until the summed probability
+reaches the probability cutoff defined in <strong>settings</strong>.</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">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"><span class="pre">RRMRotamer</span></code></a> at given <strong>index</strong></td>
-</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is invalid</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of nitrogen used as anchor for the rotamers</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of alpha carbon used as anchor for the rotamers</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of beta carbon used as anchor for the rotamers</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects in constructed
+<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
+the frame energy. Interactions to frame residues with
+same index get neglected.</li>
+<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Library from which the data is taken to construct the
+rotamers.</li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle used as input for backbone
+dependent rotamer library. Default value is a typical
+alpha helical value.</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle used as input for backbone
+dependent rotamer library. Default value is a typical
+alpha helical value.</li>
+</ul>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.RRMRotamerGroup.ApplyOneResidue">
-<code class="descname">ApplyOneResidue</code><span class="sig-paren">(</span><em>index</em>, <em>res</em><span class="optional">[</span>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamerGroup.ApplyOneResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calls ApplyOnResidue function on rotamer at position <strong>index</strong></p>
+<dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>residue</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="optional">[</span>, <em>phi=-1.0472</em>, <em>psi=-0.7854</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects. It extracts rotamers
+from <em>rot_lib</em> and adds them to the group until the summed probability
+reaches the probability cutoff defined in <strong>settings</strong>.</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>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
-default value (“”)</li>
+<li><strong>residue</strong> – Residue from which the anchor positions will be
+extracted</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects in constructed
+<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
+the frame energy. Interactions to frame residues with
+same index get neglected.</li>
+<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Library from which the data is taken to construct the
+rotamers.</li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle used as input for backbone
+dependent rotamer library. Default value is a typical
+alpha helical value.</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle used as input for backbone
+dependent rotamer library. Default value is a typical
+alpha helical value.</li>
</ul>
</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"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
-are present in <strong>res</strong> or when <strong>index</strong> is invalid</p>
+<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"><span class="pre">RuntimeError</span></code> if not all required anchor atoms
+are present in <strong>residue</strong>.</p>
</td>
</tr>
</tbody>
@@ -1157,120 +1193,206 @@ are present in <strong>res</strong> or when <strong>index</strong> is invalid</p
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.RRMRotamerGroup.Merge">
-<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 <strong>other</strong> to current <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a></p>
+<dt id="promod3.sidechain.ConstructFRMRotamerGroup">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFRMRotamerGroup</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="optional">[</span>, <em>phi=-1.0472</em>, <em>psi=-0.7854</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.ConstructFRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
+<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects. It extracts rotamers
+from <em>rot_lib</em> and adds them to the group until the summed probability
+reaches the probability cutoff defined in <strong>settings</strong>.</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"><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of nitrogen used as anchor for the rotamers</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of alpha carbon used as anchor for the rotamers</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of beta carbon used as anchor for the rotamers</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects in constructed
+<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
+the frame energy. Interactions to frame residues with
+same index get neglected.</li>
+<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Library from which the data is taken to construct the
+rotamers.</li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle used as input for backbone
+dependent rotamer library. Default value is a typical
+alpha helical value.</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle used as input for backbone
+dependent rotamer library. Default value is a typical
+alpha helical value.</li>
+</ul>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
-</dd></dl>
-
-<dl class="class">
-<dt id="promod3.sidechain.FRMRotamerGroup">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">FRMRotamerGroup</code><span class="sig-paren">(</span><em>rotamers</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"><span class="pre">FRMRotamer</span></code></a> objects for the same
-residue position. It can either be constructed by providing a list of
-<a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects or by convenience functions provided by PROMOD3.</p>
+<dl class="method">
+<dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFRMRotamerGroup</code><span class="sig-paren">(</span><em>residue</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="optional">[</span>, <em>phi=-1.0472</em>, <em>psi=-0.7854</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
+<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects. It extracts rotamers
+from <em>rot_lib</em> and adds them to the group until the summed probability
+reaches the probability cutoff defined in <strong>settings</strong>.</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"><strong>rotamers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><span class="pre">FRMRotamer</span></code></a> objects</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>residue</strong> – Residue from which the anchor positions will be
+extracted</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects in constructed
+<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
+the frame energy. Interactions to frame residues with
+same index get neglected.</li>
+<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Library from which the data is taken to construct the
+rotamers.</li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Phi backbone dihedral angle used as input for backbone
+dependent rotamer library. Default value is a typical
+alpha helical value.</li>
+<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Psi backbone dihedral angle used as input for backbone
+dependent rotamer library. Default value is a typical
+alpha helical value.</li>
+</ul>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if provided <strong>rotamers</strong> is empty</td>
+<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"><span class="pre">RuntimeError</span></code> if not all required anchor atoms
+are present in <strong>residue</strong>.</p>
+</td>
</tr>
</tbody>
</table>
+</dd></dl>
+
<dl class="method">
-<dt id="promod3.sidechain.FRMRotamerGroup.__len__">
-<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">
+<dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="sig-paren">)</span></dt>
+<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects. It extracts rotamers
+from <em>rot_lib</em> and adds them to the group until the summed probability
+reaches the probability cutoff defined in <strong>settings</strong>.</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">Returns:</th><td class="field-body">Number of rotamers in group</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of nitrogen used as anchor for the rotamers</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of alpha carbon used as anchor for the rotamers</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of beta carbon used as anchor for the rotamers</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects in constructed
+<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
+the frame energy. Interactions to frame residues with
+same index get neglected.</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"><span class="pre">RotamerLib</span></code></a>) – Library from which the data is taken to construct the
+rotamers.</li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+</ul>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.FRMRotamerGroup.__getitem__">
-<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">
+<dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>residue</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="sig-paren">)</span></dt>
+<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects. It extracts rotamers
+from <em>rot_lib</em> and adds them to the group until the summed probability
+reaches the probability cutoff defined in <strong>settings</strong>.</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">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"><span class="pre">FRMRotamer</span></code></a> at given <strong>index</strong></td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>residue</strong> – Residue from which the anchor positions will be
+extracted</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a></li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> objects in constructed
+<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
+the frame energy. Interactions to frame residues with
+same index get neglected.</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"><span class="pre">RotamerLib</span></code></a>) – Library from which the data is taken to construct the
+rotamers.</li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+</ul>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if <strong>index</strong> is invalid</td>
+<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"><span class="pre">RuntimeError</span></code> if not all required anchor atoms
+are present in <strong>residue</strong>.</p>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.FRMRotamerGroup.ApplyOneResidue">
-<code class="descname">ApplyOneResidue</code><span class="sig-paren">(</span><em>index</em>, <em>res</em><span class="optional">[</span>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplyOneResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calls ApplyOnResidue function on rotamer at position <strong>index</strong></p>
+<dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFRMRotamerGroup</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="sig-paren">)</span></dt>
+<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects. It extracts rotamers
+from <em>rot_lib</em> and adds them to the group until the summed probability
+reaches the probability cutoff defined in <strong>settings</strong>.</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>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
-default value (“”)</li>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of nitrogen used as anchor for the rotamers</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of alpha carbon used as anchor for the rotamers</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/1.3/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.3.3)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Position of beta carbon used as anchor for the rotamers</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects in constructed
+<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
+the frame energy. Interactions to frame residues with
+same index get neglected.</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"><span class="pre">RotamerLib</span></code></a>) – Library from which the data is taken to construct the
+rotamers.</li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
</ul>
</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"><span class="pre">RuntimeError</span></code> if not all required backbone atoms
-are present in <strong>res</strong> or when <strong>index</strong> is invalid</p>
-</td>
-</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
-<dt id="promod3.sidechain.FRMRotamerGroup.Merge">
-<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 <strong>other</strong> to current <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a></p>
+<dt>
+<code class="descclassname">promod3.sidechain.</code><code class="descname">ConstructFRMRotamerGroup</code><span class="sig-paren">(</span><em>residue</em>, <em>rotamer_id</em>, <em>residue_index</em>, <em>rot_lib</em>, <em>settings</em><span class="sig-paren">)</span></dt>
+<dd><p>Constructs a full group of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects. It extracts rotamers
+from <em>rot_lib</em> and adds them to the group until the summed probability
+reaches the probability cutoff defined in <strong>settings</strong>.</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"><strong>other</strong> (<a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>) – RotamerGroup to be merged in</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>residue</strong> – Residue from which the anchor positions will be
+extracted</li>
+<li><strong>rotamer_id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Type of of the constructed <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a></li>
+<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> objects in constructed
+<a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>. This matters for calculating
+the frame energy. Interactions to frame residues with
+same index get neglected.</li>
+<li><strong>rot_lib</strong> (<a class="reference internal" href="rotamer_lib.html#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a>) – Library from which the data is taken to construct the
+rotamers.</li>
+<li><strong>settings</strong> (<a class="reference internal" href="sidechain_settings.html#promod3.sidechain.RotamerSettings" title="promod3.sidechain.RotamerSettings"><code class="xref py py-class docutils literal"><span class="pre">RotamerSettings</span></code></a>) – Settings to control parametrization of the single
+particles.</li>
+</ul>
+</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"><span class="pre">RuntimeError</span></code> if not all required anchor atoms
+are present in <strong>residue</strong>.</p>
+</td>
</tr>
</tbody>
</table>
</dd></dl>
-<dl class="method">
-<dt id="promod3.sidechain.FRMRotamerGroup.CalculateInternalEnergies">
-<code class="descname">CalculateInternalEnergies</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.CalculateInternalEnergies" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculates internal energies of all rotamers in group</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThres">
-<code class="descname">ApplySelfEnergyThres</code><span class="sig-paren">(</span><span class="optional">[</span><em>thresh=30</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamerGroup.ApplySelfEnergyThres" title="Permalink to this definition">¶</a></dt>
-<dd><p>Searches rotamer with lowest self energy <strong>l_e</strong> and deletes all
-rotamers with <strong>self_energy</strong> > <strong>l_e</strong> + <strong>thresh</strong></p>
-</dd></dl>
-
-</dd></dl>
-
</div>
</div>
@@ -1283,21 +1405,27 @@ rotamers with <strong>self_energy</strong> > <strong>l_e</strong> + <strong>t
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Rotamers</a><ul>
-<li><a class="reference internal" href="#convenient-functions-for-constructing-rotamers">Convenient functions for constructing rotamers</a></li>
-<li><a class="reference internal" href="#convenient-functions-for-constructing-rotamer-groups">Convenient functions for constructing rotamer groups</a></li>
<li><a class="reference internal" href="#the-smallest-building-block-the-particle">The Smallest Building Block - The Particle</a></li>
<li><a class="reference internal" href="#id1">Rotamers</a></li>
<li><a class="reference internal" href="#rotamer-groups">Rotamer Groups</a></li>
+<li><a class="reference internal" href="#convenient-functions-for-constructing-rotamers">Convenient functions for constructing rotamers</a></li>
+<li><a class="reference internal" href="#convenient-functions-for-constructing-rotamer-groups">Convenient functions for constructing rotamer groups</a></li>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="rotamer_id.html"
- title="previous chapter">RotamerID</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="frame.html"
- title="next chapter">Frame</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li>Previous: <a href="rotamer_id.html" title="previous chapter">RotamerID</a></li>
+ <li>Next: <a href="frame.html" title="next chapter">Frame</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -1327,11 +1455,11 @@ rotamers with <strong>self_energy</strong> > <strong>l_e</strong> + <strong>t
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/sidechain/rotamer.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/rotamer_id.html b/doc/html/sidechain/rotamer_id.html
index 8b7c17f3cc14a148f541293afb6611d67cf85778..2dc41f6882fdf3c5cda4a3284cb3746881fbc1e6 100644
--- a/doc/html/sidechain/rotamer_id.html
+++ b/doc/html/sidechain/rotamer_id.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="rotamer.html" title="Rotamers"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="index.html" title="sidechain - Sidechain Modelling"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -67,6 +47,10 @@ As an example there are histidine in two possible protonation states,
that affect the hbond term or different versions of proline/cysteine.</p>
<div class="section" id="the-rotamerid">
<h2>The RotamerID<a class="headerlink" href="#the-rotamerid" title="Permalink to this headline">¶</a></h2>
+<dl class="class">
+<dt id="promod3.sidechain.RotamerID">
+<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>
<ul class="simple">
<li>ARG - Arginine</li>
<li>ASN - Asparagine</li>
@@ -96,11 +80,15 @@ that affect the hbond term or different versions of proline/cysteine.</p>
<li>ALA - Alanine</li>
<li>XXX - Invalid</li>
</ul>
+<p>The RotamerID enum can be accessed either directly as <code class="docutils literal"><span class="pre">promod3.sidechain.ARG</span></code>
+or as <code class="docutils literal"><span class="pre">promod3.sidechain.RotamerID.ARG</span></code>.</p>
+</dd></dl>
+
</div>
<div class="section" id="how-can-i-get-an-id">
<h2>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h2>
<p>The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the ost.conop.AminoAcid enum
+functions exist to get RotamerIDs from the <code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code> enum
or from amino acid three letter codes.</p>
<dl class="method">
<dt id="promod3.sidechain.TLCToRotID">
@@ -113,7 +101,7 @@ exactly the naming convention defined above.</p>
<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/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>, XXX if <strong>tlc</strong> cannot be recoginzed.</td>
+<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"><span class="pre">RotamerID</span></code></a>, XXX if <strong>tlc</strong> cannot be recoginzed.</td>
</tr>
</tbody>
</table>
@@ -132,7 +120,7 @@ defined in <code class="xref py py-class docutils literal"><span class="pre">ost
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code>) – AA enum of amino acid</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>, XXX if <strong>aa</strong> is invalid.</td>
+<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"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
</tr>
</tbody>
</table>
@@ -155,13 +143,19 @@ defined in <code class="xref py py-class docutils literal"><span class="pre">ost
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="index.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="rotamer.html"
- title="next chapter">Rotamers</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+ <li>Next: <a href="rotamer.html" title="next chapter">Rotamers</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -191,11 +185,11 @@ defined in <code class="xref py py-class docutils literal"><span class="pre">ost
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/sidechain/rotamer_id.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 7741227e822c35605c02e51e65a3cbce32ca08b1..7c7cce9761079e703a012e2e511a8eb3ea0797fc 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="graph.html" title="Coming to a solution"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="frame.html" title="Frame"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -68,15 +48,108 @@ can be gathered in rotamer libraries. Different libraries exist in the field
and their main difference is, whether the provided sidechain conformations
are dependent on their backbone or not. PROMOD3 provides you with a
<a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a> organizing rotamers for the different aminoacids
-in equidistant phi/psi bins.</p>
-<div class="section" id="the-backbone-dependent-rotamer-library">
-<h2>The Backbone Dependent Rotamer Library<a class="headerlink" href="#the-backbone-dependent-rotamer-library" title="Permalink to this headline">¶</a></h2>
-<p>The PROMOD3 <a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a> is a container for <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a>
-and is optimized for fast writing/loading from/to disk.
-Once initialized, the library is in a dynamic mode where
-rotamers can be added. No rotamers can be read at this stage. As soon as
+in equidistant phi/psi bins, as well as a simple <a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a>.
+Both libraries are containers for <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a> and are optimized
+for fast writing/loading from/to disk. Once initialized, the library is in a
+dynamic mode where rotamers can be added.
+No rotamers can be read at this stage. As soon as
all required rotamers are added, the library can be made static. This is the
mode you can get the rotamers out of it or dump it to disk.</p>
+<div class="section" id="the-non-backbone-dependent-rotamer-library">
+<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="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">
+<dt id="promod3.sidechain.RotamerLib.Save">
+<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>
+<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>filename</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of file, the library will be dumped into</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.RotamerLib.Load">
+<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>
+<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>filename</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of file, the library will be loaded from</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">RuntimeError</span></code> if file doesn’t exist</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.RotamerLib.AddRotamer">
+<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> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – 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"><span class="pre">RotamerLibEntry</span></code></a>) – the rotamer to be added</li>
+</ul>
+</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"><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="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>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>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="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> (<code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code>) – 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/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><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-class docutils literal"><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="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>
+
+</dd></dl>
+
+</div>
+<div class="section" id="the-backbone-dependent-rotamer-library">
+<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="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>
@@ -181,7 +254,7 @@ special <em>id</em> requests.</p>
</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/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><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"><span class="pre">RotamerLibEntry</span></code></a> of nonzero
-probability for given phi/psi pair</p>
+probability for given phi/psi pair sorted by their probability</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-class docutils literal"><span class="pre">RuntimeError</span></code> if no entries for <em>id</em> can be
@@ -379,8 +452,8 @@ required atoms are present in <em>res</em>.</p>
<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/ambiguous rotamers
-(TYR,VAL,PHE,ASP,GLU)</p>
+and can therefore not specifically treat symmetric rotamers
+(TYR,PHE,ASP,GLU) or rotamers with ambiguous naming in general.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -406,9 +479,9 @@ they are within the specified threshold.</p>
<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 (TYR,VAL,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>
+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>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -435,8 +508,8 @@ they are within the specified threshold.</p>
<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/ambiguous rotamers
-(TYR,VAL,PHE,ASP,GLU)</p>
+not specifically treat symmetric rotamers
+(TYR,PHE,ASP,GLU) or rotamers with ambiguous naming in general.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -462,7 +535,7 @@ considered similar</li>
<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.
-Sidechains with ambigous naming (TYR,VAL,PHE,ASP,GLU)
+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>
<table class="docutils field-list" frame="void" rules="none">
@@ -501,18 +574,25 @@ considered similar</li>
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Rotamer Library</a><ul>
+<li><a class="reference internal" href="#the-non-backbone-dependent-rotamer-library">The Non Backbone Dependent Rotamer Library</a></li>
<li><a class="reference internal" href="#the-backbone-dependent-rotamer-library">The Backbone Dependent Rotamer Library</a></li>
<li><a class="reference internal" href="#the-library-entry-type">The Library Entry Type</a></li>
</ul>
</li>
</ul>
-
- <h4>Previous topic</h4>
- <p class="topless"><a href="frame.html"
- title="previous chapter">Frame</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="graph.html"
- title="next chapter">Coming to a solution</a></p>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li>Previous: <a href="frame.html" title="previous chapter">Frame</a></li>
+ <li>Next: <a href="graph.html" title="next chapter">Coming to a solution</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -542,11 +622,11 @@ considered similar</li>
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/sidechain/rotamer_lib.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/sidechain/sidechain_settings.html b/doc/html/sidechain/sidechain_settings.html
index bab6fc96d353f6b766eff78d6268193e9ea7c042..d2515df664ebfdf45dfb4dc6a16ac7c7bd631b95 100644
--- a/doc/html/sidechain/sidechain_settings.html
+++ b/doc/html/sidechain/sidechain_settings.html
@@ -32,27 +32,7 @@
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="../py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="disulfid.html" title="Disulfid Bond Evaluation"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="graph.html" title="Coming to a solution"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -79,7 +59,7 @@ Ser,Thr and Tyr when using the convenient functions for constructing full
rotamer groups of them (see <a class="reference internal" href="rotamer.html#rotamer-group-construction-label"><span>here</span></a>).
Constructing the rotamer groups can further be controlled by assigning a max
summed probability resulting in less very unlikely rotamers added to the
-rotamer group(see <a class="reference internal" href="rotamer.html#rotamer-group-construction-label"><span>here</span></a>).</p>
+rotamer group (see <a class="reference internal" href="rotamer.html#rotamer-group-construction-label"><span>here</span></a>).</p>
<dl class="class">
<dt id="promod3.sidechain.RotamerSettings">
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerSettings</code><a class="headerlink" href="#promod3.sidechain.RotamerSettings" title="Permalink to this definition">¶</a></dt>
@@ -488,56 +468,6 @@ rotamer group(see <a class="reference internal" href="rotamer.html#rotamer-group
<code class="descname">sample_polar_hydrogens default: True</code></dt>
<dd></dd></dl>
-<dl class="attribute">
-<dt>
-<code class="descname">H_radius default: 0.49</code></dt>
-<dd></dd></dl>
-
-<dl class="attribute">
-<dt>
-<code class="descname">C_radius default: 1.68</code></dt>
-<dd></dd></dl>
-
-<dl class="attribute">
-<dt>
-<code class="descname">S_radius default: 1.71</code></dt>
-<dd></dd></dl>
-
-<dl class="attribute">
-<dt>
-<code class="descname">N_radius default: 1.28</code></dt>
-<dd></dd></dl>
-
-<dl class="attribute">
-<dt>
-<code class="descname">O_radius default: 1.29</code></dt>
-<dd></dd></dl>
-
-<dl class="attribute">
-<dt>
-<code class="descname">H_max_radius default: 1.0300</code></dt>
-<dd></dd></dl>
-
-<dl class="attribute">
-<dt>
-<code class="descname">C_max_radius default: 2.2400</code></dt>
-<dd></dd></dl>
-
-<dl class="attribute">
-<dt>
-<code class="descname">S_max_radius default: 2.2800</code></dt>
-<dd></dd></dl>
-
-<dl class="attribute">
-<dt>
-<code class="descname">N_max_radius default: 1.7067</code></dt>
-<dd></dd></dl>
-
-<dl class="attribute">
-<dt>
-<code class="descname">O_max_radius default: 1.7200</code></dt>
-<dd></dd></dl>
-
</dd></dl>
</div>
@@ -547,13 +477,19 @@ rotamer group(see <a class="reference internal" href="rotamer.html#rotamer-group
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="graph.html"
- title="previous chapter">Coming to a solution</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="disulfid.html"
- title="next chapter">Disulfid Bond Evaluation</a></p>
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../developers.html">Documentation For Developers</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
+ <li>Previous: <a href="graph.html" title="previous chapter">Coming to a solution</a></li>
+ <li>Next: <a href="disulfid.html" title="next chapter">Disulfid Bond Evaluation</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -583,11 +519,11 @@ rotamer group(see <a class="reference internal" href="rotamer.html#rotamer-group
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="../_sources/sidechain/sidechain_settings.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/doc/html/users.html b/doc/html/users.html
index aaf3c84354abaf3ebad1e647e34e817b228ac081..ea7682353f899fa8dfa3665a2aea5853850efebc 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -24,32 +24,14 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="index.html" />
- <link rel="next" title="Documentation For Developes" href="developers.html" />
+ <link rel="next" title="Documentation For Developers" href="developers.html" />
<link rel="prev" title="Welcome To ProMod3’s Documentation!" href="index.html" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
</head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <li class="right" >
- <a href="py-modindex.html" title="Python Module Index"
- >modules</a> |</li>
- <li class="right" >
- <a href="developers.html" title="Documentation For Developes"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="index.html" title="Welcome To ProMod3’s Documentation!"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="index.html">ProMod3 0 documentation</a> »</li>
- </ul>
- </div>
+ <body role="document">
<div class="document">
<div class="documentwrapper">
@@ -65,13 +47,15 @@
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
- <h4>Previous topic</h4>
- <p class="topless"><a href="index.html"
- title="previous chapter">Welcome To ProMod3’s Documentation!</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="developers.html"
- title="next chapter">Documentation For Developes</a></p>
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="index.html">Documentation overview</a><ul>
+ <li>Previous: <a href="index.html" title="previous chapter">Welcome To ProMod3’s Documentation!</a></li>
+ <li>Next: <a href="developers.html" title="next chapter">Documentation For Developers</a></li>
+ </ul></li>
+</ul>
+</div>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
@@ -101,11 +85,11 @@
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
|
<a href="_sources/users.txt"
- rel="nofollow">Page source</a></li>
+ rel="nofollow">Page source</a>
</div>
diff --git a/sidechain/doc/disulfid.rst b/sidechain/doc/disulfid.rst
index 1ccca67805134a1aeabe3ad326677656a1b84763..9a63016ec1e15e38bd139d0b20fd3965b7183c99 100644
--- a/sidechain/doc/disulfid.rst
+++ b/sidechain/doc/disulfid.rst
@@ -38,4 +38,4 @@ bonded state, if the resulting score is below 45.
between all possible subrotamer combinations gets
returned.
-.. [canutescu2003] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
+.. Already in other module .. [canutescu2003] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
diff --git a/sidechain/doc/frame.rst b/sidechain/doc/frame.rst
index b0ea5398ee092899e694193ed4518736a160c61e..06af9c3adbed83e96a256eb4035e15beec22d10f 100644
--- a/sidechain/doc/frame.rst
+++ b/sidechain/doc/frame.rst
@@ -21,11 +21,13 @@ The Frame Objects
The most simple way of constructing a frame residue is the usage
of the convenient functions provided by PROMOD3.
- :param particles: :class:`list` of :class:`Particle` objects building
- up the :class:`FrameResidue`
+ :param particles: particles building frame residue
:param residue_index: Interaction energies between the constructed frame
residue and any rotamer associated to the same
- residue index are neglected
+ residue index are neglected
+
+ :type particles: :class:`list` of :class:`Particle`
+ :type residue_index: :class:`int`
.. method:: __len__()
@@ -35,7 +37,8 @@ The Frame Objects
.. method:: __getitem__(index)
:param index: :class:`Particle` index
-
+ :type index: :class:`int`
+
:returns: :class:`Particle` at position **index**
:raises: :class:`RuntimeError` if index is invalid
@@ -48,8 +51,8 @@ The Frame Objects
Due to technical reasons, this is only possible if the rotamers are
part of rotamer groups.
- :param frame_residues: :class:`list` of :class:`FrameResidue` objects building
- the frame.
+ :param frame_residues: residues building the frame.
+ :type frame_residues: :class:`list` of :class:`FrameResidue`
.. method:: SetFrameEnergy(rotamer_group)