From 50a4df6c1fcc09e6e5ec08a41b3434666b8b7d40 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 19 Nov 2020 09:26:11 +0100
Subject: [PATCH] Updated compiled doc.
---
doc/html/actions/index.html | 4 +-
doc/html/actions/index_dev.html | 2 +-
doc/html/container/docker.html | 2 +-
doc/html/core/geometry.html | 42 ++++++------
doc/html/core/pm3argparse.html | 2 +-
doc/html/gettingstarted.html | 2 +-
doc/html/loop/all_atom.html | 48 +++++++-------
doc/html/loop/backbone.html | 66 +++++++++----------
doc/html/loop/mm_system_creation.html | 40 +++++------
doc/html/loop/structure_db.html | 34 +++++-----
doc/html/loop/torsion_sampler.html | 44 ++++++-------
doc/html/modelling/algorithms.html | 16 ++---
doc/html/modelling/gap_handling.html | 16 ++---
doc/html/modelling/loop_candidates.html | 20 +++---
doc/html/modelling/loop_closing.html | 18 ++---
doc/html/modelling/model_checking.html | 20 +++---
doc/html/modelling/monte_carlo.html | 16 ++---
doc/html/modelling/pipeline.html | 54 +++++++--------
.../modelling/sidechain_reconstruction.html | 6 +-
doc/html/scoring/backbone_score_env.html | 14 ++--
doc/html/scoring/backbone_scorers.html | 10 +--
doc/html/sidechain/disulfid.html | 12 ++--
doc/html/sidechain/rotamer.html | 24 +++----
doc/html/sidechain/rotamer_constructor.html | 26 ++++----
doc/html/sidechain/rotamer_lib.html | 4 +-
25 files changed, 271 insertions(+), 271 deletions(-)
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index 46d4aec8..03acc8c0 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -101,7 +101,7 @@ Example:</p>
</li>
</ul>
<p>Structures can be provided in PDB (<code class="docutils literal notranslate"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.1.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.2.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
chosen by file ending. Recognized File Extensions: <code class="docutils literal notranslate"><span class="pre">.ent</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb</span></code>,
<code class="docutils literal notranslate"><span class="pre">.ent.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif.gz</span></code>. At least one structure must be
given and you cannot mix file formats. Multiple structures can be given and each
@@ -183,7 +183,7 @@ detects and models disulfid bonds and reconstructs all sidechains with the
flexible rotamer model. The result is stored as <code class="file docutils literal notranslate"><span class="pre">out.pdb</span></code>.
The output filename can be controlled with the <code class="docutils literal notranslate"><span class="pre">-o</span></code> flag.</p>
<p>A structure can be provided in PDB (<code class="docutils literal notranslate"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.1.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/io/io/#ost.io.LoadEntity" title="(in OpenStructure v2.2.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal notranslate"><span class="pre">-e</span></code>). In the latter case, the format is
chosen by file ending. Recognized File Extensions: <code class="docutils literal notranslate"><span class="pre">.ent</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb</span></code>,
<code class="docutils literal notranslate"><span class="pre">.ent.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif</span></code>, <code class="docutils literal notranslate"><span class="pre">.cif.gz</span></code>.</p>
<p>Several flags control the modelling behaviour:</p>
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 560329c4..35c893b4 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -185,7 +185,7 @@ 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="https://www.OpenStructure.org">OST</a>’s <a class="reference external" href="https://www.openstructure.org/docs/2.1/base/testutils/#module-ost.testutils" title="(in OpenStructure v2.1.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.testutils</span></code></a> and Python’s
+<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>’s <a class="reference external" href="https://www.openstructure.org/docs/2.2/base/testutils/#module-ost.testutils" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.testutils</span></code></a> and Python’s
<a class="reference external" href="https://docs.python.org/3.7/library/unittest.html#unittest.TestCase" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed
as a script:</p>
<div class="highlight-default notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
index 29da9391..6156b9d2 100644
--- a/doc/html/container/docker.html
+++ b/doc/html/container/docker.html
@@ -77,7 +77,7 @@ pdbs/struct.pdb
</div>
<div class="section" id="the-compound-library">
<span id="docker-compound-lib"></span><h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
-<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">CompoundLib</span></code></a> is generated.
+<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">CompoundLib</span></code></a> is generated.
Compound libraries contain information on chemical compounds, such as their
connectivity, chemical class and one-letter-code. The compound library has
several uses, but the most important one is to provide the connectivy
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index 4957bce6..e379e2db 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -45,14 +45,14 @@
<dd class="field-odd"><ul class="simple">
<li><p><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Gromacs rule</p></li>
<li><p><strong>number</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Desired number of positions (max. 3)</p></li>
-<li><p><strong>anchors</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</p></li>
+<li><p><strong>anchors</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Constructed <em>number</em> positions.</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -64,16 +64,16 @@
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Positions of O and OXT atoms.</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -86,9 +86,9 @@ dihedral (A-B-C-D).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom A</p></li>
-<li><p><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom B</p></li>
-<li><p><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</p></li>
+<li><p><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom A</p></li>
+<li><p><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom B</p></li>
+<li><p><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of atom C</p></li>
<li><p><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Bond length (C-D)</p></li>
<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (B-C-D)</p></li>
<li><p><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</p></li>
@@ -98,7 +98,7 @@ dihedral (A-B-C-D).</p>
<dd class="field-even"><p>Position of atom D</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -111,16 +111,16 @@ C-alpha and C atoms.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Position of C atom</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Position of C-beta atom</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -133,8 +133,8 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
-<li><p><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</p></li>
+<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
+<li><p><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</p></li>
<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</p></li>
</ul>
</dd>
@@ -142,7 +142,7 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<dd class="field-even"><p>Transformation matrix</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat4</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -155,7 +155,7 @@ going through the origin.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
+<li><p><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Axis of rotation</p></li>
<li><p><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</p></li>
</ul>
</dd>
@@ -163,7 +163,7 @@ going through the origin.</p>
<dd class="field-even"><p>Rotation matrix</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Mat3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -176,7 +176,7 @@ going through the origin.</p>
<dd><p>Simple container class to store N, CA and C coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</p>
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>res</em> does not contain N, CA and C
@@ -193,7 +193,7 @@ atoms.</p>
<dd><p>Position of nitrogen / alpha carbon / carbon atom.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index a8f0fa0e..0cbcfccb 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -247,7 +247,7 @@ target sequences</p></li>
</ul>
<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
-<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
+<li><p><code class="xref py py-attr docutils literal notranslate"><span class="pre">profiles</span></code> - <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
ordered to match the target sequences.</p></li>
</ul>
<p>Exit codes related to profile input:</p>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index e8a57073..20ff1b4f 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -85,7 +85,7 @@ is conserved</p></li>
<li><p>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">loop</span></code></a> module)</p></li>
<li><p>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal notranslate"><span class="pre">sidechain</span></code></a> module)</p></li>
<li><p>Minimize energy of final model using molecular mechanics
-(using <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.1.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</p></li>
+(using <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> from OST)</p></li>
</ul>
<p>Since a good amount of time is spent in OpenMM routines to minimize energy, we
try to use the fast and multi-threaded “CPU” platform of OpenMM (should be
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index 37cfa2b5..606df709 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -80,8 +80,8 @@ process with all known positions and then update the environment whenever a
new loop is being added.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</p>
</dd>
</dl>
@@ -100,7 +100,7 @@ concatenated one after each other (indexing starts at 0)</p></li>
<dd><p>Sets full environment. Existing data is cleared first.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</p>
</dd>
@@ -128,7 +128,7 @@ means, that positions in the env. may be reset, newly set or cleared.</p>
<li><p><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</p></li>
<li><p><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</p></li>
<li><p><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</p></li>
<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</p></li>
</ul>
</dd>
@@ -194,7 +194,7 @@ a loop to reset later with <a class="reference internal" href="#promod3.loop.All
<dd class="field-odd"><p>SEQRES that was set in constructor (one sequence per chain).</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -313,7 +313,7 @@ and if found set the corresponding position, otherwise we unset it.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -351,7 +351,7 @@ out of bounds or if residues in the two containers are inconsistent
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Set position at that index.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -394,7 +394,7 @@ out of bounds or if residues in the two containers are inconsistent
<dd class="field-odd"><p>Position at given index.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom position index.</p>
@@ -494,7 +494,7 @@ if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
<dd class="field-odd"><p>Amino acid type of residue at index <em>res_index</em>.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p>
@@ -744,10 +744,10 @@ atom (N, CA, C, O).</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>All residues packed in a single chain as an OST entity.
-Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</p>
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -764,8 +764,8 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index</p></li>
-<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</p></li>
+<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -850,7 +850,7 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
<dt id="promod3.loop.AminoAcidLookup">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
<dd><p>Collection of static methods to lookup properties of amino acid types
-(<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) and
+(<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidAtom</span></code></a>) and
hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcidHydrogen</span></code></a>).</p>
<dl class="method">
<dt id="promod3.loop.AminoAcidLookup.GetOLC">
@@ -863,7 +863,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
</dd>
</dl>
</dd></dl>
@@ -882,7 +882,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumAtoms(aa)-1])</p></li>
<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
@@ -908,7 +908,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
<li><p><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumHydrogens(aa)-1])</p></li>
<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
@@ -933,7 +933,7 @@ atom.</p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
</dd>
@@ -957,7 +957,7 @@ and atom.</p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p></li>
<li><p><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Atom name</p></li>
</ul>
</dd>
@@ -979,7 +979,7 @@ hydrogens of <em>aa</em>.</p>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
</dd>
</dl>
</dd></dl>
@@ -1008,7 +1008,7 @@ hydrogens of <em>aa</em>.</p>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
</dd>
</dl>
</dd></dl>
@@ -1036,7 +1036,7 @@ hydrogens of <em>aa</em>.</p>
<dd class="field-odd"><p>Amino acid type of the given heavy atom type</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
@@ -1122,7 +1122,7 @@ when residue is peptide bound.</p>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. PRO)</p>
@@ -1146,7 +1146,7 @@ when residue is N terminal.</p>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if no such atom (i.e. H3 for PRO)</p>
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index 48cb9e68..f8d64017 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -38,7 +38,7 @@
<p>The most simple representation of structural information in ProMod3 is the
<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>. It provides a way to store the backbone positions of
residues. They provide structural manipulations, they can be manipulated and
-converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
@@ -142,7 +142,7 @@ code which is not one of the 20 default amino acids or if
<em>residues</em>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<dd class="field-odd"><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
which the backbone positions and one letter codes
are extracted.</p>
</dd>
@@ -164,7 +164,7 @@ required positions.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</p></li>
-<li><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<li><p><strong>residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – List of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
which the backbone positions are extracted.</p></li>
</ul>
</dd>
@@ -185,14 +185,14 @@ a residue not providing all necessary positions.</p>
<dd class="field-odd"><p>The whole backbone list converted to a density map.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a></p>
</dd>
</dl>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
-<li><p><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </p></li>
+<li><p><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – </p></li>
<li><p><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
<li><p><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p></li>
</ul>
@@ -208,7 +208,7 @@ a residue not providing all necessary positions.</p>
<dd class="field-odd"><p>The whole backbone list converted to an OST entity.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -222,8 +222,8 @@ be replaced, otherwise they will be added to the entity.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</p></li>
+<li><p><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</p></li>
</ul>
</dd>
</dl>
@@ -235,7 +235,7 @@ be replaced, otherwise they will be added to the entity.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </p></li>
+<li><p><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.img.ImageHandle</span></code></a>) – </p></li>
<li><p><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – </p></li>
<li><p><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p></li>
</ul>
@@ -251,7 +251,7 @@ be replaced, otherwise they will be added to the entity.</p>
<dd class="field-odd"><p></p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.AlignedCuboid</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – </p>
@@ -344,7 +344,7 @@ actual fragment at specified <em>index</em></p>
atom for residue at given index.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
@@ -367,7 +367,7 @@ atom for residue at given index.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
/ oxygen atom to this.</p></li>
</ul>
</dd>
@@ -411,7 +411,7 @@ atom for residue at given index.</p>
<dd class="field-odd"><p>Amino acid type of the residue at given index.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p>
@@ -426,7 +426,7 @@ atom for residue at given index.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -448,12 +448,12 @@ and set the amino acid type according to the given one letter code.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
-<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
-<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
+<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
+<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
<li><p><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</p></li>
</ul>
</dd>
@@ -512,12 +512,12 @@ to the given one letter code.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
-<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
-<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
-<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
-<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
-<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</p></li>
+<li><p><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</p></li>
+<li><p><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</p></li>
+<li><p><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</p></li>
+<li><p><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</p></li>
+<li><p><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</p></li>
<li><p><strong>olc</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</p></li>
</ul>
</dd>
@@ -571,7 +571,7 @@ depends on the residue following the C stem. The position is only
reconstructed if the residue handle is valid.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
+<dd class="field-odd"><p><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
element of this backbone list)</p>
</dd>
</dl>
@@ -585,7 +585,7 @@ element of this backbone list)</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
+<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
</ul>
</dd>
</dl>
@@ -601,7 +601,7 @@ element of this backbone list)</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Start index.</p></li>
<li><p><strong>to</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – End index (one past last residue to transform).</p></li>
-<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
+<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p></li>
</ul>
</dd>
</dl>
@@ -613,7 +613,7 @@ element of this backbone list)</p>
<dd><p>Applies a transformation to all positions of this list.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>transform</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p>
+<dd class="field-odd"><p><strong>transform</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</p>
</dd>
</dl>
</dd></dl>
@@ -630,12 +630,12 @@ residue <em>other_index</em> of <em>other</em> backbone list considering the
positions of the N, CA and C atoms.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index.</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</p></li>
<li><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p></li>
<li><p><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</p></li>
</ul>
@@ -652,7 +652,7 @@ positions of the N, CA and C atoms.</p>
list onto CA positions of <em>other</em> backbone list.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</p>
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index f4eb0849..e3fd0c60 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -34,8 +34,8 @@
<div class="body" role="main">
<div class="section" id="generate-ost-mol-mm-systems">
-<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.1.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
-<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.1.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
+<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
proteins, we define a system creator for loops (<a class="reference internal" href="#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal notranslate"><span class="pre">MmSystemCreator</span></code></a>) and a
specialized forcefield lookup for amino acids (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldLookup</span></code></a>).</p>
<p>The example below showcases the creation and use of an MM system:</p>
@@ -259,7 +259,7 @@ acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]<
MM simulations.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -388,7 +388,7 @@ FF specific data for amino acids in a protein. We distinguish amino acid types
<dl class="class">
<dt id="promod3.loop.ForcefieldLookup">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
+<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
<ul class="simple">
<li><p>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
<em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
@@ -491,7 +491,7 @@ for details.</p>
<dd class="field-odd"><p>Amino acid type for given <em>ff_aa</em></p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal notranslate"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</p>
@@ -589,7 +589,7 @@ for details.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Dampening factor for LJ 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
@@ -603,7 +603,7 @@ for details.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Dampening factor for electrostatic 1,4 interactions (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a></p>
@@ -616,7 +616,7 @@ for details.</p>
<code class="sig-name descname">GetMasses</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetMasses" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+<dd class="field-odd"><p>Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -636,7 +636,7 @@ for details.</p>
<code class="sig-name descname">GetCharges</code><span class="sig-paren">(</span><em class="sig-param">ff_aa</em>, <em class="sig-param">is_nter</em>, <em class="sig-param">is_cter</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.GetCharges" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+<dd class="field-odd"><p>Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -657,7 +657,7 @@ for details.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Sigma in nm for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -678,7 +678,7 @@ for details.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Epsilon in kJ/mol for each atom
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -812,7 +812,7 @@ for details.</p>
<dt id="promod3.loop.ForcefieldAminoAcid">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the amino acid types for forcefields. The first 20 values
-correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
+correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
there are values for disulfid bridges (<em>FF_CYS2</em>), d-protonated histidine
(<em>FF_HISD</em>, default for <em>ost.conop.HIS</em> is <em>FF_HISE</em>) and <em>FF_XXX</em> for unknown
types. The full list of values is:</p>
@@ -830,7 +830,7 @@ types. The full list of values is:</p>
<dd><p>Contains lists of bonds, angles, dihedrals, impropers and LJ pairs (exclusions
are the combination of all bonds and 1,3 pairs of angles and are not stored
separately). Each type of connectivity has it’s own class (see below) storing
-indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Topology</span></code></a>.
+indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Topology</span></code></a>.
The indexing of atoms for internal connectivities is in [<em>0, N-1</em>], where <em>N</em>
= <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ForcefieldLookup.GetNumAtoms()</span></code></a>. For connectivities of pairs of
residues, atoms of the first residue are in [<em>0, N1-1</em>] and atoms of the
@@ -919,7 +919,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldBondInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
+<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -969,7 +969,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
+<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1031,7 +1031,7 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define Urey-Bradley angle
-(see <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1115,8 +1115,8 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define periodic dihedral or improper (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1199,7 +1199,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
+<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1271,7 +1271,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldLJPairInfo">
<em class="property">class </em><code class="sig-prename descclassname">promod3.loop.</code><code class="sig-name descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
+<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.index_one">
<code class="sig-name descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 34537eeb..0c036f78 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -117,7 +117,7 @@ stuff to the structure db. (<a class="reference external" href="https://docs.pyt
<dt id="promod3.loop.CoordInfo.shift">
<code class="sig-name descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
<dd><p>Translation from original coordinates that has been applied before storing
-structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
+structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
</dd></dl>
</dd></dl>
@@ -255,7 +255,7 @@ database, you might want to consider two things:</p>
<ol class="arabic simple">
<li><p>Use a database of limited size to generate the actual profiles (something
in between 5000 and 10000 nonredundant chains is enough)</p></li>
-<li><p>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+<li><p>Use the <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
running in parallel</p></li>
</ol>
<dl class="class">
@@ -382,11 +382,11 @@ in the according <a class="reference internal" href="#promod3.loop.CoordInfo" ti
<dd class="field-odd"><ul class="simple">
<li><p><strong>id</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – identifier of the added structure (e.g. pdb id)</p></li>
<li><p><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Name of the chain in <em>ent</em> you want to add</p></li>
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
as specified by <em>chain_name</em>.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
<em>chain_name</em>. The profile sequence must match <em>seqres</em>.</p></li>
<li><p><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
connected stretch of residues are all connected
@@ -509,9 +509,9 @@ full entry at <em>coord_idx</em></p>
<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the returned backbone list. If not
set, the original sequence at specified location in the
database is used.</p></li>
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
superposed onto.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
superposed onto.</p></li>
</ul>
</dd>
@@ -645,7 +645,7 @@ connected stretches of residues in the database.</p>
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>Solvent accessibility for each residue of <em>fragment</em> or full entry
at <em>coord_idx</em> in square A as calculated by
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Accessibility()</span></code></a> when adding the structure to
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Accessibility()</span></code></a> when adding the structure to
the database.</p>
</dd>
<dt class="field-even">Return type</dt>
@@ -680,7 +680,7 @@ full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
model.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
@@ -710,7 +710,7 @@ full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
model.</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</dd>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
@@ -747,7 +747,7 @@ containing that data.</p></li>
probabilities as NULL model.</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><code class="xref py py-exc docutils literal notranslate"><span class="pre">RuntimeError</span></code> if <em>bb_list</em> and
@@ -765,7 +765,7 @@ frequencies in entry with <em>coord_idx</em></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</p></li>
<li><p><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
(in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal notranslate"><span class="pre">GetNumCoords()</span></code></a>-1])</p></li>
</ul>
@@ -1045,8 +1045,8 @@ and <strong>c_stem</strong> and of the same length as the <strong>frag_size</str
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</p></li>
<li><p><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of residues of the fragment</p></li>
<li><p><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
<em>extra_bins</em> additional bins surrounding the bin given by
@@ -1244,7 +1244,7 @@ linked to this object.</p></li>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
</ul>
</dd>
</dl>
@@ -1258,7 +1258,7 @@ linked to this object.</p></li>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>w</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – linear weight</p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</p></li>
</ul>
</dd>
</dl>
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index 9a1cff3d..cdb56db8 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -124,7 +124,7 @@ acids not matching any of the group definitions.</p>
<dd><p>Extracts backbone torsion angles from the structure and adds them to the appropriate histograms in the sampler.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</p>
+<dd class="field-odd"><p><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</p>
</dd>
</dl>
</dd></dl>
@@ -187,9 +187,9 @@ for details.</p>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
@@ -224,9 +224,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
@@ -256,9 +256,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>psi</em> angle</p></li>
</ul>
</dd>
@@ -292,9 +292,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – <em>phi</em> angle</p></li>
</ul>
</dd>
@@ -328,9 +328,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
@@ -366,9 +366,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
@@ -386,9 +386,9 @@ standard amino acid</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
-<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></p></li>
+<li><p><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></p></li>
<li><p><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – phi angle</p></li>
<li><p><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – psi angle</p></li>
</ul>
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index fe77be33..52fbe89c 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -84,7 +84,7 @@ of the solutions</p></li>
indices of the common subsets (rigid blocks) relative
to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>bb_list_one</strong>
onto <strong>bb_list_two</strong></p>
</dd>
@@ -98,7 +98,7 @@ onto <strong>bb_list_two</strong></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>
+<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a>
objects from which the positions are extracted</p></li>
<li><p><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
positions will be extracted</p></li>
@@ -119,9 +119,9 @@ of the solutions</p></li>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#tuple" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></a> with the first element being a
<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> defining the
column indices of the common subsets (rigid blocks)
-relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
+relative to the input <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions from the first
sequence onto the second sequence.</p>
</dd>
@@ -154,7 +154,7 @@ of the solutions</p></li>
indices of the common subsets (rigid blocks) relative
to the input <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code> objects
and the second element being a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>pos_one</strong>
onto <strong>pos_two</strong></p>
</dd>
@@ -217,8 +217,8 @@ Weird things are happening otherwise.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</p></li>
-<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</p></li>
+<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</p></li>
+<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</p></li>
<li><p><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</p></li>
<li><p><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length (num. residues) of fragments to be extracted.</p></li>
<li><p><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
@@ -301,7 +301,7 @@ want to generate</p></li>
<li><p><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
the total number is:
len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></p></li>
-<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
+<li><p><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
fragment search performance.</p></li>
<li><p><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
increases the fragment search performance</p></li>
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 2d204ee7..bb636cf9 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -50,8 +50,8 @@ invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a></p></li>
-<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></p></li>
+<li><p><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal notranslate"><span class="pre">before</span></code></a></p></li>
+<li><p><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal notranslate"><span class="pre">after</span></code></a></p></li>
<li><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seq</span></code></a></p></li>
</ul>
</dd>
@@ -99,7 +99,7 @@ are valid and:</p>
<dd class="field-odd"><p>Chain, the gap is belonging to</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ChainHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -233,13 +233,13 @@ extend the gap past another gap.</p>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.before">
<code class="sig-name descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.after">
<code class="sig-name descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
@@ -282,7 +282,7 @@ False if no new extension possible.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -317,7 +317,7 @@ valid termini.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
<li><p><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
<li><p>If -1, all possible non-terminal gaps are returned.</p></li>
<li><p>If >= 0, this restricts the max. gap-length
@@ -364,7 +364,7 @@ score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalti
<li><p><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Extend()</span></code></a>.</p></li>
<li><p><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for length of gap.</p></li>
<li><p><strong>penalties</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Penalty for each residue added to gap.</p></li>
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</p></li>
<li><p><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – <ul>
<li><p>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a>
(i.e. it stops at gaps and termini).</p></li>
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index 1c75ef55..89ab41a2 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -119,8 +119,8 @@ a fragment database.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</p></li>
<li><p><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
<em>n_stem</em> and <em>c_stem</em></p></li>
<li><p><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">FragDB</span></code></a>) – The fragment database</p></li>
@@ -221,9 +221,9 @@ not depending on a metropolis criterium.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a>) – A torsion sampler (used for all residues) or a list
@@ -261,9 +261,9 @@ candidate. This leads to an increase in number of loops.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match</p></li>
<li><p><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First pivot residue</p></li>
<li><p><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Second pivot residue</p></li>
@@ -331,7 +331,7 @@ anything is raised when calculating the scores.</p>
<code class="sig-name descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em class="sig-param">score_container</em>, <em class="sig-param">structure_db</em>, <em class="sig-param">prof</em>, <em class="sig-param">offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a score comparing the given profile <em>prof</em> starting at <em>offset</em>
with the sequence / structure profile of each candidate as extracted from
-<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
+<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
details, <em>prof.null_model</em> is used for weighting).</p>
<p>Note that for profile scores a higher “score” is better! So take care when
combining this to other scores, where it is commonly the other way around.</p>
@@ -345,7 +345,7 @@ with this DB).</p>
<li><p><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></p></li>
<li><p><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal notranslate"><span class="pre">FillFromDatabase()</span></code></a></p></li>
-<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</p></li>
+<li><p><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</p></li>
<li><p><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</p></li>
</ul>
</dd>
@@ -373,8 +373,8 @@ positions and the corresponding atoms in <em>c_stem</em>.</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal notranslate"><span class="pre">ScoringWeights</span></code></a></p></li>
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index 3022493e..eaed142d 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -73,11 +73,11 @@ to avoid moving into unfavourable regions of the backbone dihedrals.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the backbones to be closed</p></li>
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
If the residue before <em>n_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
and phi angle (-1.0472) to evaluate the first angle.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
If the residue after <em>c_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
psi angle (-0.7854) to evaluate the last angle.</p></li>
@@ -110,8 +110,8 @@ This is faster but might lead to weird backbone dihedral pairs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</p></li>
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</p></li>
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</p></li>
<li><p><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Maximal number of iterations</p></li>
<li><p><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
be closed has RMSD below the given <em>c_stem</em></p></li>
@@ -288,7 +288,7 @@ size or sequence as the initial one.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
</dd>
@@ -306,7 +306,7 @@ size or sequence as the initial one.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
</dd>
@@ -325,7 +325,7 @@ doesn’t do anything if specified residue is a glycine</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
</dd>
@@ -343,7 +343,7 @@ doesn’t do anything if specified residue is a glycine</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
</dd>
@@ -361,7 +361,7 @@ doesn’t do anything if specified residue is a glycine</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Idx of residue</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</p></li>
<li><p><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</p></li>
</ul>
</dd>
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 6758658c..7ecf5c3e 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -47,15 +47,15 @@ A ring is only added if all ring-atoms exist or if it is a proline and
three of the atoms exist (center and radii are estimated then).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</p>
+<dd class="field-odd"><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of rings to perform ring checks. Each ring is a named
tuple with:
-center (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>),
-plane (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Plane</span></code></a>),
+center (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Vec3</span></code></a>),
+plane (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/composite/#ost.geom.Plane" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Plane</span></code></a>),
radius (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>),
-residue (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</p>
+residue (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>).</p>
</dd>
</dl>
</dd></dl>
@@ -68,11 +68,11 @@ residue (<a class="reference external" href="https://www.openstructure.org/docs/
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</p></li>
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
-<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
+<dd class="field-even"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of residues (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a>) which
have a punched ring.</p>
</dd>
</dl>
@@ -87,7 +87,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal notranslate"><span class="pre">GetRings()</span></code></a>.</p></li>
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
@@ -108,7 +108,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<dd class="field-odd"><ul class="simple">
<li><p><strong>candidates</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
Offending candidates are removed from this list.</p></li>
-<li><p><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</p></li>
+<li><p><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</p></li>
<li><p><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal notranslate"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</p></li>
<li><p><strong>orig_indices</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>) – Mapping to old indexing of candidates. If given, it
must have as many elements as <em>candidates</em>.</p></li>
@@ -169,7 +169,7 @@ with <code class="docutils literal notranslate"><span class="pre">MolProbity</sp
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#dict" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code></a></p>
</dd>
<dt class="field-even">Raises</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
executable is not found.</p>
</dd>
</dl>
@@ -182,7 +182,7 @@ executable is not found.</p>
<p>See <a class="reference internal" href="#promod3.modelling.RunMolProbity" title="promod3.modelling.RunMolProbity"><code class="xref py py-func docutils literal notranslate"><span class="pre">RunMolProbity()</span></code></a> for details.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</p>
+<dd class="field-odd"><p><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</p>
</dd>
</dl>
</dd></dl>
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index 8a68c7a2..4a9cf7bb 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -448,9 +448,9 @@ avoid moving into unfavourable phi/psi ranges.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal notranslate"><span class="pre">CCD()</span></code></a>.</p></li>
<li><p><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – Sequence of the conformation to be closed.</p></li>
<li><p><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal notranslate"><span class="pre">TorsionSampler</span></code></a> / <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a>
@@ -490,9 +490,9 @@ dihedral angles as it is the case for the <a class="reference internal" href="#p
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</p></li>
</ul>
</dd>
@@ -524,9 +524,9 @@ solutions. The KICCloser simply picks the first one.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<li><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</p></li>
-<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<li><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</p></li>
<li><p><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Seed for internal random generators.</p></li>
</ul>
@@ -557,7 +557,7 @@ adapt.</p></li>
superposing the c_stem with the desired positions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<dd class="field-odd"><p><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</p>
</dd>
</dl>
@@ -588,7 +588,7 @@ here.</p></li>
superposing the n_stem with the desired positions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<dd class="field-odd"><p><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</p>
</dd>
</dl>
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index 772f4c79..59e416f6 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -107,7 +107,7 @@ and <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqre
chain follows afterwards.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -129,11 +129,11 @@ Gaps of different chains are appended one after another.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.seqres">
<code class="sig-name descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain
+<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceHandle</span></code></a> for each chain
of the target protein.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">SequenceList</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -141,14 +141,14 @@ of the target protein.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.profiles">
<code class="sig-name descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
+<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal notranslate"><span class="pre">seqres</span></code></a>). Please note, that this
attribute won’t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>. You have
to fill it manually or even better by the convenient function
<a class="reference internal" href="#promod3.modelling.SetSequenceProfiles" title="promod3.modelling.SetSequenceProfiles"><code class="xref py py-func docutils literal notranslate"><span class="pre">SetSequenceProfiles()</span></code></a>, to ensure consistency with the seqres.</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -305,7 +305,7 @@ alignment handle or an alignment handle list. Every list item is treated as a
single chain in the final raw model.</p>
<p>Each alignment handle must contain exactly two sequences and the second
sequence is considered the template sequence, which must have a
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a> attached.</p>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityView</span></code></a> attached.</p>
<p>Before extracting the coordinates, the alignments are pre-processed
according to <em>aln_preprocessing</em>.</p>
<p>This is a basic protein core modelling algorithm that copies backbone
@@ -333,7 +333,7 @@ as information about insertions and deletions in the gaps list.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
+<li><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal notranslate"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
list of alignment handles for raw model with multiple chains.</p></li>
<li><p><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True, if we wish to include ligands in the model. This
searches for ligands in all OST handles of the views
@@ -346,7 +346,7 @@ in SMTL). All ligands are added to a new chain named
(chains are consecutively named according to
characters in
‘ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz’).
-If <em>aln</em> is of type <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>,
+If <em>aln</em> is of type <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>,
<em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>.
If <em>aln</em> is of type <code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentList</span></code>,
<em>chain_names</em> is expected to be a <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
@@ -372,7 +372,7 @@ to False.</p></li>
<li><p>the second sequence does not have an attached structure</p></li>
<li><p>the residues of the template structure do not match with the
alignment sequence (note that you can set an “offset” (see
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetSequenceOffset()</span></code></a>) for the
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">SetSequenceOffset()</span></code></a>) for the
template sequence (but not for the target))</p></li>
<li><p>the target sequence has a non-zero offset (cannot be honored as
the resulting model will always start its residue numbering at 1)</p></li>
@@ -412,12 +412,12 @@ return an incomplete model.</p>
<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
alignment.</p></li>
<li><p><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
-CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.1.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
-and <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.1.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
+CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
+and <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-func docutils literal notranslate"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
Both do a similarly good job without ligands (CHARMM
slightly better), but you will want to be consistent
with the optional force fields in <cite>extra_force_fields</cite>.</p></li>
-<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
+<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
(ligand) residue cannot be parametrized with the
default force field. The force fields are tried
in the order as given and ligands without an
@@ -438,7 +438,7 @@ limited. Termini of length 1 won’t be modelled.</p></li>
<dd class="field-even"><p>Delivers the model as an OST entity.</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -596,7 +596,7 @@ environments get updated in <strong>target_mhandle</strong>.</p>
<li><p><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – This is the chain where the info goes to</p></li>
<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – First residue of the copied stretch</p></li>
<li><p><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Last residue of the copied stretch</p></li>
-<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
+<li><p><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
they’re copied over</p></li>
</ul>
</dd>
@@ -623,7 +623,7 @@ while ensuring consistency with the <a class="reference internal" href="#promod3
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal notranslate"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</p></li>
-<li><p><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</p></li>
+<li><p><strong>profiles</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -764,7 +764,7 @@ For the scondary-structure-penalty to work,
the model-template must have the appropriate
information before <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal notranslate"><span class="pre">BuildRawModel()</span></code></a> is
called (e.g. with
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.1.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</p></li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v2.2.0)"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</p></li>
<li><p><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">FullGapExtender</span></code></a> instead of
of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal notranslate"><span class="pre">GapExtender</span></code></a>. Also works in combination
with <cite>use_scoring_extender</cite>. This allows the gap
@@ -1109,7 +1109,7 @@ one is loaded if None.</p></li>
<dt id="promod3.modelling.MinimizeModelEnergy">
<code class="sig-prename descclassname">promod3.modelling.</code><code class="sig-name descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em class="sig-param">mhandle</em>, <em class="sig-param">max_iterations=12</em>, <em class="sig-param">max_iter_sd=20</em>, <em class="sig-param">max_iter_lbfgs=10</em>, <em class="sig-param">use_amber_ff=False</em>, <em class="sig-param">extra_force_fields=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Minimize energy of final model using molecular mechanics.</p>
-<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.1.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
+<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v2.2.0)"><code class="xref py py-mod docutils literal notranslate"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
It will iteratively (at most <em>max_iterations</em> times):</p>
<ul class="simple">
<li><p>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</p></li>
@@ -1135,7 +1135,7 @@ minimization is aborted. This issue is logged and added as a major issue to
<li><p><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Max. number of iterations within LBFGS method</p></li>
<li><p><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</p></li>
-<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
+<li><p><strong>extra_force_fields</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal notranslate"><span class="pre">BuildFromRawModel()</span></code></a>).</p></li>
</ul>
</dd>
@@ -1143,7 +1143,7 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
<dd class="field-even"><p>The model including all oxygens as used in the minimizer.</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">Entity</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -1214,8 +1214,8 @@ set to True, if the problem affects backbone atoms.</p></li>
<dd><p>List of residues affected by issue (or empty list if global issue).</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ResidueView</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -1282,17 +1282,17 @@ attribute yet, it is added.</p>
<p>Columns that only contain gaps (‘-‘) are removed. If no such column can be
identified, the input alignment gets returned. A new alignment gets
constructed otherwise. The sequences of the new alignment retain name, offset
-and the potentially attached <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original
+and the potentially attached <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original
sequences.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
+<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The processed alignment</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -1333,16 +1333,16 @@ ATOMSEQ: ABCDEFGHI...
<p>given a <em>min_terminal_anchor_size</em>>2. If no shift can be performed, the
input alignment gets returned. A new alignment gets constructed otherwise.
The sequences of the new alignment retain name, offset and the potentially
-attached <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original sequences.</p>
+attached <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityView</span></code></a> from the original sequences.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
+<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Input alignment</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The processed alignment</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a></p>
</dd>
</dl>
</dd></dl>
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index e46de40f..cf1a4a3d 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -38,7 +38,7 @@
<p>Two methods are provided to fully reconstruct sidechains of residues:</p>
<ul class="simple">
<li><p>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal notranslate"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
-<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p></li>
+<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">EntityHandle</span></code></a></p></li>
<li><p>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal notranslate"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
and used to reconstruct sidechains of single loops</p></li>
</ul>
@@ -91,7 +91,7 @@ and used to reconstruct sidechains of single loops</p></li>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
+<li><p><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
reconstruction gets directly applied on the structure itself.</p></li>
<li><p><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in <em>ent</em> (i.e.
containing all required atoms) should be kept rigid
@@ -195,7 +195,7 @@ environment before calling this!</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</p></li>
<li><p><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Length of loop.</p></li>
<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Chain the loop belongs to.</p></li>
<li><p><strong>start_resnum_list</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Starts of loops.</p></li>
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index 3b5a28c5..145b8ca9 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -58,8 +58,8 @@ at some point you want to restore the original state. The
task.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<dd class="field-odd"><p><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</p>
</dd>
</dl>
@@ -91,7 +91,7 @@ attached</p>
structural data was already set, all the existing data gets cleared first.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<dd class="field-odd"><p><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</p>
</dd>
@@ -113,7 +113,7 @@ positions.</p>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal notranslate"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</p></li>
-<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</p></li>
+<li><p><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</p></li>
<li><p><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</p></li>
</ul>
</dd>
@@ -241,7 +241,7 @@ providing lists of integers.</p>
<dd class="field-odd"><p>SEQRES that was set in constructor (one sequence per chain).</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceList</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -336,7 +336,7 @@ The constraint functions are built after the principle of QMEANDisCo.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</p></li>
+<li><p><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</p></li>
<li><p><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal notranslate"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
or CB atoms</p></li>
</ul>
@@ -347,7 +347,7 @@ or CB atoms</p></li>
<code class="sig-name descname">AddStructuralInfo</code><span class="sig-paren">(</span><em class="sig-param">aln</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.DiscoContainer.AddStructuralInfo" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
+<dd class="field-odd"><p><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
SEQRES and the second sequence the actual structural
info. The second sequence must have a view attached.</p>
</dd>
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index 205762ba..aebb68b2 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -336,7 +336,7 @@ called for every type of amino acids and for every <em>count</em> <= <em>max_
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</p></li>
+<li><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</p></li>
<li><p><strong>count</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Number of surrounding CB positions for which to set energy.</p></li>
<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
@@ -455,8 +455,8 @@ SetEnergy(aa2, aa1, bin, energy).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
-<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
+<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
+<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
<li><p><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</p></li>
<li><p><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</p></li>
</ul>
@@ -614,8 +614,8 @@ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
-<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
+<li><p><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</p></li>
+<li><p><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</p></li>
<li><p><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</p></li>
<li><p><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the alpha angle.</p></li>
<li><p><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Discrete bin describing the beta angle.</p></li>
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index f7ef7ce2..2d880095 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -66,10 +66,10 @@ rotamers to the result of the geometric expression.</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</p></li>
<li><p><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</p></li>
-<li><p><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</p></li>
-<li><p><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</p></li>
-<li><p><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</p></li>
-<li><p><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</p></li>
+<li><p><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</p></li>
+<li><p><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</p></li>
+<li><p><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</p></li>
+<li><p><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</p></li>
</ul>
</dd>
<dt class="field-even">Raises</dt>
@@ -98,8 +98,8 @@ possible, the one with the optimal sum of scores gets estimated.</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>rotamer_groups</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of
<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamerGroup</span></code></a>) – Every group represents a cysteine</p></li>
-<li><p><strong>ca_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</p></li>
-<li><p><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</p></li>
+<li><p><strong>ca_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</p></li>
+<li><p><strong>cb_positions</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#list" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">list</span></code></a> of <a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</p></li>
<li><p><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
as a disulfid bond</p></li>
<li><p><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index 26f4dccc..4201fcc7 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -91,7 +91,7 @@ or as <code class="docutils literal notranslate"><span class="pre">promod3.sidec
<div class="section" id="how-can-i-get-an-id">
<h3>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h3>
<p>The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
+functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
or from amino acid three letter codes.</p>
<dl class="method">
<dt id="promod3.sidechain.TLCToRotID">
@@ -114,10 +114,10 @@ exactly the naming convention defined above.</p>
<dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
to generate special IDs this way
(e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not
-defined in <a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+defined in <a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</p>
+<dd class="field-odd"><p><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</p>
@@ -210,7 +210,7 @@ evaluated by the underlying scoring function.</p>
<dd class="field-odd"><p>The position of the particle</p>
</dd>
<dt class="field-even">Return type</dt>
-<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
+<dd class="field-even"><p><a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a></p>
</dd>
</dl>
</dd></dl>
@@ -263,7 +263,7 @@ function</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
<li><p><strong>particle_type</strong> (<a class="reference internal" href="#promod3.sidechain.SCWRL4ParticleType" title="promod3.sidechain.SCWRL4ParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">SCWRL4ParticleType</span></code></a>) – The type of the particle</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
<li><p><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The charge of the particle, relevant for the hydrogen
bond term</p></li>
<li><p><strong>lone_pairs</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
@@ -272,7 +272,7 @@ particle is a potential hydrogen bond acceptor.
An example would be the Serine OG atom, where you can
represent the two lone pairs with vectors pointing
from the OG position towards the lone pair centers.</p></li>
-<li><p><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
+<li><p><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
relevant for the hydrogen bond term. If set, the
particle is a potential hydrogen bond donor. An
example would be the Serine HG hydrogen. The
@@ -300,7 +300,7 @@ function</p>
<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
<li><p><strong>radius</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#float" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">float</span></code></a>) – The hard-sphere radius of the particle, relevant for the
repulsion term.</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
</ul>
</dd>
</dl>
@@ -408,7 +408,7 @@ function</p>
<dd class="field-odd"><ul class="simple">
<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – The name of the particle</p></li>
<li><p><strong>radius</strong> (<a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>) – The type of the particle</p></li>
-<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
+<li><p><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</p></li>
</ul>
</dd>
</dl>
@@ -474,7 +474,7 @@ in this process.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
<strong>res</strong></p></li>
<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
@@ -699,7 +699,7 @@ No atoms are removed from <strong>res</strong> in this process.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</p></li>
<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1028,7 +1028,7 @@ particles of the same residue.</p></li>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</p></li>
<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1140,7 +1140,7 @@ particles of the same residue.</p></li>
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Rotamer index</p></li>
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</p></li>
<li><p><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#bool" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</p></li>
<li><p><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/stdtypes.html#str" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 45ac39c0..188163de 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -68,7 +68,7 @@ an interface implemented by scoring function specific constructors
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</p></li>
<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</p></li>
<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the required backbone atoms</p></li>
@@ -119,7 +119,7 @@ don’t show up in a rotamer).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</p></li>
<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the backbone positions</p></li>
@@ -158,7 +158,7 @@ you observe in a rotamer).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</p></li>
<li><p><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal notranslate"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</p></li>
<li><p><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the backbone positions</p></li>
@@ -237,7 +237,7 @@ any rotamers for ALA and GLY.</p>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue">
<code class="sig-name descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em class="sig-param">residue</em>, <em class="sig-param">residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
This can be useful to mark a region occupied by a ligand. Note, that
there won’t be any parametrization of hbonds in this function. All heavy
atoms of the residue will be represented as carbons and hydrogens are
@@ -245,7 +245,7 @@ skipped.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</p></li>
<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</p></li>
</ul>
@@ -259,7 +259,7 @@ construct a <a class="reference internal" href="frame.html#promod3.sidechain.Fra
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">
<code class="sig-name descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em class="sig-param">residue</em>, <em class="sig-param">residue_index</em>, <em class="sig-param">comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms based on the passed compounds library.
This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal notranslate"><span class="pre">ConstructFrameResidue()</span></code></a>,
which will be called by this function if the residue is not known by the given
@@ -275,10 +275,10 @@ as in the <code class="xref py py-class docutils literal notranslate"><span clas
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><p><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a>.</p></li>
<li><p><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> belongs to.</p></li>
-<li><p><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</p></li>
+<li><p><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
@@ -418,7 +418,7 @@ to be assigned</p></li>
<dl class="method">
<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">
<code class="sig-name descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em class="sig-param">res</em>, <em class="sig-param">res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms. It is important that the residue has
proper bonds assigned, as they influence the atom typing procedure.
Furthermore, you need hydrogens to automatically estimate the correct
@@ -436,7 +436,7 @@ If the atom has the bool properties “is_hbond_acceptor” AND
in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>. If the generic properties are not set,
every oxygen is assumed to be an hbond acceptor. But only an hbond donor
if its bound to a hydrogen (or deuterium). You can set the generic
-properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
+properties for an <a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
at.SetBoolProp(“is_hbond_donor”, False) and
at.SetBoolProp(“is_hbond_acceptor”, True). An oxygen with those
generic properties is assigned O_A_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal notranslate"><span class="pre">VINAParticleType</span></code></a>.</p></li>
@@ -458,7 +458,7 @@ corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
<a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p></li>
<li><p><strong>res_idx</strong> (<a class="reference external" href="https://docs.python.org/3.7/library/functions.html#int" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">int</span></code></a>) – Index that is set in <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal notranslate"><span class="pre">FrameResidue</span></code></a></p></li>
</ul>
@@ -476,7 +476,7 @@ corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain
as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal notranslate"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">RRMRotamer</span></code></a></p>
</dd>
<dt class="field-even">Return type</dt>
@@ -494,7 +494,7 @@ constructed <a class="reference internal" href="rotamer.html#promod3.sidechain.F
contains the atoms from <em>residue</em>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal notranslate"><span class="pre">FRMRotamer</span></code></a></p>
</dd>
<dt class="field-even">Return type</dt>
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 6670b168..382c4eb5 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -401,7 +401,7 @@ all not required chi angles with their corresponding standard deviations to
NaN.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p>
+<dd class="field-odd"><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p>
@@ -424,7 +424,7 @@ are NaN.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
-<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.1/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.1.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p></li>
+<li><p><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/2.2/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v2.2.0)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</p></li>
<li><p><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal notranslate"><span class="pre">RotamerLibEntry</span></code></a></p></li>
</ul>
</dd>
--
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