diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index 46d4aec86598f47f170e9b0dc82fceff6828e28e..03acc8c078ac24d3ae060b4247b3658346ecdff9 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 560329c4bc572b230f5c96f7faa3fd26f7f6278d..35c893b404ddcfc8d33fcb0c1e49ea75a90a83cf 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 29da9391e35446ad9a02b564dbba812dd8531275..6156b9d2c9ba9ed6431261ddae3bc4cce325433c 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 4957bce6419bbe90c93c45fbe4f05c7e3cabcabf..e379e2db97aca62d73a13378197745c0ea22dd75 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 a8f0fa0e6fe86765b4a93087be2febf0d08c443b..0cbcfccb1194e13f1628445e9fa7241b6250f7b8 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 e8a57073e8b3190d7d04623f41b610544ecbeac6..20ff1b4fa4b46126008093a01b22123b95d630cd 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 37cfa2b582489c2faa49a71da82a35e148a3a84f..606df70990b579ae9dc000f6eeca585cc72d47cf 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 48cb9e683bde2988d46f71b48cbfc71f4c0bf782..f8d64017e6e5f84a550406d6af13dd62434f3ce4 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 f4eb0849b57867b4c162c1b4b48d00d3551f9c91..e3fd0c60adc0127c59ee9e992a79bb02fceb47ea 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 34537eeb5aac1304921dbc98edaaf09fb2d5f0d3..0c036f7842f4c5ee804f04fd9136a81a083f15a6 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 9a1cff3d2049b4c1aa59de4fcd88d11a5b0fe13d..cdb56db84434b425bc4dec86202d2c0c57c0a0a0 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 fe77be330a98cf742722c45657266e3e5e38a0d5..52fbe89c8cf0175e4df0be3faf5572b2c74428ba 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 2d204ee7d9864ab6296dba3947a1ad6329dfd816..bb636cf987354b08e0b3e1e1aefcceb68d1a73cb 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 &gt;= 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 1c75ef550b37610e0a61273bca07af01ba879d6f..89ab41a29956cbc4a906d61a083d476712b298cf 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 3022493e3495ff75aa2f0c11943b26f45d22540d..eaed142d036c9382c1daaba0f9f6769b56a265d7 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 6758658c18429130aded443d4ac0c373534ba80b..7ecf5c3eda588565d42bc15174a31539d2ad37bf 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 8a68c7a2b80378d7040b79698984fba4653a15df..4a9cf7bbedf72da08008e9c0821ca753f4f9dd7b 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 772f4c79530457426ceb59e77fbe228fef2846b3..59e416f6890acd8b8e90a74b7c38d802c2d44d7a 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>&gt;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 e46de40fa21749f66e20750010211f847bef6dcf..cf1a4a3d2e32e1bf2da14921995031cdaff486f6 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 3b5a28c502d35c99afe5bb64fe8b4a5d02b335d0..145b8ca99c90a973d9ebe0c83a959427d2c4dc14 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 205762bafdc90606d1897afb71faa2dafdab761b..aebb68b2beed7d10b16c167114ff95fa9d2da67a 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> &lt;= <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 f7ef7ce2ef6ba0250c3875e7ffce685ea44411d7..2d8800954685db9e06127789b0d5d5b5a88287f7 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 26f4dccc1a1b4c321624bf7a2a835bad4b8971f1..4201fcc72369bf35b5c80dda56cd9c426d1e87e1 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 45ac39c00d7ae7d00267cbe5fd9b3435f57d6037..188163de022b7e2fd1ec974874720da82ef954a3 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 6670b168d5492c77e174ea848bfe10b9c1e4cf7f..382c4eb5bbba3e9620b278c6b47bd2ce09aebba7 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>