Update documentation

Author: actions-user

_modules/transformato/mutate.html

@@ -331,6 +331,31 @@ <h2>Description<a class="headerlink" href="#description" title="Link to this hea
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="transformato.mutate.Mutation._mutate_vdw">
+<span class="sig-name descname"><span class="pre">_mutate_vdw</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">psf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lambda_value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vdw_atom_idx</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">offset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">to_default</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/transformato/mutate.html#Mutation._mutate_vdw"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#transformato.mutate.Mutation._mutate_vdw" title="Link to this definition"></a></dt>
+<dd><p>This is used to scale the LJ parameters of the DDD and DDX atoms to zero in phase II and III</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>psf</strong> (<em>CharmmPsfFile</em>) – </p></li>
+<li><p><strong>lambda_value</strong> (<em>float</em>) – </p></li>
+<li><p><strong>vdw_atom_idx</strong> (<em>List</em><em>[</em><em>int</em><em>]</em>) – </p></li>
+<li><p><strong>offset</strong> (<em>int</em>) – </p></li>
+<li><p><strong>to_default</strong> (<em>bool</em>) – </p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py method">
+<dt class="sig sig-object py" id="transformato.mutate.Mutation._scale_epsilon_and_rmin">
+<em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">_scale_epsilon_and_rmin</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lambda_value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">psf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tlc</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/transformato/mutate.html#Mutation._scale_epsilon_and_rmin"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#transformato.mutate.Mutation._scale_epsilon_and_rmin" title="Link to this definition"></a></dt>
+<dd><p>This scales the LJ interactions (epsilon and rmin) from non-interacting DDD atom (no charge)
+to ‘real’ dummy atom (no LJ!), typically this is performed in one step, but to be sure
+we offer scalling possibility here as well</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="transformato.mutate.Mutation.mutate">
 <span class="sig-name descname"><span class="pre">mutate</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">psf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lambda_value_electrostatic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lambda_value_vdw</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">vdw_atom_idx</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">steric_mutation_to_default</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/transformato/mutate.html#Mutation.mutate"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#transformato.mutate.Mutation.mutate" title="Link to this definition"></a></dt>

_modules/transformato/state.html

@@ -220,6 +220,22 @@ <h2>Description<a class="headerlink" href="#description" title="Link to this hea
 </dl>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="transformato.state.IntermediateStateFactory._write_amber_files">
+<span class="sig-name descname"><span class="pre">_write_amber_files</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">psf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_file_base</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tlc</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">env</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/transformato/state.html#IntermediateStateFactory._write_amber_files"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#transformato.state.IntermediateStateFactory._write_amber_files" title="Link to this definition"></a></dt>
+<dd><p>Write a parm7 and rst7 file for each intermediate step, including information about the dummy atoms</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>psf</strong> (<em>AmberParm</em>) – </p></li>
+<li><p><strong>output_file_base</strong> (<em>str</em>) – </p></li>
+<li><p><strong>tlc</strong> (<em>str</em>) – </p></li>
+<li><p><strong>env</strong> (<em>str</em>) – </p></li>
+</ul>
+</dd>
+</dl>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="transformato.state.IntermediateStateFactory._write_psf">
 <em class="property"><span class="pre">static</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">_write_psf</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">psf</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_file_base</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">env</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/transformato/state.html#IntermediateStateFactory._write_psf"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#transformato.state.IntermediateStateFactory._write_psf" title="Link to this definition"></a></dt>

_modules/transformato/system.html

@@ -194,12 +194,12 @@ <h2 id="_">_</h2>
 </li>
       <li><a href="autosummary/transformato.mutate.html#transformato.mutate.ProposeMutationRoute._check_for_lp">_check_for_lp() (transformato.mutate.ProposeMutationRoute method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="autosummary/transformato.state.html#transformato.state.IntermediateStateFactory._check_hmr">_check_hmr() (transformato.state.IntermediateStateFactory method)</a>
 </li>
       <li><a href="autosummary/transformato.mutate.html#transformato.mutate.Mutation._compensate_charge">_compensate_charge() (transformato.mutate.Mutation method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="autosummary/transformato.state.html#transformato.state.IntermediateStateFactory._copy_charmm_files">_copy_charmm_files() (transformato.state.IntermediateStateFactory method)</a>
 </li>
       <li><a href="autosummary/transformato.state.html#transformato.state.IntermediateStateFactory._copy_files">_copy_files() (transformato.state.IntermediateStateFactory method)</a>
@@ -233,14 +233,20 @@ <h2 id="_">_</h2>
       <li><a href="autosummary/transformato.mutate.html#transformato.mutate.CommonCoreTransformation._mutate_atoms">_mutate_atoms() (transformato.mutate.CommonCoreTransformation method)</a>
 </li>
       <li><a href="autosummary/transformato.mutate.html#transformato.mutate.ProposeMutationRoute._mutate_to_common_core">_mutate_to_common_core() (transformato.mutate.ProposeMutationRoute method)</a>
+</li>
+      <li><a href="autosummary/transformato.mutate.html#transformato.mutate.Mutation._mutate_vdw">_mutate_vdw() (transformato.mutate.Mutation method)</a>
 </li>
       <li><a href="autosummary/transformato.state.html#transformato.state.IntermediateStateFactory._overwrite_simulation_script_parameters">_overwrite_simulation_script_parameters() (transformato.state.IntermediateStateFactory method)</a>
 </li>
       <li><a href="autosummary/transformato.system.html#transformato.system.SystemStructure._read_parameters">_read_parameters() (transformato.system.SystemStructure method)</a>
+</li>
+      <li><a href="autosummary/transformato.mutate.html#transformato.mutate.Mutation._scale_epsilon_and_rmin">_scale_epsilon_and_rmin() (transformato.mutate.Mutation static method)</a>
 </li>
       <li><a href="autosummary/transformato.mutate.html#transformato.mutate.ProposeMutationRoute._show_common_core">_show_common_core() (transformato.mutate.ProposeMutationRoute method)</a>
 </li>
       <li><a href="autosummary/transformato.mutate.html#transformato.mutate.ProposeMutationRoute._transform_common_core">_transform_common_core() (transformato.mutate.ProposeMutationRoute method)</a>
+</li>
+      <li><a href="autosummary/transformato.state.html#transformato.state.IntermediateStateFactory._write_amber_files">_write_amber_files() (transformato.state.IntermediateStateFactory method)</a>
 </li>
       <li><a href="autosummary/transformato.state.html#transformato.state.IntermediateStateFactory._write_psf">_write_psf() (transformato.state.IntermediateStateFactory static method)</a>
 </li>