Update documentation

_sources/autosummary/transformato.mutate.rst.txt

@@ -60,8 +60,6 @@ Functions
 
 
 
-.. automethod:: transformato.mutate.mutate_pure_tautomers
-
 .. automethod:: transformato.mutate.perform_mutations
 
 

autosummary/transformato.mutate.html

@@ -68,7 +68,6 @@
 </ul>
 </li>
 <li class="toctree-l3"><a class="reference internal" href="#functions">Functions</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#transformato.mutate.mutate_pure_tautomers"><code class="docutils literal notranslate"><span class="pre">mutate.mutate_pure_tautomers()</span></code></a></li>
 <li class="toctree-l4"><a class="reference internal" href="#transformato.mutate.perform_mutations"><code class="docutils literal notranslate"><span class="pre">mutate.perform_mutations()</span></code></a></li>
 </ul>
 </li>
@@ -331,31 +330,6 @@ <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>
@@ -809,21 +783,6 @@ <h3>Iterates over all atoms of the molecule and saves them as a list<a class="he
 </section>
 <section id="functions">
 <h2>Functions<a class="headerlink" href="#functions" title="Link to this heading"></a></h2>
-<dl class="py method">
-<dt class="sig sig-object py" id="transformato.mutate.mutate_pure_tautomers">
-<span class="sig-prename descclassname"><span class="pre">mutate.</span></span><span class="sig-name descname"><span class="pre">mutate_pure_tautomers</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">system1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">system2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">configuration</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">single_state</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nr_of_bonded_windows</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">4</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#transformato.mutate.mutate_pure_tautomers" title="Link to this definition"></a></dt>
-<dd><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>s1_to_s2</strong> (<a class="reference internal" href="#transformato.mutate.ProposeMutationRoute" title="transformato.mutate.ProposeMutationRoute"><em>ProposeMutationRoute</em></a>) – </p></li>
-<li><p><strong>system1</strong> (<a class="reference internal" href="transformato.system.html#transformato.system.SystemStructure" title="transformato.system.SystemStructure"><em>SystemStructure</em></a>) – </p></li>
-<li><p><strong>system2</strong> (<a class="reference internal" href="transformato.system.html#transformato.system.SystemStructure" title="transformato.system.SystemStructure"><em>SystemStructure</em></a>) – </p></li>
-<li><p><strong>nr_of_bonded_windows</strong> (<em>int</em>) – </p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
 <dl class="py method">
 <dt class="sig sig-object py" id="transformato.mutate.perform_mutations">
 <span class="sig-prename descclassname"><span class="pre">mutate.</span></span><span class="sig-name descname"><span class="pre">perform_mutations</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">i</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">mutation_list</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">list_of_heavy_atoms_to_be_mutated</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">nr_of_mutation_steps_charge</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nr_of_mutation_steps_lj_of_hydrogens</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nr_of_mutation_steps_lj_of_heavy_atoms</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nr_of_mutation_steps_cc</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">5</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">endstate_correction</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="headerlink" href="#transformato.mutate.perform_mutations" title="Link to this definition"></a></dt>

autosummary/transformato.state.html

@@ -220,22 +220,6 @@ <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>

genindex.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>
@@ -233,20 +233,14 @@ <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>
@@ -579,8 +573,6 @@ <h2 id="M">M</h2>
         <li><a href="autosummary/transformato.mutate.html#transformato.mutate.Mutation.mutate">(transformato.mutate.Mutation method)</a>
 </li>
       </ul></li>
-      <li><a href="autosummary/transformato.mutate.html#transformato.mutate.mutate_pure_tautomers">mutate_pure_tautomers() (transformato.mutate method)</a>
-</li>
       <li><a href="autosummary/transformato.mutate.html#transformato.mutate.Mutation">Mutation (class in transformato.mutate)</a>
 </li>
       <li><a href="autosummary/transformato.mutate.html#transformato.mutate.MutationDefinition">MutationDefinition (class in transformato.mutate)</a>