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ReactionMechanismGenerator · Dec 16, 2024 · a7fab29 · a7fab29
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diff --git a/genindex.html b/genindex.html
@@ -1407,6 +1407,10 @@ <h2 id="F">F</h2>
       <li><a href="reference/molecule/pathfinder.html#rmgpy.molecule.pathfinder.find_adj_lone_pair_radical_delocalization_paths">find_adj_lone_pair_radical_delocalization_paths() (in module rmgpy.molecule.pathfinder)</a>
 </li>
       <li><a href="reference/molecule/pathfinder.html#rmgpy.molecule.pathfinder.find_adj_lone_pair_radical_multiple_bond_delocalization_paths">find_adj_lone_pair_radical_multiple_bond_delocalization_paths() (in module rmgpy.molecule.pathfinder)</a>
+</li>
+      <li><a href="reference/molecule/pathfinder.html#rmgpy.molecule.pathfinder.find_adsorbate_conjugate_delocalization_paths">find_adsorbate_conjugate_delocalization_paths() (in module rmgpy.molecule.pathfinder)</a>
+</li>
+      <li><a href="reference/molecule/pathfinder.html#rmgpy.molecule.pathfinder.find_adsorbate_delocalization_paths">find_adsorbate_delocalization_paths() (in module rmgpy.molecule.pathfinder)</a>
 </li>
       <li><a href="reference/molecule/pathfinder.html#rmgpy.molecule.pathfinder.find_allyl_delocalization_paths">find_allyl_delocalization_paths() (in module rmgpy.molecule.pathfinder)</a>
 </li>
@@ -1461,11 +1465,11 @@ <h2 id="F">F</h2>
       <li><a href="reference/arkane/pdep.html#arkane.PressureDependenceJob.fit_interpolation_models">fit_interpolation_models() (arkane.PressureDependenceJob method)</a>
 </li>
       <li><a href="reference/data/statmechfit.html#rmgpy.data.statmechfit.fit_statmech_direct">fit_statmech_direct() (in module rmgpy.data.statmechfit)</a>
-</li>
-      <li><a href="reference/data/statmechfit.html#rmgpy.data.statmechfit.fit_statmech_pseudo">fit_statmech_pseudo() (in module rmgpy.data.statmechfit)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="reference/data/statmechfit.html#rmgpy.data.statmechfit.fit_statmech_pseudo">fit_statmech_pseudo() (in module rmgpy.data.statmechfit)</a>
+</li>
       <li><a href="reference/data/statmechfit.html#rmgpy.data.statmechfit.fit_statmech_pseudo_rotors">fit_statmech_pseudo_rotors() (in module rmgpy.data.statmechfit)</a>
 </li>
       <li><a href="reference/data/statmechfit.html#rmgpy.data.statmechfit.fit_statmech_to_heat_capacity">fit_statmech_to_heat_capacity() (in module rmgpy.data.statmechfit)</a>
@@ -1601,6 +1605,12 @@ <h2 id="G">G</h2>
       <li><a href="reference/molecule/resonance.html#rmgpy.molecule.resonance.generate_adj_lone_pair_radical_multiple_bond_resonance_structures">generate_adj_lone_pair_radical_multiple_bond_resonance_structures() (in module rmgpy.molecule.resonance)</a>
 </li>
       <li><a href="reference/molecule/resonance.html#rmgpy.molecule.resonance.generate_adj_lone_pair_radical_resonance_structures">generate_adj_lone_pair_radical_resonance_structures() (in module rmgpy.molecule.resonance)</a>
+</li>
+      <li><a href="reference/molecule/resonance.html#rmgpy.molecule.resonance.generate_adsorbate_conjugate_resonance_structures">generate_adsorbate_conjugate_resonance_structures() (in module rmgpy.molecule.resonance)</a>
+</li>
+      <li><a href="reference/molecule/resonance.html#rmgpy.molecule.resonance.generate_adsorbate_shift_down_resonance_structures">generate_adsorbate_shift_down_resonance_structures() (in module rmgpy.molecule.resonance)</a>
+</li>
+      <li><a href="reference/molecule/resonance.html#rmgpy.molecule.resonance.generate_adsorbate_shift_up_resonance_structures">generate_adsorbate_shift_up_resonance_structures() (in module rmgpy.molecule.resonance)</a>
 </li>
       <li><a href="reference/molecule/resonance.html#rmgpy.molecule.resonance.generate_allyl_delocalization_resonance_structures">generate_allyl_delocalization_resonance_structures() (in module rmgpy.molecule.resonance)</a>
 </li>
@@ -2298,6 +2308,8 @@ <h2 id="G">G</h2>
 </li>
       <li><a href="reference/molecule/atomtype.html#rmgpy.molecule.AtomType.get_features">get_features() (rmgpy.molecule.AtomType method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reference/qm/gaussian.html#rmgpy.qm.gaussian.GaussianMol.get_file_path">get_file_path() (rmgpy.qm.gaussian.GaussianMol method)</a>
 
       <ul>
@@ -2318,8 +2330,6 @@ <h2 id="G">G</h2>
         <li><a href="reference/qm/mopac.html#rmgpy.qm.mopac.MopacMolPM7.get_file_path">(rmgpy.qm.mopac.MopacMolPM7 method)</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="reference/molecule/molecule.html#rmgpy.molecule.Molecule.get_formula">get_formula() (rmgpy.molecule.Molecule method)</a>
 </li>
       <li><a href="reference/data/kineticsdatabase.html#rmgpy.data.kinetics.KineticsDatabase.get_forward_reaction_for_family_entry">get_forward_reaction_for_family_entry() (rmgpy.data.kinetics.KineticsDatabase method)</a>
@@ -3424,6 +3434,8 @@ <h2 id="I">I</h2>
         <li><a href="reference/molecule/groupbond.html#rmgpy.molecule.GroupBond.is_double">(rmgpy.molecule.GroupBond method)</a>
 </li>
       </ul></li>
+      <li><a href="reference/molecule/bond.html#rmgpy.molecule.Bond.is_double_or_triple">is_double_or_triple() (rmgpy.molecule.Bond method)</a>
+</li>
       <li><a href="reference/molecule/graph.html#rmgpy.molecule.graph.Graph.is_edge_in_cycle">is_edge_in_cycle() (rmgpy.molecule.graph.Graph method)</a>
 
       <ul>
@@ -3561,6 +3573,8 @@ <h2 id="I">I</h2>
 </li>
       </ul></li>
       <li><a href="reference/data/kineticsfamily.html#rmgpy.data.kinetics.KineticsFamily.is_molecule_forbidden">is_molecule_forbidden() (rmgpy.data.kinetics.KineticsFamily method)</a>
+</li>
+      <li><a href="reference/molecule/molecule.html#rmgpy.molecule.Molecule.is_multidentate">is_multidentate() (rmgpy.molecule.Molecule method)</a>
 </li>
       <li><a href="reference/molecule/atom.html#rmgpy.molecule.Atom.is_nitrogen">is_nitrogen() (rmgpy.molecule.Atom method)</a>
 

diff --git a/objects.inv b/objects.inv
diff --git a/reference/molecule/bond.html b/reference/molecule/bond.html
@@ -174,6 +174,13 @@ <h1>rmgpy.molecule.Bond<a class="headerlink" href="#rmgpy-molecule-bond" title="
 not.</p>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="rmgpy.molecule.Bond.is_double_or_triple">
+<span class="sig-name descname"><span class="pre">is_double_or_triple</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#rmgpy.molecule.Bond.is_double_or_triple" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return <code class="docutils literal notranslate"><span class="pre">True</span></code> if the bond represents a double or triple bond or <code class="docutils literal notranslate"><span class="pre">False</span></code>
+if not.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="rmgpy.molecule.Bond.is_hydrogen_bond">
 <span class="sig-name descname"><span class="pre">is_hydrogen_bond</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#rmgpy.molecule.Bond.is_hydrogen_bond" title="Permalink to this definition">¶</a></dt>
@@ -328,6 +335,7 @@ <h3><a href="../../contents.html">Table of Contents</a></h3>
 <li><a class="reference internal" href="#rmgpy.molecule.Bond.increment_order"><code class="docutils literal notranslate"><span class="pre">Bond.increment_order()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.Bond.is_benzene"><code class="docutils literal notranslate"><span class="pre">Bond.is_benzene()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.Bond.is_double"><code class="docutils literal notranslate"><span class="pre">Bond.is_double()</span></code></a></li>
+<li><a class="reference internal" href="#rmgpy.molecule.Bond.is_double_or_triple"><code class="docutils literal notranslate"><span class="pre">Bond.is_double_or_triple()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.Bond.is_hydrogen_bond"><code class="docutils literal notranslate"><span class="pre">Bond.is_hydrogen_bond()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.Bond.is_order"><code class="docutils literal notranslate"><span class="pre">Bond.is_order()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.Bond.is_quadruple"><code class="docutils literal notranslate"><span class="pre">Bond.is_quadruple()</span></code></a></li>

diff --git a/reference/molecule/molecule.html b/reference/molecule/molecule.html
@@ -879,6 +879,13 @@ <h1>rmgpy.molecule.Molecule<a class="headerlink" href="#rmgpy-molecule-molecule"
 and bond orders are considered, and ignored if <code class="docutils literal notranslate"><span class="pre">False</span></code>.</p>
 </dd></dl>
 
+<dl class="py method">
+<dt class="sig sig-object py" id="rmgpy.molecule.Molecule.is_multidentate">
+<span class="sig-name descname"><span class="pre">is_multidentate</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#rmgpy.molecule.Molecule.is_multidentate" title="Permalink to this definition">¶</a></dt>
+<dd><p>Return <code class="docutils literal notranslate"><span class="pre">True</span></code> if the adsorbate contains at least two binding sites,
+or <code class="docutils literal notranslate"><span class="pre">False</span></code> otherwise.</p>
+</dd></dl>
+
 <dl class="py method">
 <dt class="sig sig-object py" id="rmgpy.molecule.Molecule.is_proton">
 <span class="sig-name descname"><span class="pre">is_proton</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#rmgpy.molecule.Molecule.is_proton" title="Permalink to this definition">¶</a></dt>
@@ -1320,6 +1327,7 @@ <h3><a href="../../contents.html">Table of Contents</a></h3>
 <li><a class="reference internal" href="#rmgpy.molecule.Molecule.is_isomorphic"><code class="docutils literal notranslate"><span class="pre">Molecule.is_isomorphic()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.Molecule.is_linear"><code class="docutils literal notranslate"><span class="pre">Molecule.is_linear()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.Molecule.is_mapping_valid"><code class="docutils literal notranslate"><span class="pre">Molecule.is_mapping_valid()</span></code></a></li>
+<li><a class="reference internal" href="#rmgpy.molecule.Molecule.is_multidentate"><code class="docutils literal notranslate"><span class="pre">Molecule.is_multidentate()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.Molecule.is_proton"><code class="docutils literal notranslate"><span class="pre">Molecule.is_proton()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.Molecule.is_radical"><code class="docutils literal notranslate"><span class="pre">Molecule.is_radical()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.Molecule.is_subgraph_isomorphic"><code class="docutils literal notranslate"><span class="pre">Molecule.is_subgraph_isomorphic()</span></code></a></li>

diff --git a/reference/molecule/pathfinder.html b/reference/molecule/pathfinder.html
@@ -186,6 +186,34 @@ <h3>Navigation</h3>
 In direction 2 atom1 &lt;gains&gt; a lone pair, looses a radical, and atom2 gains a radical)</p>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="rmgpy.molecule.pathfinder.find_adsorbate_conjugate_delocalization_paths">
+<span class="sig-prename descclassname"><span class="pre">rmgpy.molecule.pathfinder.</span></span><span class="sig-name descname"><span class="pre">find_adsorbate_conjugate_delocalization_paths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#rmgpy.molecule.pathfinder.find_adsorbate_conjugate_delocalization_paths" title="Permalink to this definition">¶</a></dt>
+<dd><p>Find all multidentate adsorbates which have a bonding configuration X-C-C-C-X.
+Examples:</p>
+<ul class="simple">
+<li><p>XCHCHXCH/XCHCHXC, where X is the surface site. The adsorption site X
+is always placed on the left-hand side of the adatom and every adatom
+is bonded to only one surface site X.</p></li>
+</ul>
+<p>In this transition atom1 and atom5 are surface sites while atom2, atom3,
+and atom4 are carbon or nitrogen atoms.</p>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="rmgpy.molecule.pathfinder.find_adsorbate_delocalization_paths">
+<span class="sig-prename descclassname"><span class="pre">rmgpy.molecule.pathfinder.</span></span><span class="sig-name descname"><span class="pre">find_adsorbate_delocalization_paths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#rmgpy.molecule.pathfinder.find_adsorbate_delocalization_paths" title="Permalink to this definition">¶</a></dt>
+<dd><p>Find all multidentate adsorbates which have a bonding configuration X-C-C-X.
+Examples:</p>
+<ul class="simple">
+<li><p>XCXC, XCHXCH, XCXCH, where X is the surface site. The adsorption site X
+is always placed on the left-hand side of the adatom and every adatom
+is bonded to only one surface site X.</p></li>
+</ul>
+<p>In this transition atom1 and atom4 are surface sites while atom2 and atom3
+are carbon or nitrogen atoms.</p>
+</dd></dl>
+
 <dl class="py function">
 <dt class="sig sig-object py" id="rmgpy.molecule.pathfinder.find_allyl_delocalization_paths">
 <span class="sig-prename descclassname"><span class="pre">rmgpy.molecule.pathfinder.</span></span><span class="sig-name descname"><span class="pre">find_allyl_delocalization_paths</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#rmgpy.molecule.pathfinder.find_allyl_delocalization_paths" title="Permalink to this definition">¶</a></dt>
@@ -292,6 +320,8 @@ <h3><a href="../../contents.html">Table of Contents</a></h3>
 <li><a class="reference internal" href="#rmgpy.molecule.pathfinder.find_adj_lone_pair_multiple_bond_delocalization_paths"><code class="docutils literal notranslate"><span class="pre">find_adj_lone_pair_multiple_bond_delocalization_paths()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.pathfinder.find_adj_lone_pair_radical_delocalization_paths"><code class="docutils literal notranslate"><span class="pre">find_adj_lone_pair_radical_delocalization_paths()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.pathfinder.find_adj_lone_pair_radical_multiple_bond_delocalization_paths"><code class="docutils literal notranslate"><span class="pre">find_adj_lone_pair_radical_multiple_bond_delocalization_paths()</span></code></a></li>
+<li><a class="reference internal" href="#rmgpy.molecule.pathfinder.find_adsorbate_conjugate_delocalization_paths"><code class="docutils literal notranslate"><span class="pre">find_adsorbate_conjugate_delocalization_paths()</span></code></a></li>
+<li><a class="reference internal" href="#rmgpy.molecule.pathfinder.find_adsorbate_delocalization_paths"><code class="docutils literal notranslate"><span class="pre">find_adsorbate_delocalization_paths()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.pathfinder.find_allyl_delocalization_paths"><code class="docutils literal notranslate"><span class="pre">find_allyl_delocalization_paths()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.pathfinder.find_allyl_end_with_charge"><code class="docutils literal notranslate"><span class="pre">find_allyl_end_with_charge()</span></code></a></li>
 <li><a class="reference internal" href="#rmgpy.molecule.pathfinder.find_butadiene"><code class="docutils literal notranslate"><span class="pre">find_butadiene()</span></code></a></li>