From 32ef51b89f621034ad2966eeef5ed4a7ecb132bd Mon Sep 17 00:00:00 2001
From: drugilsberg <drugilsberg@users.noreply.github.com>
Date: Tue, 16 Jul 2024 07:39:21 +0000
Subject: [PATCH] deploy: 43e1233cc38383a555a3321197cbaf35317c32d1

---
 _modules/rxn/chemutils/conversion.html               | 12 ++++++------
 _modules/rxn/chemutils/miscellaneous.html            |  4 ++--
 ...rxn.chemutils.reaction_smiles.ReactionFormat.html |  2 +-
 searchindex.js                                       |  2 +-
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/_modules/rxn/chemutils/conversion.html b/_modules/rxn/chemutils/conversion.html
index a7d0cb1..dbb1a79 100644
--- a/_modules/rxn/chemutils/conversion.html
+++ b/_modules/rxn/chemutils/conversion.html
@@ -88,7 +88,7 @@ <h1>Source code for rxn.chemutils.conversion</h1><div class="highlight"><pre>
 
 <span class="kn">from</span> <span class="nn">.exceptions</span> <span class="kn">import</span> <span class="n">InvalidInchi</span><span class="p">,</span> <span class="n">InvalidMdl</span><span class="p">,</span> <span class="n">InvalidSmiles</span><span class="p">,</span> <span class="n">SanitizationError</span>
 
-<span class="n">RDLogger</span><span class="o">.</span><span class="n">logger</span><span class="p">()</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">RDLogger</span><span class="o">.</span><span class="n">CRITICAL</span><span class="p">)</span>
+<span class="n">RDLogger</span><span class="o">.</span><span class="n">logger</span><span class="p">()</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">RDLogger</span><span class="o">.</span><span class="n">CRITICAL</span><span class="p">)</span>  <span class="c1"># type: ignore[no-untyped-call]</span>
 
 
 <div class="viewcode-block" id="smiles_to_mol"><a class="viewcode-back" href="../../../generated/rxn.chemutils.conversion.smiles_to_mol.html#rxn.chemutils.conversion.smiles_to_mol">[docs]</a><span class="k">def</span> <span class="nf">smiles_to_mol</span><span class="p">(</span>
@@ -124,7 +124,7 @@ <h1>Source code for rxn.chemutils.conversion</h1><div class="highlight"><pre>
     <span class="c1"># function, either with no sanitization, or with radical finding.</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="n">sanitize</span><span class="p">:</span>
         <span class="k">if</span> <span class="n">find_radicals</span><span class="p">:</span>
-            <span class="n">sanitizations</span> <span class="o">=</span> <span class="p">[</span><span class="n">Chem</span><span class="o">.</span><span class="n">SANITIZE_FINDRADICALS</span><span class="p">]</span>
+            <span class="n">sanitizations</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">SanitizeFlags</span> <span class="o">|</span> <span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="n">Chem</span><span class="o">.</span><span class="n">SANITIZE_FINDRADICALS</span><span class="p">]</span>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">sanitizations</span> <span class="o">=</span> <span class="p">[</span><span class="n">Chem</span><span class="o">.</span><span class="n">SANITIZE_NONE</span><span class="p">]</span>
 
@@ -151,7 +151,7 @@ <h1>Source code for rxn.chemutils.conversion</h1><div class="highlight"><pre>
 <span class="sd">    Returns:</span>
 <span class="sd">        Mol instance.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">mol</span> <span class="o">=</span> <span class="n">MolFromInchi</span><span class="p">(</span><span class="n">inchi</span><span class="p">,</span> <span class="n">sanitize</span><span class="o">=</span><span class="n">sanitize</span><span class="p">,</span> <span class="n">removeHs</span><span class="o">=</span><span class="n">removeHs</span><span class="p">)</span>
+    <span class="n">mol</span><span class="p">:</span> <span class="n">Mol</span> <span class="o">=</span> <span class="n">MolFromInchi</span><span class="p">(</span><span class="n">inchi</span><span class="p">,</span> <span class="n">sanitize</span><span class="o">=</span><span class="n">sanitize</span><span class="p">,</span> <span class="n">removeHs</span><span class="o">=</span><span class="n">removeHs</span><span class="p">)</span>  <span class="c1"># type: ignore[no-untyped-call]</span>
     <span class="k">if</span> <span class="ow">not</span> <span class="n">inchi</span> <span class="ow">or</span> <span class="n">mol</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
         <span class="k">raise</span> <span class="n">InvalidInchi</span><span class="p">(</span><span class="n">inchi</span><span class="p">)</span>
 
@@ -164,7 +164,7 @@ <h1>Source code for rxn.chemutils.conversion</h1><div class="highlight"><pre>
 
 <span class="sd">    Mainly a wrapper around MolToSmiles.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">MolToSmiles</span><span class="p">(</span><span class="n">mol</span><span class="p">,</span> <span class="n">canonical</span><span class="o">=</span><span class="n">canonical</span><span class="p">,</span> <span class="n">isomericSmiles</span><span class="o">=</span><span class="n">isomericSmiles</span><span class="p">)</span>  <span class="c1"># type: ignore</span></div>
+    <span class="k">return</span> <span class="n">MolToSmiles</span><span class="p">(</span><span class="n">mol</span><span class="p">,</span> <span class="n">canonical</span><span class="o">=</span><span class="n">canonical</span><span class="p">,</span> <span class="n">isomericSmiles</span><span class="o">=</span><span class="n">isomericSmiles</span><span class="p">)</span></div>
 
 
 <div class="viewcode-block" id="mdl_to_mol"><a class="viewcode-back" href="../../../generated/rxn.chemutils.conversion.mdl_to_mol.html#rxn.chemutils.conversion.mdl_to_mol">[docs]</a><span class="k">def</span> <span class="nf">mdl_to_mol</span><span class="p">(</span><span class="n">mdl</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">sanitize</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Mol</span><span class="p">:</span>
@@ -197,7 +197,7 @@ <h1>Source code for rxn.chemutils.conversion</h1><div class="highlight"><pre>
 
 <span class="sd">    Mainly a wrapper around MolToMolBlock.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">MolToMolBlock</span><span class="p">(</span><span class="n">mol</span><span class="p">)</span>  <span class="c1"># type: ignore</span></div>
+    <span class="k">return</span> <span class="n">MolToMolBlock</span><span class="p">(</span><span class="n">mol</span><span class="p">)</span></div>
 
 
 <div class="viewcode-block" id="sanitize_mol"><a class="viewcode-back" href="../../../generated/rxn.chemutils.conversion.sanitize_mol.html#rxn.chemutils.conversion.sanitize_mol">[docs]</a><span class="k">def</span> <span class="nf">sanitize_mol</span><span class="p">(</span>
@@ -306,7 +306,7 @@ <h1>Source code for rxn.chemutils.conversion</h1><div class="highlight"><pre>
 
     <span class="c1"># Sanitization as a separate step, to enable exclusion of valence check</span>
     <span class="k">try</span><span class="p">:</span>
-        <span class="n">excluded_sanitizations</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="n">excluded_sanitizations</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">SanitizeFlags</span> <span class="o">|</span> <span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="k">if</span> <span class="ow">not</span> <span class="n">check_valence</span><span class="p">:</span>
             <span class="n">excluded_sanitizations</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Chem</span><span class="o">.</span><span class="n">SANITIZE_PROPERTIES</span><span class="p">)</span>
         <span class="n">sanitize_mol</span><span class="p">(</span><span class="n">mol</span><span class="p">,</span> <span class="n">exclude_sanitizations</span><span class="o">=</span><span class="n">excluded_sanitizations</span><span class="p">)</span>
diff --git a/_modules/rxn/chemutils/miscellaneous.html b/_modules/rxn/chemutils/miscellaneous.html
index e40da56..a53982e 100644
--- a/_modules/rxn/chemutils/miscellaneous.html
+++ b/_modules/rxn/chemutils/miscellaneous.html
@@ -151,7 +151,7 @@ <h1>Source code for rxn.chemutils.miscellaneous</h1><div class="highlight"><pre>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="n">mol</span><span class="p">:</span> <span class="n">Mol</span> <span class="o">=</span> <span class="n">AddHs</span><span class="p">(</span><span class="n">smiles_to_mol</span><span class="p">(</span><span class="n">smiles</span><span class="p">,</span> <span class="n">sanitize</span><span class="o">=</span><span class="kc">False</span><span class="p">))</span>
-    <span class="n">atoms</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">Atom</span><span class="p">]</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">GetAtoms</span><span class="p">()</span>
+    <span class="n">atoms</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="n">Atom</span><span class="p">]</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">GetAtoms</span><span class="p">()</span>  <span class="c1"># type: ignore[call-arg,no-untyped-call]</span>
     <span class="k">return</span> <span class="n">Counter</span><span class="p">(</span><span class="n">atom</span><span class="o">.</span><span class="n">GetSymbol</span><span class="p">()</span> <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">)</span></div>
 
 
@@ -394,7 +394,7 @@ <h1>Source code for rxn.chemutils.miscellaneous</h1><div class="highlight"><pre>
 <span class="sd">        mol: RDKit Mol.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">atom</span><span class="p">:</span> <span class="n">Atom</span>
-    <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">mol</span><span class="o">.</span><span class="n">GetAtoms</span><span class="p">():</span>
+    <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">mol</span><span class="o">.</span><span class="n">GetAtoms</span><span class="p">():</span>  <span class="c1"># type: ignore[call-arg,no-untyped-call]</span>
         <span class="k">if</span> <span class="n">atom</span><span class="o">.</span><span class="n">GetAtomMapNum</span><span class="p">()</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
             <span class="k">return</span> <span class="kc">True</span>
     <span class="k">return</span> <span class="kc">False</span></div>
diff --git a/generated/rxn.chemutils.reaction_smiles.ReactionFormat.html b/generated/rxn.chemutils.reaction_smiles.ReactionFormat.html
index a246027..9090507 100644
--- a/generated/rxn.chemutils.reaction_smiles.ReactionFormat.html
+++ b/generated/rxn.chemutils.reaction_smiles.ReactionFormat.html
@@ -102,7 +102,7 @@
 <h1>rxn.chemutils.reaction_smiles.ReactionFormat<a class="headerlink" href="#rxn-chemutils-reaction-smiles-reactionformat" title="Permalink to this heading"></a></h1>
 <dl class="py class">
 <dt class="sig sig-object py" id="rxn.chemutils.reaction_smiles.ReactionFormat">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">rxn.chemutils.reaction_smiles.</span></span><span class="sig-name descname"><span class="pre">ReactionFormat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">names</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">values</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">module</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qualname</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start</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">boundary</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/rxn/chemutils/reaction_smiles.html#ReactionFormat"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#rxn.chemutils.reaction_smiles.ReactionFormat" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">rxn.chemutils.reaction_smiles.</span></span><span class="sig-name descname"><span class="pre">ReactionFormat</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">names=&lt;not</span> <span class="pre">given&gt;</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">*values</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">module=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">qualname=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">type=None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start=1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">boundary=None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/rxn/chemutils/reaction_smiles.html#ReactionFormat"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#rxn.chemutils.reaction_smiles.ReactionFormat" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">RxnEnum</span></code></p>
 <p>Existing reaction SMILES formats.</p>
 <dl class="py attribute">
diff --git a/searchindex.js b/searchindex.js
index ca5a53b..76366b5 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["README", "api", "generated/rxn.chemutils", "generated/rxn.chemutils.conversion", "generated/rxn.chemutils.conversion.canonicalize_smiles", "generated/rxn.chemutils.conversion.cleanup_smiles", "generated/rxn.chemutils.conversion.inchi_to_mol", "generated/rxn.chemutils.conversion.maybe_canonicalize", "generated/rxn.chemutils.conversion.mdl_to_mol", "generated/rxn.chemutils.conversion.mdl_to_smiles", "generated/rxn.chemutils.conversion.mol_to_inchi", "generated/rxn.chemutils.conversion.mol_to_mdl", "generated/rxn.chemutils.conversion.mol_to_smiles", "generated/rxn.chemutils.conversion.remove_hydrogens", "generated/rxn.chemutils.conversion.sanitize_mol", "generated/rxn.chemutils.conversion.smiles_to_inchi", "generated/rxn.chemutils.conversion.smiles_to_mol", "generated/rxn.chemutils.conversion.split_smiles_and_fragment_info", "generated/rxn.chemutils.exceptions", "generated/rxn.chemutils.exceptions.InvalidInchi", "generated/rxn.chemutils.exceptions.InvalidMdl", "generated/rxn.chemutils.exceptions.InvalidReactionSmiles", "generated/rxn.chemutils.exceptions.InvalidSmiles", "generated/rxn.chemutils.exceptions.SanitizationError", "generated/rxn.chemutils.exceptions.UnclearWhetherTokenized", "generated/rxn.chemutils.extended_reaction_smiles", "generated/rxn.chemutils.extended_reaction_smiles.UnsupportedExtendedReactionSmiles", "generated/rxn.chemutils.extended_reaction_smiles.determine_fragment_groups", "generated/rxn.chemutils.extended_reaction_smiles.merge_molecules_from_fragment_groups", "generated/rxn.chemutils.extended_reaction_smiles.parse_extended_reaction_smiles", "generated/rxn.chemutils.extended_reaction_smiles.to_extended_reaction_smiles", "generated/rxn.chemutils.miscellaneous", "generated/rxn.chemutils.miscellaneous.apply_to_any_smiles", "generated/rxn.chemutils.miscellaneous.apply_to_smiles_groups", "generated/rxn.chemutils.miscellaneous.atom_type_counter", "generated/rxn.chemutils.miscellaneous.canonicalize_any", "generated/rxn.chemutils.miscellaneous.canonicalize_file", "generated/rxn.chemutils.miscellaneous.equivalent_smiles", "generated/rxn.chemutils.miscellaneous.get_individual_compounds", "generated/rxn.chemutils.miscellaneous.is_valid_smiles", "generated/rxn.chemutils.miscellaneous.merge_reactions", "generated/rxn.chemutils.miscellaneous.mol_has_atom_mapping", "generated/rxn.chemutils.miscellaneous.remove_chiral_centers", "generated/rxn.chemutils.miscellaneous.remove_double_bond_stereochemistry", "generated/rxn.chemutils.miscellaneous.smiles_has_atom_mapping", "generated/rxn.chemutils.miscellaneous.sort_any", "generated/rxn.chemutils.multicomponent_smiles", "generated/rxn.chemutils.multicomponent_smiles.apply_to_multicomponent_smiles", "generated/rxn.chemutils.multicomponent_smiles.canonicalize_multicomponent_smiles", "generated/rxn.chemutils.multicomponent_smiles.list_to_multicomponent_smiles", "generated/rxn.chemutils.multicomponent_smiles.multicomponent_smiles_to_list", "generated/rxn.chemutils.multicomponent_smiles.remove_duplicates_in_multicomponent_smiles", "generated/rxn.chemutils.multicomponent_smiles.sort_multicomponent_smiles", "generated/rxn.chemutils.rdf", "generated/rxn.chemutils.rdf.property_parser", "generated/rxn.chemutils.rdf.property_parser.PropertyParser", "generated/rxn.chemutils.rdf.property_parser.PropertySerializer", "generated/rxn.chemutils.rdf.property_parser.parse_properties", "generated/rxn.chemutils.rdf.property_parser.serialize_properties", "generated/rxn.chemutils.rdf.rdf_parser", "generated/rxn.chemutils.rdf.rdf_parser.IncompleteReaction", "generated/rxn.chemutils.rdf.rdf_parser.InvalidBlock", "generated/rxn.chemutils.rdf.rdf_parser.ParsedReaction", "generated/rxn.chemutils.rdf.rdf_parser.RdfParser", "generated/rxn.chemutils.rdf.rdf_parser.RdfParsingError", "generated/rxn.chemutils.rdf.rdf_parser.iterate_reactions_from_file", "generated/rxn.chemutils.rdf.rdf_reaction", "generated/rxn.chemutils.rdf.rdf_reaction.RdfReaction", "generated/rxn.chemutils.rdf.reaction_properties", "generated/rxn.chemutils.rdf.reaction_properties.Compound", "generated/rxn.chemutils.rdf.reaction_properties.ReactionProperties", "generated/rxn.chemutils.rdf.reaction_properties.find_compounds", "generated/rxn.chemutils.rdf.reaction_properties.find_compounds_with_category", "generated/rxn.chemutils.rdf.reaction_smiles_extractor", "generated/rxn.chemutils.rdf.reaction_smiles_extractor.ReactionSmilesExtractor", "generated/rxn.chemutils.rdkit_utils", "generated/rxn.chemutils.rdkit_utils.combine_mols", "generated/rxn.chemutils.reaction_combiner", "generated/rxn.chemutils.reaction_combiner.ReactionCombiner", "generated/rxn.chemutils.reaction_equation", "generated/rxn.chemutils.reaction_equation.ReactionEquation", "generated/rxn.chemutils.reaction_equation.apply_to_compound_groups", 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