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<li><a class="reference internal" href="#">pymatgen.analysis.chemenv.connectivity package</a><ul>
<li><a class="reference internal" href="#submodules">Submodules</a></li>
<li><a class="reference internal" href="#module-pymatgen.analysis.chemenv.connectivity.connected_components">pymatgen.analysis.chemenv.connectivity.connected_components module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.as_dict"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.compute_periodicity()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity_all_simple_paths_algorithm"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.compute_periodicity_all_simple_paths_algorithm()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity_cycle_basis"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.compute_periodicity_cycle_basis()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.coordination_sequence"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.coordination_sequence()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.description"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.description()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.elastic_centered_graph"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.elastic_centered_graph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.from_dict"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.from_graph"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.from_graph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.graph"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.graph</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_0d"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.is_0d</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_1d"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.is_1d</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_2d"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.is_2d</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_3d"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.is_3d</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_periodic"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.is_periodic</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.make_supergraph"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.make_supergraph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.periodicity"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.periodicity</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.periodicity_vectors"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.periodicity_vectors</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.show_graph"><code class="docutils literal notranslate"><span class="pre">ConnectedComponent.show_graph()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.draw_network"><code class="docutils literal notranslate"><span class="pre">draw_network()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.make_supergraph"><code class="docutils literal notranslate"><span class="pre">make_supergraph()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.chemenv.connectivity.connectivity_finder">pymatgen.analysis.chemenv.connectivity.connectivity_finder module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder"><code class="docutils literal notranslate"><span class="pre">ConnectivityFinder</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder.get_structure_connectivity"><code class="docutils literal notranslate"><span class="pre">ConnectivityFinder.get_structure_connectivity()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder.setup_parameters"><code class="docutils literal notranslate"><span class="pre">ConnectivityFinder.setup_parameters()</span></code></a></li>
</ul>
</li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.chemenv.connectivity.environment_nodes">pymatgen.analysis.chemenv.connectivity.environment_nodes module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ATOM"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.ATOM</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.CE_NNBCES_NBCES_LIGANDS"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.CE_NNBCES_NBCES_LIGANDS</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.COORDINATION_ENVIRONMENT"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.COORDINATION_ENVIRONMENT</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.DEFAULT_EXTENSIONS"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.DEFAULT_EXTENSIONS</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.LIGANDS_ARRANGEMENT"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.LIGANDS_ARRANGEMENT</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORING_CES"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NEIGHBORING_CES</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORING_COORDINATION_ENVIRONMENTS"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NEIGHBORING_COORDINATION_ENVIRONMENTS</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORS_LIGANDS_ARRANGEMENT"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NEIGHBORS_LIGANDS_ARRANGEMENT</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_CES"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_CES</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.atom_symbol"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.atom_symbol</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ce"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.ce</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ce_symbol"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.ce_symbol</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.coordination_environment"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.coordination_environment</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.everything_equal"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.everything_equal()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.isite"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.isite</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.mp_symbol"><code class="docutils literal notranslate"><span class="pre">AbstractEnvironmentNode.mp_symbol</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode"><code class="docutils literal notranslate"><span class="pre">EnvironmentNode</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode.coordination_environment"><code class="docutils literal notranslate"><span class="pre">EnvironmentNode.coordination_environment</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode.everything_equal"><code class="docutils literal notranslate"><span class="pre">EnvironmentNode.everything_equal()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.get_environment_node"><code class="docutils literal notranslate"><span class="pre">get_environment_node()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#module-pymatgen.analysis.chemenv.connectivity.structure_connectivity">pymatgen.analysis.chemenv.connectivity.structure_connectivity module</a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity</span></code></a><ul>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.add_bonds"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.add_bonds()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.add_sites"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.add_sites()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.as_dict"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.as_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.environment_subgraph"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.environment_subgraph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.from_dict"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.from_dict()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.get_connected_components"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.get_connected_components()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.print_links"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.print_links()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_atom_environment_subgraph"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.setup_atom_environment_subgraph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_atom_environments_subgraph"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.setup_atom_environments_subgraph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_connectivity_description"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.setup_connectivity_description()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_environment_subgraph"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.setup_environment_subgraph()</span></code></a></li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_environments_subgraph"><code class="docutils literal notranslate"><span class="pre">StructureConnectivity.setup_environments_subgraph()</span></code></a></li>
</ul>
</li>
<li><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.get_delta_image"><code class="docutils literal notranslate"><span class="pre">get_delta_image()</span></code></a></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
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<section id="module-pymatgen.analysis.chemenv.connectivity">
<span id="pymatgen-analysis-chemenv-connectivity-package"></span><h1>pymatgen.analysis.chemenv.connectivity package<a class="headerlink" href="#module-pymatgen.analysis.chemenv.connectivity" title="Link to this heading"></a></h1>
<p>Package for analyzing connectivity.</p>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Link to this heading"></a></h2>
</section>
<section id="module-pymatgen.analysis.chemenv.connectivity.connected_components">
<span id="pymatgen-analysis-chemenv-connectivity-connected-components-module"></span><h2>pymatgen.analysis.chemenv.connectivity.connected_components module<a class="headerlink" href="#module-pymatgen.analysis.chemenv.connectivity.connected_components" title="Link to this heading"></a></h2>
<p>Connected components.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ConnectedComponent</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">environments</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">links</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">environments_data</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">links_data</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">graph</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 external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L201-L905"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Describe the connected components in a structure in terms of coordination environments.</p>
<p>Constructor for the ConnectedComponent object.</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>environments</strong> – Environments in the connected component.</p></li>
<li><p><strong>links</strong> – Links between environments in the connected component.</p></li>
<li><p><strong>environments_data</strong> – Data of environment nodes.</p></li>
<li><p><strong>links_data</strong> – Data of links between environment nodes.</p></li>
<li><p><strong>graph</strong> – Graph of the connected component.</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L815-L840"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.as_dict" title="Link to this definition"></a></dt>
<dd><p>Bson-serializable dict representation of the ConnectedComponent object.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Bson-serializable dict representation of the ConnectedComponent object.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity">
<span class="sig-name descname"><span class="pre">compute_periodicity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">algorithm</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'all_simple_paths'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L377-L389"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity" 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"><p><strong>algorithm</strong> (<em>str</em>) – Algorithm to use to compute the periodicity vectors. Can be
either “all_simple_paths” or “cycle_basis”.</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity_all_simple_paths_algorithm">
<span class="sig-name descname"><span class="pre">compute_periodicity_all_simple_paths_algorithm</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L391-L474"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity_all_simple_paths_algorithm" title="Link to this definition"></a></dt>
<dd><p>Get the periodicity vectors of the connected component.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity_cycle_basis">
<span class="sig-name descname"><span class="pre">compute_periodicity_cycle_basis</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L476-L516"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.compute_periodicity_cycle_basis" title="Link to this definition"></a></dt>
<dd><p>Compute periodicity vectors of the connected component.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.coordination_sequence">
<span class="sig-name descname"><span class="pre">coordination_sequence</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">source_node</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">path_size</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">coordination</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'number'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">include_source</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 external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L267-L372"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.coordination_sequence" title="Link to this definition"></a></dt>
<dd><p>Get the coordination sequence for a given node.</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>source_node</strong> – Node for which the coordination sequence is computed.</p></li>
<li><p><strong>path_size</strong> – Maximum length of the path for the coordination sequence.</p></li>
<li><p><strong>coordination</strong> – Type of coordination sequence. The default (“number”) corresponds to the number
of environment nodes that are reachable by following paths of sizes between 1 and path_size.
For coordination “env:number”, this resulting coordination sequence is a sequence of dictionaries
mapping the type of environment to the number of such environment reachable by following paths of
sizes between 1 and path_size.</p></li>
<li><p><strong>include_source</strong> – Whether to include the source_node in the coordination sequence.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Mapping between the nth “layer” of the connected component with the corresponding coordination.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>dict</p>
</dd>
</dl>
<p class="rubric">Examples</p>
<p>The corner-sharing octahedral framework (as in perovskites) have the following coordination sequence (up to
a path of size 6) :
{1: 6, 2: 18, 3: 38, 4: 66, 5: 102, 6: 146}
Considering both the octahedrons and the cuboctahedrons of the typical BaTiO3 perovskite, the “env:number”
coordination sequence (up to a path of size 6) starting on the Ti octahedron and Ba cuboctahedron
are the following :
Starting on the Ti octahedron : {1: {‘O:6’: 6, ‘C:12’: 8}, 2: {‘O:6’: 26, ‘C:12’: 48},</p>
<blockquote>
<div><p>3: {‘O:6’: 90, ‘C:12’: 128}, 4: {‘O:6’: 194, ‘C:12’: 248},
5: {‘O:6’: 338, ‘C:12’: 408}, 6: {‘O:6’: 522, ‘C:12’: 608}}</p>
</div></blockquote>
<dl class="simple">
<dt>Starting on the Ba cuboctahedron<span class="classifier">{1: {‘O:6’: 8, ‘C:12’: 18}, 2: {‘O:6’: 48, ‘C:12’: 74},</span></dt><dd><p>3: {‘O:6’: 128, ‘C:12’: 170}, 4: {‘O:6’: 248, ‘C:12’: 306},
5: {‘O:6’: 408, ‘C:12’: 482}, 6: {‘O:6’: 608, ‘C:12’: 698}}</p>
</dd>
</dl>
<p>If include_source is set to True, the source node is included in the sequence, e.g. for the corner-sharing
octahedral framework : {0: 1, 1: 6, 2: 18, 3: 38, 4: 66, 5: 102, 6: 146}. For the “env:number” coordination
starting on a Ba cuboctahedron (as shown above), the coordination sequence is then :
{0: {‘C:12’: 1}, 1: {‘O:6’: 8, ‘C:12’: 18}, 2: {‘O:6’: 48, ‘C:12’: 74}, 3: {‘O:6’: 128, ‘C:12’: 170},</p>
<blockquote>
<div><p>4: {‘O:6’: 248, ‘C:12’: 306}, 5: {‘O:6’: 408, ‘C:12’: 482}, 6: {‘O:6’: 608, ‘C:12’: 698}}</p>
</div></blockquote>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.description">
<span class="sig-name descname"><span class="pre">description</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">full</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 external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L883-L905"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.description" 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"><p><strong>full</strong> (<em>bool</em>) – Whether to return a short or full description.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>A description of the connected component.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>str</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.elastic_centered_graph">
<span class="sig-name descname"><span class="pre">elastic_centered_graph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">start_node</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 external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L644-L756"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.elastic_centered_graph" 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"><p><strong>start_node</strong> (<em>Node</em><em>, </em><em>optional</em>) – Node to start the elastic centering from.
If not provided, the first node in the graph is used.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Elastic centered subgraph.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>nx.MultiGraph</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L842-L868"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.from_dict" title="Link to this definition"></a></dt>
<dd><p>Reconstructs the ConnectedComponent object from a dict representation of the
ConnectedComponent object created using the as_dict method.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>dct</strong> (<em>dict</em>) – dict representation of the ConnectedComponent object</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The connected component representing the links of a given set of environments.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent" title="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent">ConnectedComponent</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.from_graph">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_graph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">g</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L870-L881"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.from_graph" title="Link to this definition"></a></dt>
<dd><p>Constructor for the ConnectedComponent object from a graph of the connected component.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>g</strong> (<em>MultiGraph</em>) – Graph of the connected component.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The connected component representing the links of a given set of environments.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent" title="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent">ConnectedComponent</a></p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.graph">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">graph</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/connected_components.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.graph" title="Link to this definition"></a></dt>
<dd><p>The Networkx MultiGraph object of this connected component with environment as nodes and links
between these nodes as edges with information about the image cell difference if any.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_0d">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">is_0d</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/connected_components.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_0d" title="Link to this definition"></a></dt>
<dd><p>Whether this connected component is 0-dimensional.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_1d">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">is_1d</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/connected_components.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_1d" title="Link to this definition"></a></dt>
<dd><p>Whether this connected component is 1-dimensional.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_2d">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">is_2d</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/connected_components.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_2d" title="Link to this definition"></a></dt>
<dd><p>Whether this connected component is 2-dimensional.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_3d">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">is_3d</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/connected_components.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_3d" title="Link to this definition"></a></dt>
<dd><p>Whether this connected component is 3-dimensional.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_periodic">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">is_periodic</span></span><em class="property"><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="pre">bool</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/connected_components.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.is_periodic" title="Link to this definition"></a></dt>
<dd><p>Whether this connected component is periodic.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.make_supergraph">
<span class="sig-name descname"><span class="pre">make_supergraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">multiplicity</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L518-L526"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.make_supergraph" 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"><p><strong>multiplicity</strong> (<em>int</em>) – Multiplicity of the super graph.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Super graph of the connected component.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>nx.MultiGraph</p>
</dd>
</dl>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.periodicity">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">periodicity</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/connected_components.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.periodicity" title="Link to this definition"></a></dt>
<dd><p>Periodicity of this connected component.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.periodicity_vectors">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">periodicity_vectors</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/connected_components.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.periodicity_vectors" title="Link to this definition"></a></dt>
<dd><p>Periodicity vectors of this connected component.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.show_graph">
<span class="sig-name descname"><span class="pre">show_graph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">MultiGraph</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_file</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">None</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">drawing_type</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'internal'</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L528-L560"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.ConnectedComponent.show_graph" title="Link to this definition"></a></dt>
<dd><p>Displays the graph using the specified drawing type.</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>graph</strong> (<em>Graph</em><em>, </em><em>optional</em>) – The graph to display. If not provided, the current graph is used.</p></li>
<li><p><strong>save_file</strong> (<em>str</em><em>, </em><em>optional</em>) – The file path to save the graph image to.
If not provided, the graph is not saved.</p></li>
<li><p><strong>drawing_type</strong> (<em>str</em>) – The type of drawing to use. Can be “internal” or “external”.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.draw_network">
<span class="sig-name descname"><span class="pre">draw_network</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">env_graph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pos</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ax</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">sg</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">periodicity_vectors</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 external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L26-L125"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.draw_network" title="Link to this definition"></a></dt>
<dd><p>Draw network of environments in a matplotlib figure axes.</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>env_graph</strong> – Graph of environments.</p></li>
<li><p><strong>pos</strong> – Positions of the nodes of the environments in the 2D figure.</p></li>
<li><p><strong>ax</strong> – Axes object in which the network should be drawn.</p></li>
<li><p><strong>sg</strong> – Not used currently (drawing of supergraphs).</p></li>
<li><p><strong>periodicity_vectors</strong> – List of periodicity vectors that should be drawn.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connected_components.make_supergraph">
<span class="sig-name descname"><span class="pre">make_supergraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">multiplicity</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">periodicity_vectors</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connected_components.py#L128-L198"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connected_components.make_supergraph" title="Link to this definition"></a></dt>
<dd><p>Make super graph from a graph of environments.</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>graph</strong> – Graph of environments.</p></li>
<li><p><strong>multiplicity</strong> – Multiplicity of the super graph.</p></li>
<li><p><strong>periodicity_vectors</strong> – Periodicity vectors needed to make the super graph.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Super graph of the environments.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>nx.MultiGraph</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.chemenv.connectivity.connectivity_finder">
<span id="pymatgen-analysis-chemenv-connectivity-connectivity-finder-module"></span><h2>pymatgen.analysis.chemenv.connectivity.connectivity_finder module<a class="headerlink" href="#module-pymatgen.analysis.chemenv.connectivity.connectivity_finder" title="Link to this heading"></a></h2>
<p>Module implementing connectivity finding.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ConnectivityFinder</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">multiple_environments_choice</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 external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connectivity_finder.py#L20-L73"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Main class used to find the structure connectivity of a structure.</p>
<p>Constructor for the ConnectivityFinder.</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>multiple_environments_choice</strong> – defines the procedure to apply when</p></li>
<li><p><strong>one</strong> (<em>the environment</em><em> of </em><em>a given site is described as a "mix"</em><em> of </em><em>more than</em>)</p></li>
<li><p><strong>environments.</strong> (<em>coordination</em>)</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder.get_structure_connectivity">
<span class="sig-name descname"><span class="pre">get_structure_connectivity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">light_structure_environments</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connectivity_finder.py#L34-L67"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder.get_structure_connectivity" title="Link to this definition"></a></dt>
<dd><p>Get the structure connectivity from the coordination environments provided
as an input.</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>light_structure_environments</strong> – LightStructureEnvironments with the</p></li>
<li><p><strong>structure</strong> (<em>relevant coordination environments in the</em>)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>a StructureConnectivity object describing the connectivity of</p>
</dd>
</dl>
<p>the environments in the structure</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder.setup_parameters">
<span class="sig-name descname"><span class="pre">setup_parameters</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">multiple_environments_choice</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/connectivity_finder.py#L69-L73"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.connectivity_finder.ConnectivityFinder.setup_parameters" title="Link to this definition"></a></dt>
<dd><p>Setup of the parameters for the connectivity finder.</p>
</dd></dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.chemenv.connectivity.environment_nodes">
<span id="pymatgen-analysis-chemenv-connectivity-environment-nodes-module"></span><h2>pymatgen.analysis.chemenv.connectivity.environment_nodes module<a class="headerlink" href="#module-pymatgen.analysis.chemenv.connectivity.environment_nodes" title="Link to this heading"></a></h2>
<p>Environment nodes module.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">AbstractEnvironmentNode</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">central_site</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">i_central_site</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/environment_nodes.py#L10-L96"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Abstract class used to define an environment as a node in a graph.</p>
<p>Constructor for the AbstractEnvironmentNode object.</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>central_site</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a><em> or </em><em>subclass</em><em> of </em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a>) – central site as a pymatgen Site or
subclass of Site (e.g. PeriodicSite, …).</p></li>
<li><p><strong>i_central_site</strong> (<em>int</em>) – Index of the central site in the structure.</p></li>
</ul>
</dd>
</dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ATOM">
<span class="sig-name descname"><span class="pre">ATOM</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">6</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ATOM" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.CE_NNBCES_NBCES_LIGANDS">
<span class="sig-name descname"><span class="pre">CE_NNBCES_NBCES_LIGANDS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">-1</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.CE_NNBCES_NBCES_LIGANDS" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.COORDINATION_ENVIRONMENT">
<span class="sig-name descname"><span class="pre">COORDINATION_ENVIRONMENT</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">0</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.COORDINATION_ENVIRONMENT" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.DEFAULT_EXTENSIONS">
<span class="sig-name descname"><span class="pre">DEFAULT_EXTENSIONS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">(6,</span> <span class="pre">0)</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.DEFAULT_EXTENSIONS" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.LIGANDS_ARRANGEMENT">
<span class="sig-name descname"><span class="pre">LIGANDS_ARRANGEMENT</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">4</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.LIGANDS_ARRANGEMENT" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORING_CES">
<span class="sig-name descname"><span class="pre">NEIGHBORING_CES</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">2</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORING_CES" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORING_COORDINATION_ENVIRONMENTS">
<span class="sig-name descname"><span class="pre">NEIGHBORING_COORDINATION_ENVIRONMENTS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">2</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORING_COORDINATION_ENVIRONMENTS" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORS_LIGANDS_ARRANGEMENT">
<span class="sig-name descname"><span class="pre">NEIGHBORS_LIGANDS_ARRANGEMENT</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">5</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NEIGHBORS_LIGANDS_ARRANGEMENT" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE">
<span class="sig-name descname"><span class="pre">NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">3</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_CE" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT">
<span class="sig-name descname"><span class="pre">NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">3</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_LIGANDS_FOR_EACH_NEIGHBORING_COORDINATION_ENVIRONMENT" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_CES">
<span class="sig-name descname"><span class="pre">NUMBER_OF_NEIGHBORING_CES</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_CES" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS">
<span class="sig-name descname"><span class="pre">NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">1</span></em><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.atom_symbol">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">atom_symbol</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.atom_symbol" title="Link to this definition"></a></dt>
<dd><p>Symbol of the atom on the central site.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ce">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ce</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ce" title="Link to this definition"></a></dt>
<dd><p>Coordination environment of this node.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ce_symbol">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">ce_symbol</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.ce_symbol" title="Link to this definition"></a></dt>
<dd><p>Coordination environment of this node.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.coordination_environment">
<em class="property"><span class="pre">abstract</span><span class="w"> </span><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">coordination_environment</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.coordination_environment" title="Link to this definition"></a></dt>
<dd><p>Coordination environment of this node.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.everything_equal">
<span class="sig-name descname"><span class="pre">everything_equal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/environment_nodes.py#L62-L66"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.everything_equal" title="Link to this definition"></a></dt>
<dd><p>Check equality with respect to another AbstractEnvironmentNode using the index of the central site
as well as the central site itself.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.isite">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">isite</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.isite" title="Link to this definition"></a></dt>
<dd><p>Index of the central site.</p>
</dd></dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.mp_symbol">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">mp_symbol</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode.mp_symbol" title="Link to this definition"></a></dt>
<dd><p>Coordination environment of this node.</p>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">EnvironmentNode</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">central_site</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">i_central_site</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ce_symbol</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/environment_nodes.py#L99-L126"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode" title="Link to this definition"></a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode" title="pymatgen.analysis.chemenv.connectivity.environment_nodes.AbstractEnvironmentNode"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractEnvironmentNode</span></code></a></p>
<p>Define an environment as a node in a graph.</p>
<p>Constructor for the EnvironmentNode object.</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>central_site</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a><em> or </em><em>subclass</em><em> of </em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a>) – central site as a pymatgen Site or
subclass of Site (e.g. PeriodicSite, …).</p></li>
<li><p><strong>i_central_site</strong> (<em>int</em>) – Index of the central site in the structure.</p></li>
<li><p><strong>ce_symbol</strong> (<em>str</em>) – Symbol of the identified environment.</p></li>
</ul>
</dd>
</dl>
<dl class="py property">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode.coordination_environment">
<em class="property"><span class="pre">property</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">coordination_environment</span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/analysis/chemenv/connectivity/environment_nodes.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode.coordination_environment" title="Link to this definition"></a></dt>
<dd><p>Coordination environment of this node.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode.everything_equal">
<span class="sig-name descname"><span class="pre">everything_equal</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">other</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/environment_nodes.py#L120-L126"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.EnvironmentNode.everything_equal" title="Link to this definition"></a></dt>
<dd><p>Compare with another environment node.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>True if it is equal to the other node.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>bool</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.environment_nodes.get_environment_node">
<span class="sig-name descname"><span class="pre">get_environment_node</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">central_site</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">i_central_site</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ce_symbol</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/environment_nodes.py#L159-L170"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.environment_nodes.get_environment_node" title="Link to this definition"></a></dt>
<dd><p>Get the EnvironmentNode class or subclass for the given site and symbol.</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>central_site</strong> (<a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a><em> or </em><em>subclass</em><em> of </em><a class="reference internal" href="pymatgen.core.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a>) – Central site of the environment.</p></li>
<li><p><strong>i_central_site</strong> (<em>int</em>) – Index of the central site in the structure.</p></li>
<li><p><strong>ce_symbol</strong> – Symbol of the environment.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>An EnvironmentNode object.</p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-pymatgen.analysis.chemenv.connectivity.structure_connectivity">
<span id="pymatgen-analysis-chemenv-connectivity-structure-connectivity-module"></span><h2>pymatgen.analysis.chemenv.connectivity.structure_connectivity module<a class="headerlink" href="#module-pymatgen.analysis.chemenv.connectivity.structure_connectivity" title="Link to this heading"></a></h2>
<p>Structure connectivity class.</p>
<dl class="py class">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">StructureConnectivity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">light_structure_environment</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">connectivity_graph</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">environment_subgraphs</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 external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L43-L333"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity" title="Link to this definition"></a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">MSONable</span></code></p>
<p>Main class containing the connectivity of a structure.</p>
<p>Constructor for the StructureConnectivity object.</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>light_structure_environment</strong> – a LightStructureEnvironments object
containing the relevant local environments
for the sites in the structure.</p></li>
<li><p><strong>connectivity_graph</strong> – the networkx MultiGraph if it has already been computed,
e.g. stored in a file or dict and StructureConnectivity
is reconstructed from that file or dict.</p></li>
<li><p><strong>environment_subgraphs</strong> – the different subgraphs of environments that have
been computed if any (as for connectivity_graph, only
if it is reconstructed from a file or dict).</p></li>
</ul>
</dd>
</dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.add_bonds">
<span class="sig-name descname"><span class="pre">add_bonds</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">isite</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">site_neighbors_set</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L98-L143"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.add_bonds" title="Link to this definition"></a></dt>
<dd><p>Add the bonds for a given site index to the structure connectivity graph.</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>isite</strong> – Index of the site for which the bonds have to be added.</p></li>
<li><p><strong>site_neighbors_set</strong> – site_neighbors_set: Neighbors set of the site</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.add_sites">
<span class="sig-name descname"><span class="pre">add_sites</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L94-L96"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.add_sites" title="Link to this definition"></a></dt>
<dd><p>Add the sites in the structure connectivity graph.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.as_dict">
<span class="sig-name descname"><span class="pre">as_dict</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L291-L302"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.as_dict" title="Link to this definition"></a></dt>
<dd><p>Convert to MSONable dict.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.environment_subgraph">
<span class="sig-name descname"><span class="pre">environment_subgraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">environments_symbols</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">only_atoms</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 external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L76-L92"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.environment_subgraph" 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>environments_symbols</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – symbols of the environments to consider.</p></li>
<li><p><strong>only_atoms</strong> (<em>list</em><em>[</em><em>str</em><em>]</em>) – atoms to consider.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>The subgraph of the structure connectivity graph</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>nx.MultiGraph</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.from_dict">
<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">from_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dct</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">dict</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">Self</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L304-L333"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.from_dict" 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"><p><strong>dct</strong> (<em>dict</em>)</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>StructureConnectivity</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.get_connected_components">
<span class="sig-name descname"><span class="pre">get_connected_components</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">environments_symbols</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">only_atoms</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 external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L256-L262"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.get_connected_components" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.print_links">
<span class="sig-name descname"><span class="pre">print_links</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">→</span> <span class="sig-return-typehint"><span class="pre">None</span></span></span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L273-L289"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.print_links" title="Link to this definition"></a></dt>
<dd><p>Print all links in the graph.</p>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_atom_environment_subgraph">
<span class="sig-name descname"><span class="pre">setup_atom_environment_subgraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atom_environment</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L264-L265"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_atom_environment_subgraph" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_atom_environments_subgraph">
<span class="sig-name descname"><span class="pre">setup_atom_environments_subgraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">atoms_environments</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L270-L271"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_atom_environments_subgraph" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_connectivity_description">
<span class="sig-name descname"><span class="pre">setup_connectivity_description</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L253-L254"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_connectivity_description" title="Link to this definition"></a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_environment_subgraph">
<span class="sig-name descname"><span class="pre">setup_environment_subgraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">environments_symbols</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_atoms</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 external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L145-L251"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_environment_subgraph" title="Link to this definition"></a></dt>
<dd><p>Set up the graph for predefined environments and optionally 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>environments_symbols</strong> – Symbols of the environments for the environment subgraph.</p></li>
<li><p><strong>only_atoms</strong> – Atoms to be considered.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_environments_subgraph">
<span class="sig-name descname"><span class="pre">setup_environments_subgraph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">environments_symbols</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L267-L268"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.StructureConnectivity.setup_environments_subgraph" title="Link to this definition"></a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="pymatgen.analysis.chemenv.connectivity.structure_connectivity.get_delta_image">
<span class="sig-name descname"><span class="pre">get_delta_image</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">isite1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">isite2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">data2</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/materialsproject/pymatgen/blob/v2025.1.24/src/pymatgen/core/../analysis/chemenv/connectivity/structure_connectivity.py#L29-L40"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#pymatgen.analysis.chemenv.connectivity.structure_connectivity.get_delta_image" title="Link to this definition"></a></dt>
<dd><p>Helper method to get the delta image between one environment and another
from the ligand’s delta images.</p>
</dd></dl>
</section>
</section>
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