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<div class="section" id="module-pymatgen.analysis.graphs">
<span id="pymatgen-analysis-graphs-module"></span><h1>pymatgen.analysis.graphs module<a class="headerlink" href="#module-pymatgen.analysis.graphs" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.analysis.graphs.ConnectedSite">
<em class="property">class </em><code class="descname">ConnectedSite</code><span class="sig-paren">(</span><em>site</em>, <em>jimage</em>, <em>index</em>, <em>weight</em>, <em>dist</em><span class="sig-paren">)</span><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">tuple</span></code></p>
<p>Create new instance of ConnectedSite(site, jimage, index, weight, dist)</p>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.ConnectedSite.dist">
<code class="descname">dist</code><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.dist" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for field number 4</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.ConnectedSite.index">
<code class="descname">index</code><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.index" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for field number 2</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.ConnectedSite.jimage">
<code class="descname">jimage</code><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.jimage" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for field number 1</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.ConnectedSite.site">
<code class="descname">site</code><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.site" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for field number 0</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.ConnectedSite.weight">
<code class="descname">weight</code><a class="headerlink" href="#pymatgen.analysis.graphs.ConnectedSite.weight" title="Permalink to this definition">¶</a></dt>
<dd><p>Alias for field number 3</p>
</dd></dl>
</dd></dl>
<dl class="exception">
<dt id="pymatgen.analysis.graphs.MolGraphSplitError">
<em class="property">exception </em><code class="descname">MolGraphSplitError</code><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MolGraphSplitError"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MolGraphSplitError" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">Exception</span></code></p>
</dd></dl>
<dl class="class">
<dt id="pymatgen.analysis.graphs.MoleculeGraph">
<em class="property">class </em><code class="descname">MoleculeGraph</code><span class="sig-paren">(</span><em>molecule</em>, <em>graph_data=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>This is a class for annotating a Molecule with
bond information, stored in the form of a graph. A “bond” does
not necessarily have to be a chemical bond, but can store any
kind of information that connects two Sites.</p>
<p>If constructing this class manually, use the <cite>with_empty_graph</cite>
method or <cite>with_local_env_strategy</cite> method (using an algorithm
provided by the <cite>local_env</cite> module, such as O’Keeffe).</p>
<p>This class that contains connection information:
relationships between sites represented by a Graph structure,
and an associated structure object.</p>
<p>This class uses the NetworkX package to store and operate
on the graph itself, but contains a lot of helper methods
to make associating a graph with a given molecule easier.</p>
<p>Use cases for this include storing bonding information,
NMR J-couplings, Heisenberg exchange parameters, etc.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> – Molecule object</p></li>
<li><p><strong>graph_data</strong> – dict containing graph information in</p></li>
</ul>
</dd>
</dl>
<p>dict format (not intended to be constructed manually,
see as_dict method for format)</p>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.add_edge">
<code class="descname">add_edge</code><span class="sig-paren">(</span><em>from_index</em>, <em>to_index</em>, <em>weight=None</em>, <em>warn_duplicates=True</em>, <em>edge_properties=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.add_edge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.add_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Add edge to graph.</p>
<p>Since physically a ‘bond’ (or other connection
between sites) doesn’t have a direction, from_index,
from_jimage can be swapped with to_index, to_jimage.</p>
<p>However, images will always always be shifted so that
from_index < to_index and from_jimage becomes (0, 0, 0).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – index of site connecting from</p></li>
<li><p><strong>to_index</strong> – index of site connecting to</p></li>
<li><p><strong>(</strong><strong>float</strong><strong>)</strong> (<em>weight</em>) – e.g. bond length</p></li>
<li><p><strong>(</strong><strong>bool</strong><strong>)</strong> (<em>warn_duplicates</em>) – if True, will warn if</p></li>
</ul>
</dd>
</dl>
<p>trying to add duplicate edges (duplicate edges will not
be added in either case)
:param edge_properties (dict): any other information to
store on graph edges, similar to Structure’s site_properties
:return:</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.alter_edge">
<code class="descname">alter_edge</code><span class="sig-paren">(</span><em>from_index</em>, <em>to_index</em>, <em>new_weight=None</em>, <em>new_edge_properties=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.alter_edge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.alter_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Alters either the weight or the edge_properties of
an edge in the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>new_weight</strong> – alter_edge does not require</p></li>
</ul>
</dd>
</dl>
<p>that weight be altered. As such, by default, this
is None. If weight is to be changed, it should be a
float.
:param new_edge_properties: alter_edge does not require
that edge_properties be altered. As such, by default,
this is None. If any edge properties are to be changed,
it should be a dictionary of edge properties to be changed.
:return:</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>As in :Class: <cite>pymatgen.core.Molecule</cite> except
with using <cite>to_dict_of_dicts</cite> from NetworkX
to store graph information.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.break_edge">
<code class="descname">break_edge</code><span class="sig-paren">(</span><em>from_index</em>, <em>to_index</em>, <em>allow_reverse=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.break_edge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.break_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove an edge from the MoleculeGraph</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>allow_reverse</strong> – If allow_reverse is True, then break_edge will</p></li>
</ul>
</dd>
</dl>
<p>attempt to break both (from_index, to_index) and, failing that,
will attempt to break (to_index, from_index).
:return:</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.build_unique_fragments">
<code class="descname">build_unique_fragments</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.build_unique_fragments"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.build_unique_fragments" title="Permalink to this definition">¶</a></dt>
<dd><p>Find all possible fragment combinations of the MoleculeGraphs (in other
words, all connected induced subgraphs)</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.diff">
<code class="descname">diff</code><span class="sig-paren">(</span><em>other</em>, <em>strict=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.diff"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.diff" title="Permalink to this definition">¶</a></dt>
<dd><p>Compares two MoleculeGraphs. Returns dict with
keys ‘self’, ‘other’, ‘both’ with edges that are
present in only one MoleculeGraph (‘self’ and
‘other’), and edges that are present in both.</p>
<p>The Jaccard distance is a simple measure of the
dissimilarity between two MoleculeGraphs (ignoring
edge weights), and is defined by 1 - (size of the
intersection / size of the union) of the sets of
edges. This is returned with key ‘dist’.</p>
<p>Important note: all node indices are in terms
of the MoleculeGraph this method is called
from, not the ‘other’ MoleculeGraph: there
is no guarantee the node indices will be the
same if the underlying Molecules are ordered
differently.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>other</strong> – MoleculeGraph</p></li>
<li><p><strong>strict</strong> – if False, will compare bonds</p></li>
</ul>
</dd>
</dl>
<p>from different Molecules, with node indices
replaced by Specie strings, will not count
number of occurrences of bonds
:return:</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.draw_graph_to_file">
<code class="descname">draw_graph_to_file</code><span class="sig-paren">(</span><em>filename='graph'</em>, <em>diff=None</em>, <em>hide_unconnected_nodes=False</em>, <em>hide_image_edges=True</em>, <em>edge_colors=False</em>, <em>node_labels=False</em>, <em>weight_labels=False</em>, <em>image_labels=False</em>, <em>color_scheme='VESTA'</em>, <em>keep_dot=False</em>, <em>algo='fdp'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.draw_graph_to_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.draw_graph_to_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Draws graph using GraphViz.</p>
<p>The networkx graph object itself can also be drawn
with networkx’s in-built graph drawing methods, but
note that this might give misleading results for
multigraphs (edges are super-imposed on each other).</p>
<p>If visualization is difficult to interpret,
<cite>hide_image_edges</cite> can help, especially in larger
graphs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>filename</strong> – filename to output, will detect filetype</p>
</dd>
</dl>
<p>from extension (any graphviz filetype supported, such as
pdf or png)
:param diff (StructureGraph): an additional graph to
compare with, will color edges red that do not exist in diff
and edges green that are in diff graph but not in the
reference graph
:param hide_unconnected_nodes: if True, hide unconnected
nodes
:param hide_image_edges: if True, do not draw edges that
go through periodic boundaries
:param edge_colors (bool): if True, use node colors to
color edges
:param node_labels (bool): if True, label nodes with
species and site index
:param weight_labels (bool): if True, label edges with
weights
:param image_labels (bool): if True, label edges with
their periodic images (usually only used for debugging,
edges to periodic images always appear as dashed lines)
:param color_scheme (str): “VESTA” or “JMOL”
:param keep_dot (bool): keep GraphViz .dot file for later
visualization
:param algo: any graphviz algo, “neato” (for simple graphs)
or “fdp” (for more crowded graphs) usually give good outputs
:return:</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.edge_weight_name">
<code class="descname">edge_weight_name</code><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.edge_weight_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Name of the edge weight property of graph</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>return</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.edge_weight_unit">
<code class="descname">edge_weight_unit</code><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.edge_weight_unit" title="Permalink to this definition">¶</a></dt>
<dd><p>Units of the edge weight property of graph</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>return</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.find_rings">
<code class="descname">find_rings</code><span class="sig-paren">(</span><em>including=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.find_rings"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.find_rings" title="Permalink to this definition">¶</a></dt>
<dd><p>Find ring structures in the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>including</strong> – list of site indices. If</p>
</dd>
</dl>
<p>including is not None, then find_rings will
only return those rings including the specified
sites. By default, this parameter is None, and
all rings will be returned.
:return: dict {index:cycle}. Each
entry will be a ring (cycle, in graph theory terms) including the index
found in the Molecule. If there is no cycle including an index, the
value will be an empty list.</p>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.from_dict">
<em class="property">classmethod </em><code class="descname">from_dict</code><span class="sig-paren">(</span><em>d</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.from_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>As in :Class: <cite>pymatgen.core.Molecule</cite> except
restoring graphs using <cite>from_dict_of_dicts</cite>
from NetworkX to restore graph information.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.get_connected_sites">
<code class="descname">get_connected_sites</code><span class="sig-paren">(</span><em>n</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.get_connected_sites"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.get_connected_sites" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a named tuple of neighbors of site n:
periodic_site, jimage, index, weight.
Index is the index of the corresponding site
in the original structure, weight can be
None if not defined.
:param n: index of Site in Molecule
:param jimage: lattice vector of site
:return: list of ConnectedSite tuples,
sorted by closest first</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.get_coordination_of_site">
<code class="descname">get_coordination_of_site</code><span class="sig-paren">(</span><em>n</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.get_coordination_of_site"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.get_coordination_of_site" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the number of neighbors of site n.
In graph terms, simply returns degree
of node corresponding to site n.
:param n: index of site
:return (int):</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.insert_node">
<code class="descname">insert_node</code><span class="sig-paren">(</span><em>i</em>, <em>species</em>, <em>coords</em>, <em>validate_proximity=False</em>, <em>site_properties=None</em>, <em>edges=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.insert_node"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.insert_node" title="Permalink to this definition">¶</a></dt>
<dd><p>A wrapper around Molecule.insert(), which also incorporates the new
site into the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>i</strong> – Index at which to insert the new site</p></li>
<li><p><strong>species</strong> – Species for the new site</p></li>
<li><p><strong>coords</strong> – 3x1 array representing coordinates of the new site</p></li>
<li><p><strong>validate_proximity</strong> – For Molecule.insert(); if True (default
False), distance will be checked to ensure that site can be safely
added.</p></li>
<li><p><strong>site_properties</strong> – Site properties for Molecule</p></li>
<li><p><strong>edges</strong> – List of dicts representing edges to be added to the
MoleculeGraph. These edges must include the index of the new site i,
and all indices used for these edges should reflect the
MoleculeGraph AFTER the insertion, NOT before. Each dict should at
least have a “to_index” and “from_index” key, and can also have a
“weight” and a “properties” key.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.isomorphic_to">
<code class="descname">isomorphic_to</code><span class="sig-paren">(</span><em>other</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.isomorphic_to"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.isomorphic_to" title="Permalink to this definition">¶</a></dt>
<dd><p>Checks if the graphs of two MoleculeGraphs are isomorphic to one
another. In order to prevent problems with misdirected edges, both
graphs are converted into undirected nx.Graph objects.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>other</strong> – MoleculeGraph object to be compared.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>bool</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.name">
<code class="descname">name</code><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.name" title="Permalink to this definition">¶</a></dt>
<dd><p>Name of graph</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>return</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.remove_nodes">
<code class="descname">remove_nodes</code><span class="sig-paren">(</span><em>indices</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.remove_nodes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.remove_nodes" title="Permalink to this definition">¶</a></dt>
<dd><p>A wrapper for Molecule.remove_sites().</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>indices</strong> – list of indices in the current Molecule (and graph) to
be removed.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.replace_group">
<code class="descname">replace_group</code><span class="sig-paren">(</span><em>index</em>, <em>func_grp</em>, <em>strategy</em>, <em>bond_order=1</em>, <em>graph_dict=None</em>, <em>strategy_params=None</em>, <em>reorder=True</em>, <em>extend_structure=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.replace_group"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.replace_group" title="Permalink to this definition">¶</a></dt>
<dd><p>Builds off of Molecule.substitute and MoleculeGraph.substitute_group
to replace a functional group in self.molecule with a functional group.
This method also amends self.graph to incorporate the new functional
group.</p>
<p>TODO: Figure out how to replace into a ring structure.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> – Index of atom to substitute.</p></li>
<li><p><strong>func_grp</strong> – <p>Substituent molecule. There are three options:</p>
<ol class="arabic simple">
<li><p>Providing an actual molecule as the input. The first atom
must be a DummySpecie X, indicating the position of
nearest neighbor. The second atom must be the next
nearest atom. For example, for a methyl group
substitution, func_grp should be X-CH3, where X is the
first site and C is the second site. What the code will
do is to remove the index site, and connect the nearest
neighbor to the C atom in CH3. The X-C bond indicates the
directionality to connect the atoms.</p></li>
<li><p>A string name. The molecule will be obtained from the
relevant template in func_groups.json.</p></li>
<li><p>A MoleculeGraph object.</p></li>
</ol>
</p></li>
<li><p><strong>strategy</strong> – Class from pymatgen.analysis.local_env.</p></li>
<li><p><strong>bond_order</strong> – A specified bond order to calculate the bond
length between the attached functional group and the nearest
neighbor site. Defaults to 1.</p></li>
<li><p><strong>graph_dict</strong> – Dictionary representing the bonds of the functional
group (format: {(u, v): props}, where props is a dictionary of
properties, including weight. If None, then the algorithm
will attempt to automatically determine bonds using one of
a list of strategies defined in pymatgen.analysis.local_env.</p></li>
<li><p><strong>strategy_params</strong> – dictionary of keyword arguments for strategy.
If None, default parameters will be used.</p></li>
<li><p><strong>reorder</strong> – bool, representing if graph nodes need to be reordered
following the application of the local_env strategy</p></li>
<li><p><strong>extend_structure</strong> – If True (default), then a large artificial box
will be placed around the Molecule, because some strategies assume
periodic boundary conditions.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.set_node_attributes">
<code class="descname">set_node_attributes</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.set_node_attributes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.set_node_attributes" title="Permalink to this definition">¶</a></dt>
<dd><p>Replicates molecule site properties (specie, coords, etc.) in the
MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.sort">
<code class="descname">sort</code><span class="sig-paren">(</span><em>key=None</em>, <em>reverse=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.sort"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.sort" title="Permalink to this definition">¶</a></dt>
<dd><p>Same as Molecule.sort(), also remaps nodes in graph.
:param key:
:param reverse:
:return:</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.split_molecule_subgraphs">
<code class="descname">split_molecule_subgraphs</code><span class="sig-paren">(</span><em>bonds</em>, <em>allow_reverse=False</em>, <em>alterations=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.split_molecule_subgraphs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.split_molecule_subgraphs" title="Permalink to this definition">¶</a></dt>
<dd><p>Split MoleculeGraph into two or more MoleculeGraphs by
breaking a set of bonds. This function uses
MoleculeGraph.break_edge repeatedly to create
disjoint graphs (two or more separate molecules).
This function does not only alter the graph
information, but also changes the underlying
Moledules.
If the bonds parameter does not include sufficient
bonds to separate two molecule fragments, then this
function will fail.
Currently, this function naively assigns the charge
of the total molecule to a single submolecule. A
later effort will be to actually accurately assign
charge.
NOTE: This function does not modify the original
MoleculeGraph. It creates a copy, modifies that, and
returns two or more new MoleculeGraph objects.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>bonds</strong> – list of tuples (from_index, to_index)</p>
</dd>
</dl>
<p>representing bonds to be broken to split the MoleculeGraph.
:param alterations: a dict {(from_index, to_index): alt},
where alt is a dictionary including weight and/or edge
properties to be changed following the split.
:param allow_reverse: If allow_reverse is True, then break_edge will
attempt to break both (from_index, to_index) and, failing that,
will attempt to break (to_index, from_index).
:return: list of MoleculeGraphs</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.substitute_group">
<code class="descname">substitute_group</code><span class="sig-paren">(</span><em>index</em>, <em>func_grp</em>, <em>strategy</em>, <em>bond_order=1</em>, <em>graph_dict=None</em>, <em>strategy_params=None</em>, <em>reorder=True</em>, <em>extend_structure=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.substitute_group"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.substitute_group" title="Permalink to this definition">¶</a></dt>
<dd><p>Builds off of Molecule.substitute to replace an atom in self.molecule
with a functional group. This method also amends self.graph to
incorporate the new functional group.</p>
<p>NOTE: using a MoleculeGraph will generally produce a different graph
compared with using a Molecule or str (when not using graph_dict).
This is because of the reordering that occurs when using some of the
local_env strategies.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>index</strong> – Index of atom to substitute.</p></li>
<li><p><strong>func_grp</strong> – <p>Substituent molecule. There are three options:</p>
<ol class="arabic simple">
<li><p>Providing an actual molecule as the input. The first atom
must be a DummySpecie X, indicating the position of
nearest neighbor. The second atom must be the next
nearest atom. For example, for a methyl group
substitution, func_grp should be X-CH3, where X is the
first site and C is the second site. What the code will
do is to remove the index site, and connect the nearest
neighbor to the C atom in CH3. The X-C bond indicates the
directionality to connect the atoms.</p></li>
<li><p>A string name. The molecule will be obtained from the
relevant template in func_groups.json.</p></li>
<li><p>A MoleculeGraph object.</p></li>
</ol>
</p></li>
<li><p><strong>strategy</strong> – Class from pymatgen.analysis.local_env.</p></li>
<li><p><strong>bond_order</strong> – A specified bond order to calculate the bond
length between the attached functional group and the nearest
neighbor site. Defaults to 1.</p></li>
<li><p><strong>graph_dict</strong> – Dictionary representing the bonds of the functional
group (format: {(u, v): props}, where props is a dictionary of
properties, including weight. If None, then the algorithm
will attempt to automatically determine bonds using one of
a list of strategies defined in pymatgen.analysis.local_env.</p></li>
<li><p><strong>strategy_params</strong> – dictionary of keyword arguments for strategy.
If None, default parameters will be used.</p></li>
<li><p><strong>reorder</strong> – bool, representing if graph nodes need to be reordered
following the application of the local_env strategy</p></li>
<li><p><strong>extend_structure</strong> – If True (default), then a large artificial box
will be placed around the Molecule, because some strategies assume
periodic boundary conditions.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="staticmethod">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.with_edges">
<em class="property">static </em><code class="descname">with_edges</code><span class="sig-paren">(</span><em>molecule</em>, <em>edges</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.with_edges"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.with_edges" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructor for MoleculeGraph, using pre-existing or pre-defined edges
with optional edge parameters.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> – Molecule object</p></li>
<li><p><strong>edges</strong> – dict representing the bonds of the functional
group (format: {(u, v): props}, where props is a dictionary of
properties, including weight. Props should be None if no
additional properties are to be specified.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>mg, a MoleculeGraph</p>
</dd>
</dl>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.with_empty_graph">
<em class="property">classmethod </em><code class="descname">with_empty_graph</code><span class="sig-paren">(</span><em>molecule</em>, <em>name='bonds'</em>, <em>edge_weight_name=None</em>, <em>edge_weight_units=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.with_empty_graph"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.with_empty_graph" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructor for MoleculeGraph, returns a MoleculeGraph
object with an empty graph (no edges, only nodes defined
that correspond to Sites in Molecule).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>(</strong><strong>Molecule</strong><strong>)</strong> (<em>molecule</em>) – </p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> (<em>edge_weight_name</em>) – name of graph, e.g. “bonds”</p></li>
<li><p><strong>(</strong><strong>str</strong><strong>)</strong> – name of edge weights,</p></li>
</ul>
</dd>
</dl>
<p>e.g. “bond_length” or “exchange_constant”
:param edge_weight_units (str): name of edge weight units
e.g. “Å” or “eV”
:return (MoleculeGraph):</p>
</dd></dl>
<dl class="staticmethod">
<dt id="pymatgen.analysis.graphs.MoleculeGraph.with_local_env_strategy">
<em class="property">static </em><code class="descname">with_local_env_strategy</code><span class="sig-paren">(</span><em>molecule</em>, <em>strategy</em>, <em>reorder=True</em>, <em>extend_structure=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#MoleculeGraph.with_local_env_strategy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.MoleculeGraph.with_local_env_strategy" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructor for MoleculeGraph, using a strategy
from :Class: <cite>pymatgen.analysis.local_env</cite>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> – Molecule object</p></li>
<li><p><strong>strategy</strong> – an instance of a
:Class: <cite>pymatgen.analysis.local_env.NearNeighbors</cite> object</p></li>
<li><p><strong>reorder</strong> – bool, representing if graph nodes need to be reordered
following the application of the local_env strategy</p></li>
<li><p><strong>extend_structure</strong> – If True (default), then a large artificial box
will be placed around the Molecule, because some strategies assume
periodic boundary conditions.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>mg, a MoleculeGraph</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.analysis.graphs.StructureGraph">
<em class="property">class </em><code class="descname">StructureGraph</code><span class="sig-paren">(</span><em>structure</em>, <em>graph_data=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">monty.json.MSONable</span></code></p>
<p>This is a class for annotating a Structure with
bond information, stored in the form of a graph. A “bond” does
not necessarily have to be a chemical bond, but can store any
kind of information that connects two Sites.</p>
<p>If constructing this class manually, use the <cite>with_empty_graph</cite>
method or <cite>with_local_env_strategy</cite> method (using an algorithm
provided by the <cite>local_env</cite> module, such as O’Keeffe).</p>
<p>This class that contains connection information:
relationships between sites represented by a Graph structure,
and an associated structure object.</p>
<p>This class uses the NetworkX package to store and operate
on the graph itself, but contains a lot of helper methods
to make associating a graph with a given crystallographic
structure easier.</p>
<p>Use cases for this include storing bonding information,
NMR J-couplings, Heisenberg exchange parameters, etc.</p>
<p>For periodic graphs, class stores information on the graph
edges of what lattice image the edge belongs to.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>structure</strong> – a Structure object</p></li>
<li><p><strong>graph_data</strong> – dict containing graph information in</p></li>
</ul>
</dd>
</dl>
<p>dict format (not intended to be constructed manually,
see as_dict method for format)</p>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.add_edge">
<code class="descname">add_edge</code><span class="sig-paren">(</span><em>from_index</em>, <em>to_index</em>, <em>from_jimage=(0</em>, <em>0</em>, <em>0)</em>, <em>to_jimage=None</em>, <em>weight=None</em>, <em>warn_duplicates=True</em>, <em>edge_properties=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.add_edge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.add_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Add edge to graph.</p>
<p>Since physically a ‘bond’ (or other connection
between sites) doesn’t have a direction, from_index,
from_jimage can be swapped with to_index, to_jimage.</p>
<p>However, images will always always be shifted so that
from_index < to_index and from_jimage becomes (0, 0, 0).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – index of site connecting from</p></li>
<li><p><strong>to_index</strong> – index of site connecting to</p></li>
<li><p><strong>(</strong><strong>tuple of ints</strong><strong>)</strong> (<em>from_jimage</em>) – lattice vector of periodic</p></li>
</ul>
</dd>
</dl>
<p>image, e.g. (1, 0, 0) for periodic image in +x direction
:param to_jimage (tuple of ints): lattice vector of image
:param weight (float): e.g. bond length
:param warn_duplicates (bool): if True, will warn if
trying to add duplicate edges (duplicate edges will not
be added in either case)
:param edge_properties (dict): any other information to
store on graph edges, similar to Structure’s site_properties
:return:</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.alter_edge">
<code class="descname">alter_edge</code><span class="sig-paren">(</span><em>from_index</em>, <em>to_index</em>, <em>to_jimage=None</em>, <em>new_weight=None</em>, <em>new_edge_properties=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.alter_edge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.alter_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Alters either the weight or the edge_properties of
an edge in the StructureGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>to_jimage</strong> – tuple</p></li>
<li><p><strong>new_weight</strong> – alter_edge does not require</p></li>
</ul>
</dd>
</dl>
<p>that weight be altered. As such, by default, this
is None. If weight is to be changed, it should be a
float.
:param new_edge_properties: alter_edge does not require
that edge_properties be altered. As such, by default,
this is None. If any edge properties are to be changed,
it should be a dictionary of edge properties to be changed.
:return:</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.as_dict">
<code class="descname">as_dict</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.as_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.as_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>As in :Class: <cite>pymatgen.core.Structure</cite> except
with using <cite>to_dict_of_dicts</cite> from NetworkX
to store graph information.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.break_edge">
<code class="descname">break_edge</code><span class="sig-paren">(</span><em>from_index</em>, <em>to_index</em>, <em>to_jimage=None</em>, <em>allow_reverse=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.break_edge"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.break_edge" title="Permalink to this definition">¶</a></dt>
<dd><p>Remove an edge from the StructureGraph. If no image is given, this method will fail.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>from_index</strong> – int</p></li>
<li><p><strong>to_index</strong> – int</p></li>
<li><p><strong>to_jimage</strong> – tuple</p></li>
<li><p><strong>allow_reverse</strong> – If allow_reverse is True, then break_edge will</p></li>
</ul>
</dd>
</dl>
<p>attempt to break both (from_index, to_index) and, failing that,
will attempt to break (to_index, from_index).
:return:</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.diff">
<code class="descname">diff</code><span class="sig-paren">(</span><em>other</em>, <em>strict=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.diff"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.diff" title="Permalink to this definition">¶</a></dt>
<dd><p>Compares two StructureGraphs. Returns dict with
keys ‘self’, ‘other’, ‘both’ with edges that are
present in only one StructureGraph (‘self’ and
‘other’), and edges that are present in both.</p>
<p>The Jaccard distance is a simple measure of the
dissimilarity between two StructureGraphs (ignoring
edge weights), and is defined by 1 - (size of the
intersection / size of the union) of the sets of
edges. This is returned with key ‘dist’.</p>
<p>Important note: all node indices are in terms
of the StructureGraph this method is called
from, not the ‘other’ StructureGraph: there
is no guarantee the node indices will be the
same if the underlying Structures are ordered
differently.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>other</strong> – StructureGraph</p></li>
<li><p><strong>strict</strong> – if False, will compare bonds</p></li>
</ul>
</dd>
</dl>
<p>from different Structures, with node indices
replaced by Specie strings, will not count
number of occurrences of bonds
:return:</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.draw_graph_to_file">
<code class="descname">draw_graph_to_file</code><span class="sig-paren">(</span><em>filename='graph'</em>, <em>diff=None</em>, <em>hide_unconnected_nodes=False</em>, <em>hide_image_edges=True</em>, <em>edge_colors=False</em>, <em>node_labels=False</em>, <em>weight_labels=False</em>, <em>image_labels=False</em>, <em>color_scheme='VESTA'</em>, <em>keep_dot=False</em>, <em>algo='fdp'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.draw_graph_to_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.draw_graph_to_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Draws graph using GraphViz.</p>
<p>The networkx graph object itself can also be drawn
with networkx’s in-built graph drawing methods, but
note that this might give misleading results for
multigraphs (edges are super-imposed on each other).</p>
<p>If visualization is difficult to interpret,
<cite>hide_image_edges</cite> can help, especially in larger
graphs.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>filename</strong> – filename to output, will detect filetype</p>
</dd>
</dl>
<p>from extension (any graphviz filetype supported, such as
pdf or png)
:param diff (StructureGraph): an additional graph to
compare with, will color edges red that do not exist in diff
and edges green that are in diff graph but not in the
reference graph
:param hide_unconnected_nodes: if True, hide unconnected
nodes
:param hide_image_edges: if True, do not draw edges that
go through periodic boundaries
:param edge_colors (bool): if True, use node colors to
color edges
:param node_labels (bool): if True, label nodes with
species and site index
:param weight_labels (bool): if True, label edges with
weights
:param image_labels (bool): if True, label edges with
their periodic images (usually only used for debugging,
edges to periodic images always appear as dashed lines)
:param color_scheme (str): “VESTA” or “JMOL”
:param keep_dot (bool): keep GraphViz .dot file for later
visualization
:param algo: any graphviz algo, “neato” (for simple graphs)
or “fdp” (for more crowded graphs) usually give good outputs
:return:</p>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.StructureGraph.edge_weight_name">
<code class="descname">edge_weight_name</code><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.edge_weight_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Name of the edge weight property of graph</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>return</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.StructureGraph.edge_weight_unit">
<code class="descname">edge_weight_unit</code><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.edge_weight_unit" title="Permalink to this definition">¶</a></dt>
<dd><p>Units of the edge weight property of graph</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>return</p>
</dd>
</dl>
</dd></dl>
<dl class="classmethod">
<dt id="pymatgen.analysis.graphs.StructureGraph.from_dict">
<em class="property">classmethod </em><code class="descname">from_dict</code><span class="sig-paren">(</span><em>d</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.from_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>As in :Class: <cite>pymatgen.core.Structure</cite> except
restoring graphs using <cite>from_dict_of_dicts</cite>
from NetworkX to restore graph information.</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.get_connected_sites">
<code class="descname">get_connected_sites</code><span class="sig-paren">(</span><em>n</em>, <em>jimage=(0</em>, <em>0</em>, <em>0)</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.get_connected_sites"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.get_connected_sites" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns a named tuple of neighbors of site n:
periodic_site, jimage, index, weight.
Index is the index of the corresponding site
in the original structure, weight can be
None if not defined.
:param n: index of Site in Structure
:param jimage: lattice vector of site
:return: list of ConnectedSite tuples,
sorted by closest first</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.get_coordination_of_site">
<code class="descname">get_coordination_of_site</code><span class="sig-paren">(</span><em>n</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.get_coordination_of_site"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.get_coordination_of_site" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the number of neighbors of site n.
In graph terms, simply returns degree
of node corresponding to site n.
:param n: index of site
:return (int):</p>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.get_subgraphs_as_molecules">
<code class="descname">get_subgraphs_as_molecules</code><span class="sig-paren">(</span><em>use_weights=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.get_subgraphs_as_molecules"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.get_subgraphs_as_molecules" title="Permalink to this definition">¶</a></dt>
<dd><p>Retrieve subgraphs as molecules, useful for extracting
molecules from periodic crystals.</p>
<p>Will only return unique molecules, not any duplicates
present in the crystal (a duplicate defined as an
isomorphic subgraph).</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>(</strong><strong>bool</strong><strong>)</strong> (<em>use_weights</em>) – If True, only treat subgraphs</p>
</dd>
</dl>
<p>as isomorphic if edges have the same weights. Typically,
this means molecules will need to have the same bond
lengths to be defined as duplicates, otherwise bond
lengths can differ. This is a fairly robust approach,
but will treat e.g. enantiomers as being duplicates.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>list of unique Molecules in Structure</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.insert_node">
<code class="descname">insert_node</code><span class="sig-paren">(</span><em>i</em>, <em>species</em>, <em>coords</em>, <em>coords_are_cartesian=False</em>, <em>validate_proximity=False</em>, <em>site_properties=None</em>, <em>edges=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.insert_node"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.insert_node" title="Permalink to this definition">¶</a></dt>
<dd><p>A wrapper around Molecule.insert(), which also incorporates the new
site into the MoleculeGraph.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>i</strong> – Index at which to insert the new site</p></li>
<li><p><strong>species</strong> – Species for the new site</p></li>
<li><p><strong>coords</strong> – 3x1 array representing coordinates of the new site</p></li>
<li><p><strong>coords_are_cartesian</strong> – Whether coordinates are cartesian.
Defaults to False.</p></li>
<li><p><strong>validate_proximity</strong> – For Molecule.insert(); if True (default
False), distance will be checked to ensure that site can be safely
added.</p></li>
<li><p><strong>site_properties</strong> – Site properties for Molecule</p></li>
<li><p><strong>edges</strong> – List of dicts representing edges to be added to the
MoleculeGraph. These edges must include the index of the new site i,
and all indices used for these edges should reflect the
MoleculeGraph AFTER the insertion, NOT before. Each dict should at
least have a “to_index” and “from_index” key, and can also have a
“weight” and a “properties” key.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.analysis.graphs.StructureGraph.name">
<code class="descname">name</code><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.name" title="Permalink to this definition">¶</a></dt>
<dd><p>Name of graph</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>return</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.remove_nodes">
<code class="descname">remove_nodes</code><span class="sig-paren">(</span><em>indices</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.remove_nodes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.remove_nodes" title="Permalink to this definition">¶</a></dt>
<dd><p>A wrapper for Molecule.remove_sites().</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>indices</strong> – list of indices in the current Molecule (and graph) to
be removed.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.set_node_attributes">
<code class="descname">set_node_attributes</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.set_node_attributes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.set_node_attributes" title="Permalink to this definition">¶</a></dt>
<dd><p>Gives each node a “specie” and a “coords” attribute, updated with the
current species and coordinates.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p></p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.graphs.StructureGraph.sort">
<code class="descname">sort</code><span class="sig-paren">(</span><em>key=None</em>, <em>reverse=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/graphs.html#StructureGraph.sort"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.graphs.StructureGraph.sort" title="Permalink to this definition">¶</a></dt>
<dd><p>Same as Structure.sort(), also remaps nodes in graph.
:param key:
:param reverse:
:return:</p>
</dd></dl>