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<div class="section" id="module-pymatgen.analysis.fragmenter">
<span id="pymatgen-analysis-fragmenter-module"></span><h1>pymatgen.analysis.fragmenter module<a class="headerlink" href="#module-pymatgen.analysis.fragmenter" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.analysis.fragmenter.Fragmenter">
<em class="property">class </em><code class="descname">Fragmenter</code><span class="sig-paren">(</span><em>molecule</em>, <em>edges=None</em>, <em>depth=1</em>, <em>open_rings=True</em>, <em>opt_steps=10000</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/fragmenter.html#Fragmenter"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.fragmenter.Fragmenter" 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>Standard constructor for molecule fragmentation</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>molecule</strong> (<a class="reference internal" href="pymatgen.core.structure.html#pymatgen.core.structure.Molecule" title="pymatgen.core.structure.Molecule"><em>Molecule</em></a>) – The molecule to fragment</p></li>
<li><p><strong>edges</strong> (<em>list</em>) – List of index pairs that define graph edges, aka molecule bonds. If not
set, edges will be determined with OpenBabel.</p></li>
<li><p><strong>depth</strong> (<em>int</em>) – The number of levels of iterative fragmentation to perform, where each
level will include fragments obtained by breaking one bond of a fragment
one level up. Defaults to 1. However, if set to 0, instead all possible
fragments are generated using an alternative, non-iterative scheme.</p></li>
<li><p><strong>open_rings</strong> (<em>bool</em>) – Whether or not to open any rings encountered during fragmentation.
Defaults to False. If true, any bond that fails to yield disconnected
graphs when broken is instead removed and the entire structure is
optimized with OpenBabel in order to obtain a good initial guess for
an opened geometry that can then be put back into QChem to be
optimized without the ring just reforming.</p></li>
<li><p><strong>opt_steps</strong> (<em>int</em>) – Number of optimization steps when opening rings. Defaults to 1000.</p></li>
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<dl class="function">
<dt id="pymatgen.analysis.fragmenter.open_ring">
<code class="descname">open_ring</code><span class="sig-paren">(</span><em>mol_graph</em>, <em>bond</em>, <em>opt_steps</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/fragmenter.html#open_ring"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.fragmenter.open_ring" title="Permalink to this definition">¶</a></dt>
<dd><p>Function to actually open a ring using OpenBabel’s local opt. Given a molecule
graph and a bond, convert the molecule graph into an OpenBabel molecule, remove
the given bond, perform the local opt with the number of steps determined by
self.steps, and then convert the resulting structure back into a molecule graph
to be returned.</p>
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