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<title>pymatgen.analysis.structure_prediction.substitution_probability module — pymatgen 2019.5.1 documentation</title>
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<div class="section" id="module-pymatgen.analysis.structure_prediction.substitution_probability">
<span id="pymatgen-analysis-structure-prediction-substitution-probability-module"></span><h1>pymatgen.analysis.structure_prediction.substitution_probability module<a class="headerlink" href="#module-pymatgen.analysis.structure_prediction.substitution_probability" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor">
<em class="property">class </em><code class="descname">SubstitutionPredictor</code><span class="sig-paren">(</span><em>lambda_table=None</em>, <em>alpha=-5</em>, <em>threshold=0.001</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/structure_prediction/substitution_probability.html#SubstitutionPredictor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor" title="Permalink 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>Predicts likely substitutions either to or from a given composition
or species list using the SubstitutionProbability</p>
<dl class="method">
<dt id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.composition_prediction">
<code class="descname">composition_prediction</code><span class="sig-paren">(</span><em>composition</em>, <em>to_this_composition=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/structure_prediction/substitution_probability.html#SubstitutionPredictor.composition_prediction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.composition_prediction" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns charged balanced substitutions from a starting or ending
composition.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>composition</strong> – starting or ending composition</p></li>
<li><p><strong>to_this_composition</strong> – If true, substitutions with this as a final composition
will be found. If false, substitutions with this as a
starting composition will be found (these are slightly
different)</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>List of predictions in the form of dictionaries.
If to_this_composition is true, the values of the dictionary
will be from the list species. If false, the keys will be
from that list.</p>
</dd>
</dl>
</dd></dl>
<dl class="method">
<dt id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.list_prediction">
<code class="descname">list_prediction</code><span class="sig-paren">(</span><em>species</em>, <em>to_this_composition=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/structure_prediction/substitution_probability.html#SubstitutionPredictor.list_prediction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionPredictor.list_prediction" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>species</strong> – list of species</p></li>
<li><p><strong>to_this_composition</strong> – If true, substitutions with this as a final composition
will be found. If false, substitutions with this as a
starting composition will be found (these are slightly
different)</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>List of predictions in the form of dictionaries.
If to_this_composition is true, the values of the dictionary
will be from the list species. If false, the keys will be
from that list.</p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability">
<em class="property">class </em><code class="descname">SubstitutionProbability</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/analysis/structure_prediction/substitution_probability.html#SubstitutionProbability"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability" title="pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability"><code class="xref py py-class docutils literal notranslate"><span class="pre">pymatgen.analysis.structure_prediction.substitution_probability.SubstitutionProbability</span></code></a></p>
<p>This class finds substitution probabilities given lists of atoms
to substitute. The inputs make more sense if you look through the
from_defaults static method.</p>
<p>The substitution prediction algorithm is presented in:
Hautier, G., Fischer, C., Ehrlacher, V., Jain, A., and Ceder, G. (2011)
Data Mined Ionic Substitutions for the Discovery of New Compounds.
Inorganic Chemistry, 50(2), 656-663. doi:10.1021/ic102031h</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lambda_table</strong> – json table of the weight functions lambda if None,
will use the default lambda.json table</p></li>
<li><p><strong>alpha</strong> – weight function for never observed substitutions</p></li>
</ul>
</dd>
</dl>
</dd></dl>
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