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<title>pymatgen.core.bonds module — pymatgen 2019.5.1 documentation</title>
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<div class="section" id="module-pymatgen.core.bonds">
<span id="pymatgen-core-bonds-module"></span><h1>pymatgen.core.bonds module<a class="headerlink" href="#module-pymatgen.core.bonds" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="pymatgen.core.bonds.CovalentBond">
<em class="property">class </em><code class="descname">CovalentBond</code><span class="sig-paren">(</span><em>site1</em>, <em>site2</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/bonds.html#CovalentBond"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.bonds.CovalentBond" 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>Defines a covalent bond between two sites.</p>
<p>Initializes a covalent bond between two sites.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>site1</strong> (<a class="reference internal" href="pymatgen.core.sites.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a>) – First site.</p></li>
<li><p><strong>site2</strong> (<a class="reference internal" href="pymatgen.core.sites.html#pymatgen.core.sites.Site" title="pymatgen.core.sites.Site"><em>Site</em></a>) – Second site.</p></li>
</ul>
</dd>
</dl>
<dl class="method">
<dt id="pymatgen.core.bonds.CovalentBond.get_bond_order">
<code class="descname">get_bond_order</code><span class="sig-paren">(</span><em>tol=0.2</em>, <em>default_bl=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/bonds.html#CovalentBond.get_bond_order"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.bonds.CovalentBond.get_bond_order" title="Permalink to this definition">¶</a></dt>
<dd><p>The bond order according the distance between the two sites
:param tol: Relative tolerance to test.</p>
<blockquote>
<div><p>(1 + tol) * the longest bond distance is considered
to be the threshold length for a bond to exist.
(1 - tol) * the shortest bond distance is considered
to be the shortest possible bond length
Defaults to 0.2.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>default_bl</strong> – If a particular type of bond does not exist,
use this bond length as a default value
(bond order = 1). If None, a ValueError will be thrown.</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Float value of bond order. For example, for C-C bond in
benzene, return 1.7.</p>
</dd>
</dl>
</dd></dl>
<dl class="staticmethod">
<dt id="pymatgen.core.bonds.CovalentBond.is_bonded">
<em class="property">static </em><code class="descname">is_bonded</code><span class="sig-paren">(</span><em>site1</em>, <em>site2</em>, <em>tol=0.2</em>, <em>bond_order=None</em>, <em>default_bl=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/bonds.html#CovalentBond.is_bonded"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.bonds.CovalentBond.is_bonded" title="Permalink to this definition">¶</a></dt>
<dd><p>Test if two sites are bonded, up to a certain limit.
:param site1: First site
:type site1: Site
:param site2: Second site
:type site2: Site
:param tol: Relative tolerance to test. Basically, the code</p>
<blockquote>
<div><p>checks if the distance between the sites is less than (1 +
tol) * typical bond distances. Defaults to 0.2, i.e.,
20% longer.</p>
</div></blockquote>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bond_order</strong> – Bond order to test. If None, the code simply checks
against all possible bond data. Defaults to None.</p></li>
<li><p><strong>default_bl</strong> – If a particular type of bond does not exist, use this
bond length. If None, a ValueError will be thrown.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Boolean indicating whether two sites are bonded.</p>
</dd>
</dl>
</dd></dl>
<dl class="attribute">
<dt id="pymatgen.core.bonds.CovalentBond.length">
<code class="descname">length</code><a class="headerlink" href="#pymatgen.core.bonds.CovalentBond.length" title="Permalink to this definition">¶</a></dt>
<dd><p>Length of the bond.</p>
</dd></dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.core.bonds.get_bond_length">
<code class="descname">get_bond_length</code><span class="sig-paren">(</span><em>sp1</em>, <em>sp2</em>, <em>bond_order=1</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/bonds.html#get_bond_length"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.bonds.get_bond_length" title="Permalink to this definition">¶</a></dt>
<dd><p>Get the bond length between two species.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sp1</strong> (<a class="reference internal" href="pymatgen.core.periodic_table.html#pymatgen.core.periodic_table.Specie" title="pymatgen.core.periodic_table.Specie"><em>Specie</em></a>) – First specie.</p></li>
<li><p><strong>sp2</strong> (<a class="reference internal" href="pymatgen.core.periodic_table.html#pymatgen.core.periodic_table.Specie" title="pymatgen.core.periodic_table.Specie"><em>Specie</em></a>) – Second specie.</p></li>
<li><p><strong>bond_order</strong> – For species with different possible bond orders,
this allows one to obtain the bond length for a particular bond
order. For example, to get the C=C bond length instead of the
C-C bond length, this should be set to 2. Defaults to 1.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Bond length in Angstrom. If no data is available, the sum of the atomic
radius is used.</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.core.bonds.get_bond_order">
<code class="descname">get_bond_order</code><span class="sig-paren">(</span><em>sp1</em>, <em>sp2</em>, <em>dist</em>, <em>tol=0.2</em>, <em>default_bl=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/bonds.html#get_bond_order"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.bonds.get_bond_order" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculate the bond order given the distance of 2 species</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sp1</strong> (<a class="reference internal" href="pymatgen.core.periodic_table.html#pymatgen.core.periodic_table.Specie" title="pymatgen.core.periodic_table.Specie"><em>Specie</em></a>) – First specie.</p></li>
<li><p><strong>sp2</strong> (<a class="reference internal" href="pymatgen.core.periodic_table.html#pymatgen.core.periodic_table.Specie" title="pymatgen.core.periodic_table.Specie"><em>Specie</em></a>) – Second specie.</p></li>
<li><p><strong>dist</strong> – Their distance in angstrom</p></li>
<li><p><strong>tol</strong> (<em>float</em>) – Relative tolerance to test. Basically, the code
checks if the distance between the sites is larger than
(1 + tol) * the longest bond distance or smaller than
(1 - tol) * the shortest bond distance to determine if
they are bonded or the distance is too short.
Defaults to 0.2.</p></li>
<li><p><strong>default_bl</strong> – If a particular type of bond does not exist, use this
bond length (bond order = 1). If None, a ValueError will be thrown.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>Float value of bond order. For example, for C-C bond in benzene,
return 1.7.</p>
</dd>
</dl>
</dd></dl>
<dl class="function">
<dt id="pymatgen.core.bonds.obtain_all_bond_lengths">
<code class="descname">obtain_all_bond_lengths</code><span class="sig-paren">(</span><em>sp1</em>, <em>sp2</em>, <em>default_bl=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/pymatgen/core/bonds.html#obtain_all_bond_lengths"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#pymatgen.core.bonds.obtain_all_bond_lengths" title="Permalink to this definition">¶</a></dt>
<dd><p>Obtain bond lengths for all bond orders from bond length database</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sp1</strong> (<a class="reference internal" href="pymatgen.core.periodic_table.html#pymatgen.core.periodic_table.Specie" title="pymatgen.core.periodic_table.Specie"><em>Specie</em></a>) – First specie.</p></li>
<li><p><strong>sp2</strong> (<a class="reference internal" href="pymatgen.core.periodic_table.html#pymatgen.core.periodic_table.Specie" title="pymatgen.core.periodic_table.Specie"><em>Specie</em></a>) – Second specie.</p></li>
<li><p><strong>default_bl</strong> – If a particular type of bond does not exist, use this
bond length as a default value (bond order = 1).
If None, a ValueError will be thrown.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>A dict mapping bond order to bond length in angstrom</p>
</dd>
</dl>
</dd></dl>
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