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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<title>OBConformerSearch Class Reference</title>
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<li class="navelem"><a class="el" href="namespaceOpenBabel.shtml">OpenBabel</a> </li>
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</ul>
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</div>
<div class="header">
<div class="summary">
<a href="#pub-methods">Public Member Functions</a> </div>
<div class="headertitle">
<div class="title">OBConformerSearch Class Reference<div class="ingroups"><a class="el" href="group__conformer.shtml">Conformer Searching</a></div></div> </div>
</div>
<div class="contents">
<!-- doxytag: class="OpenBabel::OBConformerSearch" -->
<p><code>#include <<a class="el" href="conformersearch_8h_source.shtml">openbabel/conformersearch.h</a>></code></p>
<p><a href="classOpenBabel_1_1OBConformerSearch-members.shtml">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a3d54183d8351d93903a41fb8e2d6eb7e">OBConformerSearch</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a92682a05ad305ecfb357868cda17b6c8">~OBConformerSearch</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a9084f759abbf98766f3fed69c14b568a">Setup</a> (const <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> &mol, int numConformers=30, int numChildren=5, int mutability=5, int convergence=25)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a5ee2e4f8c4c9cc9fed9949e54b8c728e">SetNumConformers</a> (int numConformers)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a25b1f90c4963a806ac4aa898f542afa3">SetNumChildren</a> (int numChildren)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a375b8f03c5cd5fd162cea6bd78c14356">SetMutability</a> (int mutability)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a259d7fb57066383560678537a93d79ad">SetConvergence</a> (int convergence)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a045f339459d9cc1892cfe9dcdbed2b60">SetFixedBonds</a> (const <a class="el" href="classOpenBabel_1_1OBBitVec.shtml">OBBitVec</a> &fixedBonds)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a95879a373f39c05163d27941df8c18c6">SetFilter</a> (<a class="el" href="classOpenBabel_1_1OBConformerFilter.shtml">OBConformerFilter</a> *filter)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#ab6e866e55e02b792a2b3837ee949bbfd">SetScore</a> (<a class="el" href="classOpenBabel_1_1OBConformerScore.shtml">OBConformerScore</a> *score)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#af648d58ec31e39dff6af003f8e6b5ca4">Search</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const <a class="el" href="namespaceOpenBabel.shtml#ad5ae0fb6c3d3406efb549fbc9f8c26f0">RotorKeys</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a6753356d193ce72d72d1fc1cfee74639">GetRotorKeys</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml#a908a9729ddc64dd383f093ab30a0aae3">GetConformers</a> (<a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> &mol)</td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Conformer searching using genetic algorithm. See <a class="el" href="group__conformer.shtml">Conformer Searching</a>. </p>
<dl class="since"><dt><b>Since:</b></dt><dd>2.3 </dd></dl>
<dl><dt><b>Examples: </b></dt><dd>
<p><a class="el" href="obconformersearch_default_8cpp-example.shtml#_a6">obconformersearch_default.cpp</a>.</p>
</dd>
</dl></div><hr/><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="a3d54183d8351d93903a41fb8e2d6eb7e"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::OBConformerSearch" ref="a3d54183d8351d93903a41fb8e2d6eb7e" args="()" -->
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<table class="memname">
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<td class="memname"><a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml">OBConformerSearch</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
</div>
</div>
<a class="anchor" id="a92682a05ad305ecfb357868cda17b6c8"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::~OBConformerSearch" ref="a92682a05ad305ecfb357868cda17b6c8" args="()" -->
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<td class="memname">~<a class="el" href="classOpenBabel_1_1OBConformerSearch.shtml">OBConformerSearch</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
</div>
</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a9084f759abbf98766f3fed69c14b568a"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::Setup" ref="a9084f759abbf98766f3fed69c14b568a" args="(const OBMol &mol, int numConformers=30, int numChildren=5, int mutability=5, int convergence=25)" -->
<div class="memitem">
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<td class="memname">bool Setup </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> & </td>
<td class="paramname"><em>mol</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>numConformers</em> = <code>30</code>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>numChildren</em> = <code>5</code>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>mutability</em> = <code>5</code>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>convergence</em> = <code>25</code> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Setup this instance with the specified molecule.</p>
<dl><dt><b>Parameters:</b></dt><dd>
<table class="params">
<tr><td class="paramname">mol</td><td>The molecule with initial conformer. </td></tr>
<tr><td class="paramname">numConformers</td><td>The number of conformers that should be generated. This is also the number of conformers selected for each generation. </td></tr>
<tr><td class="paramname">numChildren</td><td>When a new generation is generated, for each of the numConformers conformers, numChildren children are created. </td></tr>
<tr><td class="paramname">mutability</td><td>The mutability determines how frequent a permutation occurs when generating the next generation. </td></tr>
<tr><td class="paramname">convergence</td><td>The number of identical generations before considering the process converged. </td></tr>
</table>
</dd>
</dl>
<dl><dt><b>Examples: </b></dt><dd><a class="el" href="obconformersearch_default_8cpp-example.shtml#a7">obconformersearch_default.cpp</a>.</dd>
</dl>
</div>
</div>
<a class="anchor" id="a5ee2e4f8c4c9cc9fed9949e54b8c728e"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::SetNumConformers" ref="a5ee2e4f8c4c9cc9fed9949e54b8c728e" args="(int numConformers)" -->
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<td class="memname">void SetNumConformers </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>numConformers</em></td><td>)</td>
<td><code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Set the number of conformers. </p>
</div>
</div>
<a class="anchor" id="a25b1f90c4963a806ac4aa898f542afa3"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::SetNumChildren" ref="a25b1f90c4963a806ac4aa898f542afa3" args="(int numChildren)" -->
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<td class="memname">void SetNumChildren </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>numChildren</em></td><td>)</td>
<td><code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Set the number of children generated for each parent. </p>
</div>
</div>
<a class="anchor" id="a375b8f03c5cd5fd162cea6bd78c14356"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::SetMutability" ref="a375b8f03c5cd5fd162cea6bd78c14356" args="(int mutability)" -->
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<td class="memname">void SetMutability </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>mutability</em></td><td>)</td>
<td><code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Set the mutability. </p>
</div>
</div>
<a class="anchor" id="a259d7fb57066383560678537a93d79ad"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::SetConvergence" ref="a259d7fb57066383560678537a93d79ad" args="(int convergence)" -->
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<td class="memname">void SetConvergence </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>convergence</em></td><td>)</td>
<td><code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Set the convergence (i.e. number of generations that did not change the score before considering the iteration converged). </p>
</div>
</div>
<a class="anchor" id="a045f339459d9cc1892cfe9dcdbed2b60"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::SetFixedBonds" ref="a045f339459d9cc1892cfe9dcdbed2b60" args="(const OBBitVec &fixedBonds)" -->
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<td class="memname">void SetFixedBonds </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenBabel_1_1OBBitVec.shtml">OBBitVec</a> & </td>
<td class="paramname"><em>fixedBonds</em></td><td>)</td>
<td><code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Set the bonds to be fixed. </p>
</div>
</div>
<a class="anchor" id="a95879a373f39c05163d27941df8c18c6"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::SetFilter" ref="a95879a373f39c05163d27941df8c18c6" args="(OBConformerFilter *filter)" -->
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<td class="memname">void SetFilter </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBConformerFilter.shtml">OBConformerFilter</a> * </td>
<td class="paramname"><em>filter</em></td><td>)</td>
<td><code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Set the filter method used to check if a newly generated is acceptable. Typical examples are a steric filter or electrostatic energy filter. The filters make a binary selection and one group will be scored in the next step. A number of filters are provided by default but implementing a custom filter is easy.</p>
<p>There is also a <a class="el" href="classOpenBabel_1_1OBConformerFilters.shtml" title="Class for combining OBConformerFilter objects.">OBConformerFilters</a> class to make it easy to use multiple filters. </p>
</div>
</div>
<a class="anchor" id="ab6e866e55e02b792a2b3837ee949bbfd"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::SetScore" ref="ab6e866e55e02b792a2b3837ee949bbfd" args="(OBConformerScore *score)" -->
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<td class="memname">void SetScore </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBConformerScore.shtml">OBConformerScore</a> * </td>
<td class="paramname"><em>score</em></td><td>)</td>
<td><code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>All acceptable conformers are scored to select the fittest conformers from the population. A higher score means the conformer is desired in the final set or next generation. Typical scoring would be force field energy to find the lowest energy conformer. Another example is the highest RMSD between conformer i and the closest conformer to create a diverse set of conformers. Diversity could also be expressed in other ways and implementing a scoring class is easy. </p>
</div>
</div>
<a class="anchor" id="af648d58ec31e39dff6af003f8e6b5ca4"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::Search" ref="af648d58ec31e39dff6af003f8e6b5ca4" args="()" -->
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<td class="memname">void Search </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Perform conformer search using a genetic algorithm. </p>
<dl><dt><b>Examples: </b></dt><dd><a class="el" href="obconformersearch_default_8cpp-example.shtml#a8">obconformersearch_default.cpp</a>.</dd>
</dl>
</div>
</div>
<a class="anchor" id="a6753356d193ce72d72d1fc1cfee74639"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::GetRotorKeys" ref="a6753356d193ce72d72d1fc1cfee74639" args="() const " -->
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<td class="memname">const <a class="el" href="namespaceOpenBabel.shtml#ad5ae0fb6c3d3406efb549fbc9f8c26f0">RotorKeys</a>& GetRotorKeys </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const<code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl><dt><b>Examples: </b></dt><dd><a class="el" href="obconformersearch_default_8cpp-example.shtml#a9">obconformersearch_default.cpp</a>.</dd>
</dl>
</div>
</div>
<a class="anchor" id="a908a9729ddc64dd383f093ab30a0aae3"></a><!-- doxytag: member="OpenBabel::OBConformerSearch::GetConformers" ref="a908a9729ddc64dd383f093ab30a0aae3" args="(OBMol &mol)" -->
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<td class="memname">void GetConformers </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> & </td>
<td class="paramname"><em>mol</em></td><td>)</td>
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<dl><dt><b>Examples: </b></dt><dd><a class="el" href="obconformersearch_default_8cpp-example.shtml#a10">obconformersearch_default.cpp</a>.</dd>
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<hr/>The documentation for this class was generated from the following files:<ul>
<li><a class="el" href="conformersearch_8h_source.shtml">conformersearch.h</a></li>
<li><a class="el" href="conformersearch_8cpp.shtml">conformersearch.cpp</a></li>
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