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<li class="navelem"><a class="el" href="namespaceOpenBabel.shtml">OpenBabel</a> </li>
<li class="navelem"><a class="el" href="classOpenBabel_1_1OBChargeModel.shtml">OBChargeModel</a> </li>
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<a href="#pub-types">Public Types</a> |
<a href="#pub-methods">Public Member Functions</a> |
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<div class="title">OBChargeModel Class Reference</div> </div>
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<!-- doxytag: class="OpenBabel::OBChargeModel" --><!-- doxytag: inherits="OpenBabel::OBPlugin" -->
<p><code>#include <<a class="el" href="chargemodel_8h_source.shtml">openbabel/chargemodel.h</a>></code></p>
<div class="dynheader">
Inheritance diagram for OBChargeModel:</div>
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<area shape="rect" id="node2" href="classOpenBabel_1_1OBPlugin.shtml" title="Base class for all types of dynamic classes discovered at runtime." alt="" coords="29,5,112,35"/></map>
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<p><a href="classOpenBabel_1_1OBChargeModel-members.shtml">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef std::map< const char <br class="typebreak"/>
*, <a class="el" href="classOpenBabel_1_1OBPlugin.shtml">OBPlugin</a> *, <a class="el" href="structOpenBabel_1_1CharPtrLess.shtml">CharPtrLess</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga0fd3c807ed3341c33070c93b14739bc8">PluginMapType</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef <br class="typebreak"/>
PluginMapType::const_iterator </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga8fac85f5497f873a2dd8734b47f0bdc0">PluginIterator</a></td></tr>
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#a45db88b29eb37e9dd105bf4032e421d2">TypeID</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#a5169afc2e696bcdc3069120e4088b484">ComputeCharges</a> (<a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> &)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const std::vector< double > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#ab389d7d8e54da1b05bd936cb82deb650">GetFormalCharges</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const std::vector< double > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#a4466833d6a376b5a0f975ffe41716bba">GetPartialCharges</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#a9b1ae06b444f49a68b2e2c8ac9a0c534">GetDipoleMoment</a> (<a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> &)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga4a6b8d1611d5d963fc29982cc1ebcbf7">Description</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gae0859fdbf134af95a8231eb32c73b7db">Display</a> (std::string &txt, const char *param, const char *ID=NULL)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenBabel_1_1OBPlugin.shtml">OBPlugin</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga9399e9568ab809d714385f1b237a9335">MakeInstance</a> (const std::vector< std::string > &)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga3e0b39e1326de703012f81ac2be7feba">Init</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga753a34173c6750388d33e5294556790f">GetID</a> () const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="group__plugins.shtml#ga0fd3c807ed3341c33070c93b14739bc8">PluginMapType</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gaabc1385cbe63145ffec6edf1f2c3be98">GetMap</a> () const =0</td></tr>
<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenBabel_1_1OBPlugin.shtml">OBPlugin</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga295dc7f1b94da710821c562bff3e7c97">GetPlugin</a> (const char *Type, const char *ID)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static bool </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gaf95953a5793333ba51e978c4a0a00103">ListAsVector</a> (const char *PluginID, const char *param, std::vector< std::string > &vlist)</td></tr>
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<tr><td class="memItemLeft" align="right" valign="top">static std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gaba22c5352d36c7f058299af7ddffb03e">ListAsString</a> (const char *PluginID, const char *param=NULL)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static std::string </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga84fc973fdf4bba5a6b0e2d402077991c">FirstLine</a> (const char *txt)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__plugins.shtml#ga8fac85f5497f873a2dd8734b47f0bdc0">PluginIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga1d4d73999ab0518ee471c635bd0a7e87">Begin</a> (const char *PluginID)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__plugins.shtml#ga8fac85f5497f873a2dd8734b47f0bdc0">PluginIterator</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga9a330280c1cd2e7119dac87a6fd0b762">End</a> (const char *PluginID)</td></tr>
<tr><td colspan="2"><h2><a name="pro-methods"></a>
Protected Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#aefec0fbdf06bb4199614da22f1a9deee">FillChargeVectors</a> (<a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> &mol)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">virtual double </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#a38074e4c8bdf55f4c0fc5f66bf8e8065">DipoleScalingFactor</a> ()</td></tr>
<tr><td colspan="2"><h2><a name="pro-static-methods"></a>
Static Protected Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__plugins.shtml#ga0fd3c807ed3341c33070c93b14739bc8">PluginMapType</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gac40457336d7b12bb632b4ac4e8955a3a">PluginMap</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="group__plugins.shtml#ga0fd3c807ed3341c33070c93b14739bc8">PluginMapType</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#gadfcf9fda27cfbc4301fc94517a4250ef">GetTypeMap</a> (const char *PluginID)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static <a class="el" href="classOpenBabel_1_1OBPlugin.shtml">OBPlugin</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga1e58b1811ec8c1b88254ee46ccef0b78">BaseFindType</a> (<a class="el" href="group__plugins.shtml#ga0fd3c807ed3341c33070c93b14739bc8">PluginMapType</a> &Map, const char *ID)</td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#aacfd3c312da07c274fddf70535d5485e">m_partialCharges</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector< double > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#adfe2c37552d808ee93749e89ba1e1030">m_formalCharges</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="group__plugins.shtml#ga1f8d25dafb0bc13814ca451035f67955">_id</a></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Atomic partial charge models. </p>
<dl class="since"><dt><b>Since:</b></dt><dd>version 2.3</dd></dl>
<p>Classes derived from <a class="el" href="classOpenBabel_1_1OBChargeModel.shtml" title="Atomic partial charge models.">OBChargeModel</a> implement different atomic partial charge models. It is intended to allow assinging partial charges beyond the traditional Gasteiger-Marsili sigma charges previously used in Open Babel. A --partialcharge method is provided for the babel command-line, allowing you to override the Gasteiger charge assignment and use other charge models.</p>
<p>The advantage of plugin classes is that no existing code has to be modified when a new class is added. You can list those that are present by babel -L charges or from a menu item in the GUI.</p>
<p>Any <a class="el" href="classOpenBabel_1_1OBChargeModel.shtml" title="Atomic partial charge models.">OBChargeModel</a> derived class works like other plugins and needs to to have a constructor, a function returning a short description, and a <a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#a5169afc2e696bcdc3069120e4088b484">ComputeCharges()</a> function which does the work. A single global instance of the class needs to be instantiated to define the ID, by which the class is subsequently accessed.</p>
<p>Once <a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#a5169afc2e696bcdc3069120e4088b484">ComputeCharges()</a> has been called, the atoms of the molecule can be queried for partial or formal charges using <a class="el" href="classOpenBabel_1_1OBAtom.shtml#aeccf78db112723467e7756a5734c82b9">OBAtom::GetPartialCharge()</a> or in vector form from the model itself:</p>
<div class="fragment"><pre class="fragment"> OBMol inputMolecule;
OBChargeModel *mmffCharges = OBChargeModel::FindType(<span class="stringliteral">"mmff94"</span>);
<span class="keyword">const</span> std::vector<double> partialCharges;
<span class="keywordflow">if</span> (mmffCharges && mmffCharges->ComputeCharges(inputMolecule)) {
partialCharges = mmffCharges->GetPartialCharges();
}
</pre></div><p>Note: Formal charges are also returned as floating point values, since some charge models consider delocalized charges (e.g., 0.5 for an O in a carboxylate CO2- group).</p>
<div class="fragment"><pre class="fragment"> OBChargeModel *gasteiger = OBChargeModel::FindType(<span class="stringliteral">"gasteiger"</span>);
<span class="keywordflow">if</span> (gasteiger) {
cout << <span class="stringliteral">" gasteiger: "</span> << dipoleMagnitude(gasteiger->GetDipoleMoment(mol));
}
</pre></div><p>By default, Open Babel 2.3 includes Gasteiger and MMFF94 partial charges. If the Eigen matrix library is found when compiling, the QEq and QTPIE methods will be added. Future releases will likely add additional charge models, including the EEM method. </p>
</div><hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a45db88b29eb37e9dd105bf4032e421d2"></a><!-- doxytag: member="OpenBabel::OBChargeModel::TypeID" ref="a45db88b29eb37e9dd105bf4032e421d2" args="()" -->
<div class="memitem">
<div class="memproto">
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<td class="memname">const char* TypeID </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td><code> [inline, virtual]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Redefined by each plugin type: "formats", "fingerprints", etc. </p>
<p>Reimplemented from <a class="el" href="group__plugins.shtml#ga45dfda1fb13d3c26ab7f8f7631e3351c">OBPlugin</a>.</p>
</div>
</div>
<a class="anchor" id="a5169afc2e696bcdc3069120e4088b484"></a><!-- doxytag: member="OpenBabel::OBChargeModel::ComputeCharges" ref="a5169afc2e696bcdc3069120e4088b484" args="(OBMol &)" -->
<div class="memitem">
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<td class="memname">virtual bool ComputeCharges </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> & </td>
<td class="paramname"></td><td>)</td>
<td><code> [inline, virtual]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>whether partial charges were successfully assigned to this molecule </dd></dl>
<dl class="note"><dt><b>Note:</b></dt><dd>The method should fill m_partialCharges and m_formalCharges as well </dd></dl>
</div>
</div>
<a class="anchor" id="ab389d7d8e54da1b05bd936cb82deb650"></a><!-- doxytag: member="OpenBabel::OBChargeModel::GetFormalCharges" ref="ab389d7d8e54da1b05bd936cb82deb650" args="() const " -->
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<td class="memname">const std::vector<double>& GetFormalCharges </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const<code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>a vector of the formal charges on each atom, indexed from 0 This method returns floating point formal charges since some charge models consider fractional charges (e.g., 0.5 for an oxygen in a carboxylate CO2- group). </dd></dl>
<dl class="note"><dt><b>Note:</b></dt><dd>If <a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#a5169afc2e696bcdc3069120e4088b484">ComputeCharges()</a> has not been called, this will return an empty vector </dd></dl>
</div>
</div>
<a class="anchor" id="a4466833d6a376b5a0f975ffe41716bba"></a><!-- doxytag: member="OpenBabel::OBChargeModel::GetPartialCharges" ref="a4466833d6a376b5a0f975ffe41716bba" args="() const " -->
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<td class="memname">const std::vector<double>& GetPartialCharges </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td> const<code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<dl class="return"><dt><b>Returns:</b></dt><dd>a vector of the partial charges on each atom, indexed from 0 </dd></dl>
<dl class="note"><dt><b>Note:</b></dt><dd>If <a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#a5169afc2e696bcdc3069120e4088b484">ComputeCharges()</a> has not been called, this will return an empty vector </dd></dl>
</div>
</div>
<a class="anchor" id="a9b1ae06b444f49a68b2e2c8ac9a0c534"></a><!-- doxytag: member="OpenBabel::OBChargeModel::GetDipoleMoment" ref="a9b1ae06b444f49a68b2e2c8ac9a0c534" args="(OBMol &)" -->
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<td class="memname"><a class="el" href="classOpenBabel_1_1vector3.shtml">vector3</a> GetDipoleMoment </td>
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<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 class="return"><dt><b>Returns:</b></dt><dd>a vector of the dipole moment from this molecule </dd></dl>
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<a class="anchor" id="aefec0fbdf06bb4199614da22f1a9deee"></a><!-- doxytag: member="OpenBabel::OBChargeModel::FillChargeVectors" ref="aefec0fbdf06bb4199614da22f1a9deee" args="(OBMol &mol)" -->
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<td class="memname">void FillChargeVectors </td>
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<td class="paramtype"><a class="el" href="classOpenBabel_1_1OBMol.shtml">OBMol</a> & </td>
<td class="paramname"><em>mol</em></td><td>)</td>
<td><code> [protected]</code></td>
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<p>Fill the internal partial and formal charge vectors (convenience function) </p>
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<a class="anchor" id="a38074e4c8bdf55f4c0fc5f66bf8e8065"></a><!-- doxytag: member="OpenBabel::OBChargeModel::DipoleScalingFactor" ref="a38074e4c8bdf55f4c0fc5f66bf8e8065" args="()" -->
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<td class="memname">virtual double DipoleScalingFactor </td>
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<td><code> [inline, protected, virtual]</code></td>
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<p>Provide a scaling factor for the dipole moment -- ideally calibrated from many molecules. </p>
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<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="aacfd3c312da07c274fddf70535d5485e"></a><!-- doxytag: member="OpenBabel::OBChargeModel::m_partialCharges" ref="aacfd3c312da07c274fddf70535d5485e" args="" -->
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<td class="memname">std::vector<double> <a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#aacfd3c312da07c274fddf70535d5485e">m_partialCharges</a><code> [protected]</code></td>
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<a class="anchor" id="adfe2c37552d808ee93749e89ba1e1030"></a><!-- doxytag: member="OpenBabel::OBChargeModel::m_formalCharges" ref="adfe2c37552d808ee93749e89ba1e1030" args="" -->
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<td class="memname">std::vector<double> <a class="el" href="classOpenBabel_1_1OBChargeModel.shtml#adfe2c37552d808ee93749e89ba1e1030">m_formalCharges</a><code> [protected]</code></td>
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<hr/>The documentation for this class was generated from the following files:<ul>
<li><a class="el" href="chargemodel_8h_source.shtml">chargemodel.h</a></li>
<li><a class="el" href="chargemodel_8cpp.shtml">chargemodel.cpp</a></li>
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