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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_1OBCisTransStereo.shtml">OBCisTransStereo</a> </li>
<li class="navelem"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml">Config</a> </li>
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<a href="#pub-methods">Public Member Functions</a> </div>
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<div class="title">OBCisTransStereo::Config Struct Reference</div> </div>
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<!-- doxytag: class="OpenBabel::OBCisTransStereo::Config" -->
<p><code>#include <<a class="el" href="cistrans_8h_source.shtml">openbabel/stereo/cistrans.h</a>></code></p>
<p><a href="structOpenBabel_1_1OBCisTransStereo_1_1Config-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="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a539a941e29cde8d13e413c515d9801cd">Config</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#acf25320b7c10321198305519ad78680c">Config</a> (unsigned long _begin, unsigned long _end, const <a class="el" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">OBStereo::Refs</a> &_refs, <a class="el" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">OBStereo::Shape</a> _shape=OBStereo::ShapeU)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a929278c4f025d8340ab65d86696386e4">operator==</a> (const <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml">Config</a> &other) const </td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a3f058aa3902997deaaefc72fe0355477">operator!=</a> (const <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml">Config</a> &other) const </td></tr>
<tr><td colspan="2"><h2><a name="pub-attribs"></a>
Public Attributes</h2></td></tr>
<tr><td colspan="2"><div class="groupHeader">Data members defining stereochemistry.</div></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">unsigned long </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a43ec7ce807e545cea2247cd68bc7b7e9">begin</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">unsigned long </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#ac31c5196f50f192d5db1d85180b05aaf">end</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">OBStereo::Refs</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a3e3f2a8fefc9f694040bbb8685cb61e1">refs</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">OBStereo::Shape</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a77f6538bd30b4203bd2b2bba33c28c85">shape</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#ad137707f900f599f5f403d9639e2aec3">specified</a></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><p>Stereochemical configuration for double-bond cis/trans stereochemistry. </p>
<p>The config struct represents the stereochemistry in a well defined way. For cis/trans stereo bonds, the following data members define the spacial arrengement of the atoms.</p>
<ul>
<li><a class="el" href="structOpenBabel_1_1OBStereo.shtml#aff913cc7d694153b33e2b3ac168a6350">OBStereo::Ref</a> <code>begin:</code> The begin atom for the double bond.</li>
<li><a class="el" href="structOpenBabel_1_1OBStereo.shtml#aff913cc7d694153b33e2b3ac168a6350">OBStereo::Ref</a> <code>end:</code> The end atom for the double bond.</li>
<li><a class="el" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">OBStereo::Refs</a> <code>refs:</code> The 4 atoms connected to the double bond.</li>
<li><a class="el" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">OBStereo::Shape</a> <code>shape:</code> The shape formed by the <code>refs</code> by connecting them in the same order as they occur in <code>refs</code>.</li>
</ul>
<div class="image">
<img src="cistrans.png" alt="cistrans.png"/>
</div>
<div class="image">
<img src="SPshapes.png" alt="SPshapes.png"/>
</div>
<p>Only <code>begin</code> and <code>end</code> are specific for <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">OBCisTransStereo::Config</a>. The other data members occur in all <a class="el" href="classOpenBabel_1_1OBTetraPlanarStereo.shtml" title="Base class for handling and storing planar stereochemistry with 4 reference atoms.">OBTetraPlanarStereo</a> derived classes. </p>
</div><hr/><h2>Constructor & Destructor Documentation</h2>
<a class="anchor" id="a539a941e29cde8d13e413c515d9801cd"></a><!-- doxytag: member="OpenBabel::OBCisTransStereo::Config::Config" ref="a539a941e29cde8d13e413c515d9801cd" args="()" -->
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<td class="memname"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml">Config</a> </td>
<td>(</td>
<td class="paramname"></td><td>)</td>
<td><code> [inline]</code></td>
</tr>
</table>
</div>
<div class="memdoc">
<p>Default constructor. Initializes <code>begin</code> and <code>end</code> to <a class="el" href="structOpenBabel_1_1OBStereo.shtml#aba01db17f4a2bfbc3db60dc172972a25a7295d9aeb6e0e6f3a5b77aa0ce7ed0db" title="No Ref set (invalid Ref)">OBStereo::NoRef</a> and <code>shape</code> to <a class="el" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37ca0ab366e13e0cfd59ccb06cd77b673bca">OBStereo::ShapeU</a>. </p>
</div>
</div>
<a class="anchor" id="acf25320b7c10321198305519ad78680c"></a><!-- doxytag: member="OpenBabel::OBCisTransStereo::Config::Config" ref="acf25320b7c10321198305519ad78680c" args="(unsigned long _begin, unsigned long _end, const OBStereo::Refs &_refs, OBStereo::Shape _shape=OBStereo::ShapeU)" -->
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<td class="memname"><a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml">Config</a> </td>
<td>(</td>
<td class="paramtype">unsigned long </td>
<td class="paramname"><em>_begin</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">unsigned long </td>
<td class="paramname"><em>_end</em>, </td>
</tr>
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<td class="paramkey"></td>
<td></td>
<td class="paramtype">const <a class="el" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">OBStereo::Refs</a> & </td>
<td class="paramname"><em>_refs</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">OBStereo::Shape</a> </td>
<td class="paramname"><em>_shape</em> = <code>OBStereo::ShapeU</code> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td><code> [inline]</code></td>
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<p>Constructor with all parameters.</p>
<dl><dt><b>Parameters:</b></dt><dd>
<table class="params">
<tr><td class="paramname">_begin</td><td>The double bond begin atom id. </td></tr>
<tr><td class="paramname">_end</td><td>The double bond end atom id. </td></tr>
<tr><td class="paramname">_refs</td><td>The 4 reference ids. </td></tr>
<tr><td class="paramname">_shape</td><td>The shape for the 4 reference ids. </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a929278c4f025d8340ab65d86696386e4"></a><!-- doxytag: member="OpenBabel::OBCisTransStereo::Config::operator==" ref="a929278c4f025d8340ab65d86696386e4" args="(const Config &other) const " -->
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<td class="memname">bool operator== </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml">Config</a> & </td>
<td class="paramname"><em>other</em></td><td>)</td>
<td> const</td>
</tr>
</table>
</div>
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<p>Equal to operator. Comparing <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">OBCisTransStereo::Config</a> structs is done using the information stored in the struct's data members (i.e. begin, end, refs and shape).</p>
<p>There are a number of cases resuling in false being returned:</p>
<ul>
<li><code>begin</code> and <code>end</code> don't match (is checked using the 2 combinations)</li>
<li>One of the Refs lists does not contain 4 elements.</li>
<li>2 or more <a class="el" href="structOpenBabel_1_1OBStereo.shtml#aba01db17f4a2bfbc3db60dc172972a25a02b1798105615b9c057d777fd19f1015" title="Implicit Ref (i.e. hydrogen, N lone pair, ...).">OBStereo::ImplicitRef</a> values in a single <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a> struct</li>
<li>(The two <code>refs</code> don't share a single common element)</li>
</ul>
<p>In the simplest case where both <code>refs</code> contain exactly the same elements (<a class="el" href="structOpenBabel_1_1OBStereo.shtml#abb14ec41d65b0dc4d49707a713da483f">OBStereo::ContainsSameRefs()</a>), coould include <a class="el" href="structOpenBabel_1_1OBStereo.shtml#aba01db17f4a2bfbc3db60dc172972a25a02b1798105615b9c057d777fd19f1015" title="Implicit Ref (i.e. hydrogen, N lone pair, ...).">OBStereo::ImplicitRef</a>), both <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a> struct are normalized to <a class="el" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37ca0ab366e13e0cfd59ccb06cd77b673bca">OBStereo::ShapeU</a> starting with the same element. After this normalization, there are two possible orientations to overlay the shape on the double bond. From the illustration below, it can be seen only <code>refs</code>[2] has to be checked in order to conclude both <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a> structs have the same stereochemistry.</p>
<div class="fragment"><pre class="fragment">
1 4 1 4 1------4
\ / | | |
C==C | | |
/ \ | | |
2 3 2------3 2------3
1 2 3 4 1 2 3 4
| | | | <- in any case, refs[0] & refs[2] remain unchanged
1 2 3 4 1 4 3 2
</pre></div><p>When comparing a <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a> struct with explicit hydrogen(s) to one with implicit hydrogen(s), both <code>refs</code> are also normalized to <a class="el" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37ca0ab366e13e0cfd59ccb06cd77b673bca">OBStereo::ShapeU</a> starting with the same common element. This shared element cannot be <a class="el" href="structOpenBabel_1_1OBStereo.shtml#aba01db17f4a2bfbc3db60dc172972a25a02b1798105615b9c057d777fd19f1015" title="Implicit Ref (i.e. hydrogen, N lone pair, ...).">OBStereo::ImplicitRef</a>. Depending on the position of the <a class="el" href="structOpenBabel_1_1OBStereo.shtml#aba01db17f4a2bfbc3db60dc172972a25a02b1798105615b9c057d777fd19f1015" title="Implicit Ref (i.e. hydrogen, N lone pair, ...).">OBStereo::ImplicitRef</a> element(s) in the <code>refs</code>, 3 cases are possible:</p>
<div class="fragment"><pre class="fragment">
refs[2] != OBStereo::ImplicitId:
(analog to the case above where they contained the same elements )
1 2 3 4
| | <- refs[0] & refs[2] remain unchanged
1 H 3 H
else:
1 2 3 4
| | <- refs[0] & refs[3] remain unchanged
1 H H 4
1 2 3 4
| | <- refs[0] & refs[1] remain unchanged
1 2 H H
</pre></div><p>In each case, the orientation of the U shape is also defined since there can be only one <a class="el" href="structOpenBabel_1_1OBStereo.shtml#aba01db17f4a2bfbc3db60dc172972a25a02b1798105615b9c057d777fd19f1015" title="Implicit Ref (i.e. hydrogen, N lone pair, ...).">OBStereo::ImplicitRef</a> for each side of the double bond.</p>
<dl class="return"><dt><b>Returns:</b></dt><dd>True if both <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a> structs represent the stereochemistry. </dd></dl>
</div>
</div>
<a class="anchor" id="a3f058aa3902997deaaefc72fe0355477"></a><!-- doxytag: member="OpenBabel::OBCisTransStereo::Config::operator!=" ref="a3f058aa3902997deaaefc72fe0355477" args="(const Config &other) const " -->
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<td class="memname">bool operator!= </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml">Config</a> & </td>
<td class="paramname"><em>other</em></td><td>)</td>
<td> const<code> [inline]</code></td>
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<p>Not equal to operator. This is the inverse of the Equal to operator==.</p>
<dl class="return"><dt><b>Returns:</b></dt><dd>True if the two <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a> structs represent a different stereochemistry. </dd></dl>
</div>
</div>
<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="a43ec7ce807e545cea2247cd68bc7b7e9"></a><!-- doxytag: member="OpenBabel::OBCisTransStereo::Config::begin" ref="a43ec7ce807e545cea2247cd68bc7b7e9" args="" -->
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<td class="memname">unsigned long <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a43ec7ce807e545cea2247cd68bc7b7e9">begin</a></td>
</tr>
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<div class="memdoc">
<p>Referenced by <a class="el" href="namespaceOpenBabel.shtml#a62d602f9ffb93ae1f37c2d3bbf010d77">OpenBabel::CanonicalLabels()</a>, and <a class="el" href="classOpenBabel_1_1OBBuilder.shtml#a6898b04c792072e4ace54885e9ff7b10">OBBuilder::CorrectStereoBonds()</a>.</p>
</div>
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<a class="anchor" id="ac31c5196f50f192d5db1d85180b05aaf"></a><!-- doxytag: member="OpenBabel::OBCisTransStereo::Config::end" ref="ac31c5196f50f192d5db1d85180b05aaf" args="" -->
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<td class="memname">unsigned long <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#ac31c5196f50f192d5db1d85180b05aaf">end</a></td>
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<p>Referenced by <a class="el" href="namespaceOpenBabel.shtml#a62d602f9ffb93ae1f37c2d3bbf010d77">OpenBabel::CanonicalLabels()</a>, and <a class="el" href="classOpenBabel_1_1OBBuilder.shtml#a6898b04c792072e4ace54885e9ff7b10">OBBuilder::CorrectStereoBonds()</a>.</p>
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<a class="anchor" id="a3e3f2a8fefc9f694040bbb8685cb61e1"></a><!-- doxytag: member="OpenBabel::OBCisTransStereo::Config::refs" ref="a3e3f2a8fefc9f694040bbb8685cb61e1" args="" -->
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<td class="memname"><a class="el" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">OBStereo::Refs</a> <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a3e3f2a8fefc9f694040bbb8685cb61e1">refs</a></td>
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<p>The 4 reference ids. </p>
<p>Referenced by <a class="el" href="classOpenBabel_1_1OBBuilder.shtml#a6898b04c792072e4ace54885e9ff7b10">OBBuilder::CorrectStereoBonds()</a>.</p>
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<a class="anchor" id="a77f6538bd30b4203bd2b2bba33c28c85"></a><!-- doxytag: member="OpenBabel::OBCisTransStereo::Config::shape" ref="a77f6538bd30b4203bd2b2bba33c28c85" args="" -->
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<td class="memname"><a class="el" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">OBStereo::Shape</a> <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a77f6538bd30b4203bd2b2bba33c28c85">shape</a></td>
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<p>The shape of the 4 reference ids. </p>
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<a class="anchor" id="ad137707f900f599f5f403d9639e2aec3"></a><!-- doxytag: member="OpenBabel::OBCisTransStereo::Config::specified" ref="ad137707f900f599f5f403d9639e2aec3" args="" -->
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<td class="memname">bool <a class="el" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#ad137707f900f599f5f403d9639e2aec3">specified</a></td>
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<p>True if the stereochemistry is specified. When false, the described special orientation is only accidental (i.e. unspecified). </p>
<p>Referenced by <a class="el" href="namespaceOpenBabel.shtml#a62d602f9ffb93ae1f37c2d3bbf010d77">OpenBabel::CanonicalLabels()</a>.</p>
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<hr/>The documentation for this struct was generated from the following file:<ul>
<li><a class="el" href="cistrans_8h_source.shtml">cistrans.h</a></li>
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