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<div class="title">squareplanar.h</div> </div>
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<a href="squareplanar_8h.shtml">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/**********************************************************************</span>
<a name="l00002"></a>00002 <span class="comment"> squareplanar.h - Class for handling and storing squareplanar stereochemistry.</span>
<a name="l00003"></a>00003 <span class="comment"></span>
<a name="l00004"></a>00004 <span class="comment"> Copyright (C) 2009-2010 by Tim Vandermeersch</span>
<a name="l00005"></a>00005 <span class="comment"></span>
<a name="l00006"></a>00006 <span class="comment"> This file is part of the Open Babel project.</span>
<a name="l00007"></a>00007 <span class="comment"> For more information, see <http://openbabel.org/></span>
<a name="l00008"></a>00008 <span class="comment"></span>
<a name="l00009"></a>00009 <span class="comment"> This program is free software; you can redistribute it and/or modify</span>
<a name="l00010"></a>00010 <span class="comment"> it under the terms of the GNU General Public License as published by</span>
<a name="l00011"></a>00011 <span class="comment"> the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00012"></a>00012 <span class="comment"> (at your option) any later version.</span>
<a name="l00013"></a>00013 <span class="comment"></span>
<a name="l00014"></a>00014 <span class="comment"> This program is distributed in the hope that it will be useful,</span>
<a name="l00015"></a>00015 <span class="comment"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00016"></a>00016 <span class="comment"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<a name="l00017"></a>00017 <span class="comment"> GNU General Public License for more details.</span>
<a name="l00018"></a>00018 <span class="comment"></span>
<a name="l00019"></a>00019 <span class="comment"> You should have received a copy of the GNU General Public License</span>
<a name="l00020"></a>00020 <span class="comment"> along with this program; if not, write to the Free Software</span>
<a name="l00021"></a>00021 <span class="comment"> Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA</span>
<a name="l00022"></a>00022 <span class="comment"> 02110-1301, USA.</span>
<a name="l00023"></a>00023 <span class="comment"> **********************************************************************/</span>
<a name="l00024"></a>00024 <span class="preprocessor">#ifndef OB_SQUAREPLANAR_H</span>
<a name="l00025"></a>00025 <span class="preprocessor"></span><span class="preprocessor">#define OB_SQUAREPLANAR_H</span>
<a name="l00026"></a>00026 <span class="preprocessor"></span>
<a name="l00027"></a>00027 <span class="preprocessor">#include <<a class="code" href="tetraplanar_8h.shtml" title="Base class for handling and storing planar stereochemistry with 4 reference atoms.">openbabel/stereo/tetraplanar.h</a>></span>
<a name="l00028"></a>00028 <span class="preprocessor">#include <vector></span>
<a name="l00029"></a>00029
<a name="l00030"></a>00030 <span class="keyword">namespace </span>OpenBabel {
<a name="l00031"></a>00031
<a name="l00034"></a>00034
<a name="l00048"></a><a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml">00048</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml" title="Class for handling and storing square planar stereochemistry.">OBSquarePlanarStereo</a> : <span class="keyword">public</span> <a class="code" href="classOpenBabel_1_1OBTetraPlanarStereo.shtml" title="Base class for handling and storing planar stereochemistry with 4 reference atoms.">OBTetraPlanarStereo</a>
<a name="l00049"></a>00049 {
<a name="l00050"></a>00050 <span class="keyword">public</span>:
<a name="l00070"></a>00070 <span class="preprocessor">#ifndef SWIG</span>
<a name="l00071"></a><a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml">00071</a> <span class="preprocessor"></span> <span class="keyword">struct </span>OBAPI <a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml" title="Stereochemical configuration for square planar stereocenters.">Config</a>
<a name="l00072"></a>00072 {
<a name="l00077"></a><a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml#a539a941e29cde8d13e413c515d9801cd">00077</a> <a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml" title="Stereochemical configuration for square planar stereocenters.">Config</a>() : center(<a class="code" href="structOpenBabel_1_1OBStereo.shtml" title="Placeholder for enums & Ref/Refs related functions.">OBStereo</a>::NoRef), shape(<a class="code" href="structOpenBabel_1_1OBStereo.shtml" title="Placeholder for enums & Ref/Refs related functions.">OBStereo</a>::ShapeU),
<a name="l00078"></a>00078 specified(true)
<a name="l00079"></a>00079 { }
<a name="l00087"></a><a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml#a3932e85a5b2cc866ab349584485a5b1c">00087</a> <a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml" title="Stereochemical configuration for square planar stereocenters.">Config</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> _center, <span class="keyword">const</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">OBStereo::Refs</a> &_refs,
<a name="l00088"></a>00088 <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">OBStereo::Shape</a> _shape = <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37ca0ab366e13e0cfd59ccb06cd77b673bca">OBStereo::ShapeU</a>) : center(_center),
<a name="l00089"></a>00089 refs(_refs), shape(_shape), specified(true)
<a name="l00090"></a>00090 { }
<a name="l00155"></a>00155 <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenBabel.shtml#ac001b331f648fbbd8590576f59d4d2ab">operator==</a>(<span class="keyword">const</span> <a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml" title="Stereochemical configuration for square planar stereocenters.">Config</a> &other) <span class="keyword">const</span>;
<a name="l00161"></a><a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml#a3f058aa3902997deaaefc72fe0355477">00161</a> <span class="keywordtype">bool</span> operator!=(<span class="keyword">const</span> <a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml" title="Stereochemical configuration for square planar stereocenters.">Config</a> &other)<span class="keyword"> const</span>
<a name="l00162"></a>00162 <span class="keyword"> </span>{
<a name="l00163"></a>00163 <span class="keywordflow">return</span> !(*<span class="keyword">this</span> == other);
<a name="l00164"></a>00164 }
<a name="l00165"></a>00165
<a name="l00170"></a><a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml#a822b3ed2ceea391277903da02d1fd0a2">00170</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml#a822b3ed2ceea391277903da02d1fd0a2">center</a>; <span class="comment">//<! The central atom id.</span>
<a name="l00171"></a><a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml#a3e3f2a8fefc9f694040bbb8685cb61e1">00171</a> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">OBStereo::Refs</a> <a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml#a3e3f2a8fefc9f694040bbb8685cb61e1" title="The 4 reference ids.">refs</a>;
<a name="l00172"></a><a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml#a77f6538bd30b4203bd2b2bba33c28c85">00172</a> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">OBStereo::Shape</a> <a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml#a77f6538bd30b4203bd2b2bba33c28c85" title="The shape of the 4 reference ids.">shape</a>;
<a name="l00173"></a><a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml#ad137707f900f599f5f403d9639e2aec3">00173</a> <span class="keywordtype">bool</span> specified;
<a name="l00174"></a>00174
<a name="l00175"></a>00175
<a name="l00176"></a>00176 };
<a name="l00177"></a>00177 <span class="preprocessor">#endif</span>
<a name="l00178"></a>00178 <span class="preprocessor"></span>
<a name="l00181"></a>00181 <a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml" title="Class for handling and storing square planar stereochemistry.">OBSquarePlanarStereo</a>(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *mol);
<a name="l00185"></a>00185 <span class="keyword">virtual</span> ~<a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml" title="Class for handling and storing square planar stereochemistry.">OBSquarePlanarStereo</a>();
<a name="l00186"></a>00186
<a name="l00189"></a>00189
<a name="l00193"></a><a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml#a25d3547525ae04f2769c976552a55b34">00193</a> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7">OBStereo::Type</a> <a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml#a25d3547525ae04f2769c976552a55b34">GetType</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7a793d15fd6e6d225fcddc0cf4b65259d3" title="Square-planar stereochemistry.">OBStereo::SquarePlanar</a>; }
<a name="l00198"></a>00198 <span class="keywordtype">bool</span> IsValid() <span class="keyword">const</span>;
<a name="l00199"></a>00199
<a name="l00203"></a>00203 <span class="preprocessor">#ifndef SWIG</span>
<a name="l00204"></a>00204 <span class="preprocessor"></span> <span class="keywordtype">void</span> SetConfig(<span class="keyword">const</span> Config &config);
<a name="l00208"></a>00208 Config GetConfig(<a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">OBStereo::Shape</a> shape = <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37ca0ab366e13e0cfd59ccb06cd77b673bca">OBStereo::ShapeU</a>) <span class="keyword">const</span>;
<a name="l00213"></a>00213 Config GetConfig(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> start,
<a name="l00214"></a>00214 <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">OBStereo::Shape</a> shape = <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37ca0ab366e13e0cfd59ccb06cd77b673bca">OBStereo::ShapeU</a>) <span class="keyword">const</span>;
<a name="l00215"></a>00215 <span class="preprocessor">#endif</span>
<a name="l00216"></a>00216 <span class="preprocessor"></span>
<a name="l00222"></a>00222 <span class="keywordtype">bool</span> <a class="code" href="namespaceOpenBabel.shtml#ac001b331f648fbbd8590576f59d4d2ab">operator==</a>(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml" title="Class for handling and storing square planar stereochemistry.">OBSquarePlanarStereo</a> &other) <span class="keyword">const</span>;
<a name="l00228"></a><a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml#ac0773f2ca467c400db0a32bf809dbd9f">00228</a> <span class="keywordtype">bool</span> operator!=(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml" title="Class for handling and storing square planar stereochemistry.">OBSquarePlanarStereo</a> &other)<span class="keyword"> const</span>
<a name="l00229"></a>00229 <span class="keyword"> </span>{
<a name="l00230"></a>00230 <span class="keywordflow">return</span> !(*<span class="keyword">this</span> == other);
<a name="l00231"></a>00231 }
<a name="l00233"></a>00233
<a name="l00234"></a>00234 <span class="comment">/*</span>
<a name="l00235"></a>00235 <span class="comment"> * Implement OBGenericData::Clone().</span>
<a name="l00236"></a>00236 <span class="comment"> */</span>
<a name="l00237"></a>00237 <a class="code" href="classOpenBabel_1_1OBGenericData.shtml" title="Base class for generic data.">OBGenericData</a>* Clone(<a class="code" href="classOpenBabel_1_1OBBase.shtml" title="Base Class.">OBBase</a> *mol) <span class="keyword">const</span>;
<a name="l00238"></a>00238
<a name="l00240"></a>00240
<a name="l00241"></a>00241
<a name="l00244"></a>00244 <span class="keywordtype">bool</span> IsTrans(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> id1, <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> id2) <span class="keyword">const</span>;
<a name="l00248"></a>00248 <span class="keywordtype">bool</span> IsCis(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> id1, <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> id2) <span class="keyword">const</span>;
<a name="l00253"></a>00253 <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> GetTransRef(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">id</span>) <span class="keyword">const</span>;
<a name="l00257"></a>00257 std::vector<unsigned long> GetCisRefs(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">id</span>) <span class="keyword">const</span>;
<a name="l00259"></a>00259
<a name="l00260"></a>00260 <span class="keyword">private</span>:
<a name="l00261"></a>00261 Config m_cfg;
<a name="l00262"></a>00262 <span class="comment">// The following function sits behind GetCisRef and GetTransRef</span>
<a name="l00263"></a>00263 <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> GetCisOrTransRef(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">id</span>, <span class="keywordtype">bool</span> getcisref) <span class="keyword">const</span>;
<a name="l00264"></a>00264 };
<a name="l00266"></a>00266 <span class="comment">// end addtogroup doxygen</span>
<a name="l00267"></a>00267
<a name="l00268"></a>00268 } <span class="comment">// namespace OpenBabel</span>
<a name="l00269"></a>00269
<a name="l00270"></a>00270 <span class="preprocessor">#ifndef SWIG</span>
<a name="l00271"></a>00271 <span class="preprocessor"></span><span class="keyword">namespace </span>std {
<a name="l00272"></a>00272
<a name="l00275"></a>00275
<a name="l00291"></a>00291 OBAPI ostream& <a class="code" href="namespaceOpenBabel.shtml#a70c653ee69fdbd27f77d430e4aed3cad" title="Prints a representation of the vector as a row vector of the form "<0.1,1,2>".">operator<<</a>(ostream &out, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBSquarePlanarStereo.shtml" title="Class for handling and storing square planar stereochemistry.">OpenBabel::OBSquarePlanarStereo</a> &ct);
<a name="l00305"></a>00305 OBAPI ostream& <a class="code" href="namespaceOpenBabel.shtml#a70c653ee69fdbd27f77d430e4aed3cad" title="Prints a representation of the vector as a row vector of the form "<0.1,1,2>".">operator<<</a>(ostream &out, <span class="keyword">const</span> <a class="code" href="structOpenBabel_1_1OBSquarePlanarStereo_1_1Config.shtml" title="Stereochemical configuration for square planar stereocenters.">OpenBabel::OBSquarePlanarStereo::Config</a> &cfg);
<a name="l00306"></a>00306
<a name="l00308"></a>00308
<a name="l00309"></a>00309 } <span class="comment">// namespace std</span>
<a name="l00310"></a>00310 <span class="preprocessor">#endif // Not SWIG</span>
<a name="l00311"></a>00311 <span class="preprocessor"></span>
<a name="l00312"></a>00312 <span class="preprocessor">#endif</span>
<a name="l00313"></a>00313 <span class="preprocessor"></span>
</pre></div></div>
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Generated on Thu Oct 13 2011 16:08:08 by <a href="http://www.doxygen.org/"><img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.7.5.1.
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