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<div class="title">cistrans.h</div> </div>
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<a href="cistrans_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"> cistrans.h - Class for handling and storing cis/trans 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_CISTRANS_H</span>
<a name="l00025"></a>00025 <span class="preprocessor"></span><span class="preprocessor">#define OB_CISTRANS_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="l00075"></a><a class="code" href="classOpenBabel_1_1OBCisTransStereo.shtml">00075</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBCisTransStereo.shtml" title="Class for handling and storing cis/trans stereochemistry.">OBCisTransStereo</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="l00076"></a>00076 {
<a name="l00077"></a>00077 <span class="keyword">public</span>:
<a name="l00098"></a>00098 <span class="preprocessor">#ifndef SWIG</span>
<a name="l00099"></a><a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml">00099</a> <span class="preprocessor"></span> <span class="keyword">struct </span>OBAPI <a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a>
<a name="l00100"></a>00100 {
<a name="l00105"></a><a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a539a941e29cde8d13e413c515d9801cd">00105</a> <a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a>() : begin(<a class="code" href="structOpenBabel_1_1OBStereo.shtml" title="Placeholder for enums & Ref/Refs related functions.">OBStereo</a>::NoRef), end(<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="l00106"></a>00106 specified(true)
<a name="l00107"></a>00107 { }
<a name="l00116"></a><a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#acf25320b7c10321198305519ad78680c">00116</a> <a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> _begin, <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> _end, <span class="keyword">const</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">OBStereo::Refs</a> &_refs,
<a name="l00117"></a>00117 <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>) : begin(_begin), end(_end),
<a name="l00118"></a>00118 refs(_refs), shape(_shape), specified(true)
<a name="l00119"></a>00119 { }
<a name="l00184"></a>00184 <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_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a> &other) <span class="keyword">const</span>;
<a name="l00190"></a><a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a3f058aa3902997deaaefc72fe0355477">00190</a> <span class="keywordtype">bool</span> operator!=(<span class="keyword">const</span> <a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">Config</a> &other)<span class="keyword"> const</span>
<a name="l00191"></a>00191 <span class="keyword"> </span>{
<a name="l00192"></a>00192 <span class="keywordflow">return</span> !(*<span class="keyword">this</span> == other);
<a name="l00193"></a>00193 }
<a name="l00194"></a>00194
<a name="l00199"></a><a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#ac31c5196f50f192d5db1d85180b05aaf">00199</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> begin, <a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#ac31c5196f50f192d5db1d85180b05aaf">end</a>; <span class="comment">//<! The double bond begin and end ids.</span>
<a name="l00200"></a><a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a3e3f2a8fefc9f694040bbb8685cb61e1">00200</a> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#aa6d4491769cb9af32f3ea22e9f9a66c4">OBStereo::Refs</a> <a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a3e3f2a8fefc9f694040bbb8685cb61e1" title="The 4 reference ids.">refs</a>;
<a name="l00201"></a><a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a77f6538bd30b4203bd2b2bba33c28c85">00201</a> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a55b506070847a13554f8b879c1bfb37c">OBStereo::Shape</a> <a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#a77f6538bd30b4203bd2b2bba33c28c85" title="The shape of the 4 reference ids.">shape</a>;
<a name="l00202"></a><a class="code" href="structOpenBabel_1_1OBCisTransStereo_1_1Config.shtml#ad137707f900f599f5f403d9639e2aec3">00202</a> <span class="keywordtype">bool</span> specified;
<a name="l00203"></a>00203
<a name="l00204"></a>00204
<a name="l00205"></a>00205 };
<a name="l00206"></a>00206 <span class="preprocessor">#endif</span>
<a name="l00207"></a>00207 <span class="preprocessor"></span>
<a name="l00210"></a>00210 <a class="code" href="classOpenBabel_1_1OBCisTransStereo.shtml" title="Class for handling and storing cis/trans stereochemistry.">OBCisTransStereo</a>(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *mol);
<a name="l00214"></a>00214 <span class="keyword">virtual</span> ~<a class="code" href="classOpenBabel_1_1OBCisTransStereo.shtml" title="Class for handling and storing cis/trans stereochemistry.">OBCisTransStereo</a>();
<a name="l00215"></a>00215
<a name="l00218"></a>00218
<a name="l00222"></a><a class="code" href="classOpenBabel_1_1OBCisTransStereo.shtml#a25d3547525ae04f2769c976552a55b34">00222</a> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7">OBStereo::Type</a> <a class="code" href="classOpenBabel_1_1OBCisTransStereo.shtml#a25d3547525ae04f2769c976552a55b34">GetType</a>()<span class="keyword"> const </span>{ <span class="keywordflow">return</span> <a class="code" href="structOpenBabel_1_1OBStereo.shtml#a1d1cfd8ffb84e947f82999c682b666a7abf2462b166f389c17adccf7a95941396" title="cis/trans double bond">OBStereo::CisTrans</a>; }
<a name="l00230"></a>00230 <span class="keywordtype">bool</span> IsValid() <span class="keyword">const</span>;
<a name="l00231"></a>00231
<a name="l00235"></a>00235 <span class="preprocessor">#ifndef SWIG</span>
<a name="l00236"></a>00236 <span class="preprocessor"></span> <span class="keywordtype">void</span> SetConfig(<span class="keyword">const</span> Config &config);
<a name="l00240"></a>00240 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="l00245"></a>00245 Config GetConfig(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> start,
<a name="l00246"></a>00246 <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="l00247"></a>00247 <span class="preprocessor">#endif</span>
<a name="l00248"></a>00248 <span class="preprocessor"></span>
<a name="l00254"></a>00254 <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_1OBCisTransStereo.shtml" title="Class for handling and storing cis/trans stereochemistry.">OBCisTransStereo</a> &other) <span class="keyword">const</span>;
<a name="l00260"></a><a class="code" href="classOpenBabel_1_1OBCisTransStereo.shtml#ac2d04819b59f3a4ec2c1505344dcd62c">00260</a> <span class="keywordtype">bool</span> operator!=(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBCisTransStereo.shtml" title="Class for handling and storing cis/trans stereochemistry.">OBCisTransStereo</a> &other)<span class="keyword"> const</span>
<a name="l00261"></a>00261 <span class="keyword"> </span>{
<a name="l00262"></a>00262 <span class="keywordflow">return</span> !(*<span class="keyword">this</span> == other);
<a name="l00263"></a>00263 }
<a name="l00265"></a>00265
<a name="l00266"></a>00266 <span class="comment">/*</span>
<a name="l00267"></a>00267 <span class="comment"> * Implement OBGenericData::Clone().</span>
<a name="l00268"></a>00268 <span class="comment"> */</span>
<a name="l00269"></a>00269 <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="l00270"></a>00270
<a name="l00271"></a>00271
<a name="l00273"></a>00273
<a name="l00274"></a>00274
<a name="l00301"></a>00301 <span class="keywordtype">bool</span> IsOnSameAtom(<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="l00305"></a>00305 <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="l00309"></a>00309 <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="l00314"></a>00314 <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="l00319"></a>00319 <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> GetCisRef(<span class="keywordtype">unsigned</span> <span class="keywordtype">long</span> <span class="keywordtype">id</span>) <span class="keyword">const</span>;
<a name="l00321"></a>00321
<a name="l00322"></a>00322 <span class="keyword">private</span>:
<a name="l00323"></a>00323 Config m_cfg;
<a name="l00324"></a>00324 <span class="comment">// The following function sits behind GetCisRef and GetTransRef</span>
<a name="l00325"></a>00325 <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="l00326"></a>00326 };
<a name="l00328"></a>00328
<a name="l00329"></a>00329 } <span class="comment">// namespace OpenBabel</span>
<a name="l00330"></a>00330
<a name="l00331"></a>00331 <span class="preprocessor">#ifndef SWIG</span>
<a name="l00332"></a>00332 <span class="preprocessor"></span><span class="keyword">namespace </span>std {
<a name="l00333"></a>00333
<a name="l00336"></a>00336
<a name="l00353"></a>00353 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_1OBCisTransStereo.shtml" title="Class for handling and storing cis/trans stereochemistry.">OpenBabel::OBCisTransStereo</a> &ct);
<a name="l00368"></a>00368 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_1OBCisTransStereo_1_1Config.shtml" title="Stereochemical configuration for double-bond cis/trans stereochemistry.">OpenBabel::OBCisTransStereo::Config</a> &cfg);
<a name="l00369"></a>00369
<a name="l00371"></a>00371
<a name="l00372"></a>00372 } <span class="comment">// namespace std</span>
<a name="l00373"></a>00373 <span class="preprocessor">#endif // Not SWIG</span>
<a name="l00374"></a>00374 <span class="preprocessor"></span>
<a name="l00375"></a>00375 <span class="preprocessor">#endif</span>
<a name="l00376"></a>00376 <span class="preprocessor"></span>
</pre></div></div>
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