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<div class="title">isomorphism.h</div> </div>
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<a href="isomorphism_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"> isomophism.h - OBIsomorphismMapper class for finding isomorphisms.</span>
<a name="l00003"></a>00003 <span class="comment"></span>
<a name="l00004"></a>00004 <span class="comment"> Copyright (C) 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_ISOMORPHISM_H</span>
<a name="l00025"></a>00025 <span class="preprocessor"></span><span class="preprocessor">#define OB_ISOMORPHISM_H</span>
<a name="l00026"></a>00026 <span class="preprocessor"></span>
<a name="l00027"></a>00027 <span class="preprocessor">#include <<a class="code" href="mol_8h.shtml" title="Handle molecules. Declarations of OBMol, OBAtom, OBBond, OBResidue. (the main header for Open Babel)...">openbabel/mol.h</a>></span>
<a name="l00028"></a>00028
<a name="l00029"></a>00029 <span class="keyword">namespace </span>OpenBabel {
<a name="l00030"></a>00030
<a name="l00031"></a>00031 <span class="keyword">class </span>OBQuery;
<a name="l00032"></a>00032
<a name="l00035"></a>00035
<a name="l00076"></a><a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml">00076</a> <span class="keyword">class </span>OBAPI <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml" title="Abstract class defining interface for isomorphism (i.e. substructure) searches.">OBIsomorphismMapper</a>
<a name="l00077"></a>00077 {
<a name="l00078"></a>00078 <span class="keyword">public</span>:
<a name="l00083"></a><a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#a97df663c0fc8a3ba6e9113802cac5c82">00083</a> <span class="keyword">typedef</span> std::vector< std::pair<unsigned int,unsigned int> > <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#a97df663c0fc8a3ba6e9113802cac5c82">Mapping</a>;
<a name="l00088"></a><a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#af45ae29000944170414da618d8d5d677">00088</a> <span class="keyword">typedef</span> std::vector< Mapping > <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#af45ae29000944170414da618d8d5d677">Mappings</a>;
<a name="l00089"></a>00089
<a name="l00095"></a>00095 <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml" title="Abstract class defining interface for isomorphism (i.e. substructure) searches.">OBIsomorphismMapper</a>(<a class="code" href="classOpenBabel_1_1OBQuery.shtml" title="A substructure query.">OBQuery</a> *query);
<a name="l00096"></a>00096 <span class="keyword">virtual</span> ~<a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml" title="Abstract class defining interface for isomorphism (i.e. substructure) searches.">OBIsomorphismMapper</a>();
<a name="l00097"></a>00097
<a name="l00106"></a>00106 <span class="keyword">static</span> <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml" title="Abstract class defining interface for isomorphism (i.e. substructure) searches.">OBIsomorphismMapper</a>* GetInstance(<a class="code" href="classOpenBabel_1_1OBQuery.shtml" title="A substructure query.">OBQuery</a> *query, <span class="keyword">const</span> std::string &algorithm = std::string(<span class="stringliteral">"VF2"</span>));
<a name="l00107"></a>00107
<a name="l00116"></a>00116 <span class="keyword">virtual</span> <span class="keywordtype">void</span> MapFirst(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *queried, <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#a97df663c0fc8a3ba6e9113802cac5c82">Mapping</a> &map, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &mask = <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a>()) = 0;
<a name="l00127"></a>00127 <span class="keyword">virtual</span> <span class="keywordtype">void</span> MapUnique(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *queried, <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#af45ae29000944170414da618d8d5d677">Mappings</a> &maps, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &mask = <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a>()) = 0;
<a name="l00139"></a>00139 <span class="keyword">virtual</span> <span class="keywordtype">void</span> MapAll(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *queried, <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#af45ae29000944170414da618d8d5d677">Mappings</a> &maps, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &mask = <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a>(), std::size_t maxMemory = 3000000) = 0;
<a name="l00140"></a>00140
<a name="l00147"></a><a class="code" href="classOpenBabel_1_1OBIsomorphismMapper_1_1Functor.shtml">00147</a> <span class="keyword">class </span><a class="code" href="classOpenBabel_1_1OBIsomorphismMapper_1_1Functor.shtml" title="Functor base class to be used in combination with MapGeneric.">Functor</a>
<a name="l00148"></a>00148 {
<a name="l00149"></a>00149 <span class="keyword">public</span>:
<a name="l00150"></a><a class="code" href="classOpenBabel_1_1OBIsomorphismMapper_1_1Functor.shtml#ab890a520140b6cc0c5f5fe05a6bf4f10">00150</a> <span class="keyword">virtual</span> <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper_1_1Functor.shtml#ab890a520140b6cc0c5f5fe05a6bf4f10">~Functor</a>() {}
<a name="l00158"></a>00158 <span class="keyword">virtual</span> <span class="keywordtype">bool</span> operator()(<a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#a97df663c0fc8a3ba6e9113802cac5c82">Mapping</a> &map) = 0;
<a name="l00159"></a>00159 };
<a name="l00168"></a>00168 <span class="keyword">virtual</span> <span class="keywordtype">void</span> MapGeneric(Functor &functor, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *queried, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &mask = <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a>()) = 0;
<a name="l00169"></a>00169
<a name="l00170"></a>00170
<a name="l00174"></a><a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#a3f1b7a8e3d742835665503376bf8643d">00174</a> <span class="keywordtype">void</span> <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#a3f1b7a8e3d742835665503376bf8643d">SetTimeout</a>(<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> seconds) { m_timeout = seconds; }
<a name="l00175"></a>00175
<a name="l00176"></a>00176 <span class="keyword">protected</span>:
<a name="l00177"></a><a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#a095cd6b4cbaab0cba9c46ea592ed899c">00177</a> <a class="code" href="classOpenBabel_1_1OBQuery.shtml" title="A substructure query.">OBQuery</a> *<a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#a095cd6b4cbaab0cba9c46ea592ed899c" title="The search query.">m_query</a>;
<a name="l00178"></a><a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#acda4225670d6511a6b4055aa91a387f9">00178</a> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#acda4225670d6511a6b4055aa91a387f9" title="The timeout in seconds.">m_timeout</a>;
<a name="l00179"></a>00179 };
<a name="l00180"></a>00180
<a name="l00181"></a><a class="code" href="group__substructure.shtml#ga4edd651fb377c60f3b7ac2f48b7f5e57">00181</a> <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="group__substructure.shtml#ga4edd651fb377c60f3b7ac2f48b7f5e57">MapsTo</a>(<span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#a97df663c0fc8a3ba6e9113802cac5c82">OBIsomorphismMapper::Mapping</a> &map, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> queryIndex, <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> &queriedIndex)
<a name="l00182"></a>00182 {
<a name="l00183"></a>00183 OBIsomorphismMapper::Mapping::const_iterator i;
<a name="l00184"></a>00184 <span class="keywordflow">for</span> (i = map.begin(); i != map.end(); ++i)
<a name="l00185"></a>00185 <span class="keywordflow">if</span> (i->first == queryIndex) {
<a name="l00186"></a>00186 queriedIndex = i->second;
<a name="l00187"></a>00187 <span class="keywordflow">return</span> <span class="keyword">true</span>;
<a name="l00188"></a>00188 }
<a name="l00189"></a>00189
<a name="l00190"></a>00190 <span class="keywordflow">return</span> <span class="keyword">false</span>;
<a name="l00191"></a>00191 }
<a name="l00192"></a>00192
<a name="l00193"></a>00193
<a name="l00199"></a><a class="code" href="group__substructure.shtml#ga9373f6c3f788157de6f03c9403be34c4">00199</a> <span class="keyword">typedef</span> <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#a97df663c0fc8a3ba6e9113802cac5c82">OBIsomorphismMapper::Mapping</a> <a class="code" href="group__substructure.shtml#ga9373f6c3f788157de6f03c9403be34c4" title="A single automorphic permutation.">Automorphism</a>;
<a name="l00205"></a><a class="code" href="group__substructure.shtml#ga6179e6c11d4f797e8d0ef6ac5c9f25a8">00205</a> <span class="keyword">typedef</span> <a class="code" href="classOpenBabel_1_1OBIsomorphismMapper.shtml#af45ae29000944170414da618d8d5d677">OBIsomorphismMapper::Mappings</a> <a class="code" href="group__substructure.shtml#ga6179e6c11d4f797e8d0ef6ac5c9f25a8" title="A group of automorphic permutations.">Automorphisms</a>;
<a name="l00206"></a>00206
<a name="l00224"></a>00224 OBAPI <span class="keywordtype">bool</span> <a class="code" href="group__substructure.shtml#ga16841a730cf92c8e51a804ad8d746307">FindAutomorphisms</a>(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *mol, std::vector<OBIsomorphismMapper::Mapping> &aut, <span class="keyword">const</span> std::vector<unsigned int> &symmetry_classes,
<a name="l00225"></a>00225 <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &mask = <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a>(), std::size_t maxMemory = 3000000);
<a name="l00234"></a>00234 OBAPI <span class="keywordtype">bool</span> <a class="code" href="group__substructure.shtml#ga16841a730cf92c8e51a804ad8d746307">FindAutomorphisms</a>(<a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *mol, std::vector<OBIsomorphismMapper::Mapping> &aut, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &mask = <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a>(),
<a name="l00235"></a>00235 std::size_t maxMemory = 3000000);
<a name="l00236"></a>00236
<a name="l00248"></a>00248 OBAPI <span class="keywordtype">void</span> <a class="code" href="group__substructure.shtml#ga16841a730cf92c8e51a804ad8d746307">FindAutomorphisms</a>(<a class="code" href="classOpenBabel_1_1OBIsomorphismMapper_1_1Functor.shtml" title="Functor base class to be used in combination with MapGeneric.">OBIsomorphismMapper::Functor</a> &functor, <a class="code" href="classOpenBabel_1_1OBMol.shtml" title="Molecule Class.">OBMol</a> *mol,
<a name="l00249"></a>00249 <span class="keyword">const</span> std::vector<unsigned int> &symmetry_classes, <span class="keyword">const</span> <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a> &mask = <a class="code" href="classOpenBabel_1_1OBBitVec.shtml" title="A speed-optimized vector of bits.">OBBitVec</a>());
<a name="l00250"></a>00250
<a name="l00365"></a>00365
<a name="l00366"></a>00366
<a name="l00367"></a>00367 }
<a name="l00368"></a>00368
<a name="l00369"></a>00369 <span class="preprocessor">#endif</span>
<a name="l00370"></a>00370 <span class="preprocessor"></span>
</pre></div></div>
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