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46bfbba903
add reaction depiction; add ChemicalReactionToRxnBlock(); This stuff needs more testing and so far has only been built on linux.
84 lines
3.4 KiB
C++
84 lines
3.4 KiB
C++
// $Id$
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//
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// Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
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// All rights reserved.
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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//
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// * Redistributions of source code must retain the above copyright
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// notice, this list of conditions and the following disclaimer.
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// * Redistributions in binary form must reproduce the above
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// copyright notice, this list of conditions and the following
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// disclaimer in the documentation and/or other materials provided
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// with the distribution.
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// * Neither the name of Novartis Institutes for BioMedical Research Inc.
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// nor the names of its contributors may be used to endorse or promote
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// products derived from this software without specific prior written permission.
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//
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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#include <GraphMol/ChemReactions/Reaction.h>
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#include <GraphMol/ChemReactions/ReactionParser.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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#include <sstream>
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namespace RDKit {
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//! returns the reaction SMARTS for a reaction
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std::string ChemicalReactionToRxnSmarts(ChemicalReaction &rxn){
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std::string res="";
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for(MOL_SPTR_VECT::const_iterator iter=rxn.beginReactantTemplates();
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iter != rxn.endReactantTemplates();++iter){
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if(iter!=rxn.beginReactantTemplates()) res +=".";
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res += MolToSmarts(**iter,true);
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}
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res += ">>";
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for(MOL_SPTR_VECT::const_iterator iter=rxn.beginProductTemplates();
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iter != rxn.endProductTemplates();++iter){
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if(iter!=rxn.beginProductTemplates()) res +=".";
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res += MolToSmarts(**iter,true);
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}
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return res;
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};
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#if 1
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//! returns an RXN block for a reaction
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std::string ChemicalReactionToRxnBlock(const ChemicalReaction &rxn){
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std::ostringstream res;
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res<<"$RXN\n\n RDKit\n\n";
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res<<std::setw(3)<<rxn.getNumReactantTemplates()<<std::setw(3)<<rxn.getNumProductTemplates()<<"\n";
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for(MOL_SPTR_VECT::const_iterator iter=rxn.beginReactantTemplates();
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iter != rxn.endReactantTemplates();++iter){
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// to write the mol block, we need ring information:
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MolOps::findSSSR(**iter);
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res<<"$MOL\n";
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res << MolToMolBlock(**iter,true,-1,false);
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}
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for(MOL_SPTR_VECT::const_iterator iter=rxn.beginProductTemplates();
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iter != rxn.endProductTemplates();++iter){
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// to write the mol block, we need ring information:
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MolOps::findSSSR(**iter);
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res<<"$MOL\n";
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res << MolToMolBlock(**iter,true,-1,false);
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}
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return res.str();
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};
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#endif
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}
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