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84 lines
2.9 KiB
C++
84 lines
2.9 KiB
C++
// $Id$
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//
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// Copyright (C) 2003-2010 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "SubstructUtils.h"
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#include <RDGeneral/utils.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <boost/dynamic_bitset.hpp>
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namespace RDKit{
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bool atomCompat(const ATOM_SPTR a1,const ATOM_SPTR a2){
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PRECONDITION(a1,"bad atom");
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PRECONDITION(a2,"bad atom");
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//std::cerr << "\t\tatomCompat: "<< a1 << " " << a1->getIdx() << "-" << a2 << " " << a2->getIdx() << std::endl;
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bool res = a1->Match(a2);
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return res;
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}
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bool chiralAtomCompat(const ATOM_SPTR a1,const ATOM_SPTR a2){
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PRECONDITION(a1,"bad atom");
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PRECONDITION(a2,"bad atom");
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//std::cerr << "\t\tatomCompat: "<< a1 << " " << a1->getIdx() << "-" << a2 << " " << a2->getIdx() << std::endl;
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bool res = a1->Match(a2);
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if(res){
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if(a1->hasProp("_CIPCode") || a2->hasProp("_CIPCode")){
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// if either atom has a CIPCode, they need to both have it and match:
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if(a1->hasProp("_CIPCode") && a2->hasProp("_CIPCode")){
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std::string s1,s2;
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a1->getProp("_CIPCode",s1);
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a2->getProp("_CIPCode",s2);
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if(s1!=s2) res=false;
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} else {
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res=false;
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}
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}
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}
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return res;
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}
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bool bondCompat(const BOND_SPTR b1,const BOND_SPTR b2){
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PRECONDITION(b1,"bad bond");
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PRECONDITION(b2,"bad bond");
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bool res = b1->Match(b2);
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//std::cout << "\t\tbondCompat: "<< b1->getIdx() << "-" << b2->getIdx() << ": " << res << std::endl;
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return res;
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}
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void removeDuplicates(std::vector<MatchVectType> &v,unsigned int nAtoms){
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//
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// This works by tracking the indices of the atoms in each match vector.
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// This can lead to unexpected behavior when looking at rings and queries
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// that don't specify bond orders. For example querying this molecule:
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// C1CCC=1
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// with the pattern constructed from SMARTS C~C~C~C will return a
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// single match, despite the fact that there are 4 different paths
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// when valence is considered. The defense of this behavior is
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// that the 4 paths are equivalent in the semantics of the query.
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// Also, OELib returns the same results
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//
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std::vector< boost::dynamic_bitset<> > seen;
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std::vector<MatchVectType> res;
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for(std::vector<MatchVectType>::const_iterator i=v.begin();i!=v.end();++i){
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boost::dynamic_bitset<> val(nAtoms);
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for(MatchVectType::const_iterator ci=i->begin();ci!=i->end();++ci){
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val.set(ci->second);
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}
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if(std::find(seen.begin(),seen.end(),val)==seen.end()){
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// it's something new
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res.push_back(*i);
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seen.push_back(val);
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}
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}
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v = res;
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}
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}
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