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95a92282d1
o rdkit gains a RDKit::common_properties namespace that contains common string value properties o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns true/false on success or failure. This is used to optimize access. o rdkit learns how to pass property keys by reference, not value. A new namespace has been added to RDKit, common_properties that contains the std::string values for commonly used properties. This helps to avoid typos in string values but also avoids a creation of std::strings from character values. All accessors (has/get/clear and getPropIfPresent) now pass the key by reference. Additionally, getPropIfPresent removes the double lookup of hasProp/getProp which can be a significant speedup in the smiles and smarts parsers (10-20%)
89 lines
3.2 KiB
C++
89 lines
3.2 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,bool useQueryQueryMatches){
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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;
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if(useQueryQueryMatches && a1->hasQuery() && a2->hasQuery()){
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res = static_cast<QueryAtom *>(a1.get())->QueryMatch(static_cast<QueryAtom *>(a2.get()));
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} else {
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res = a1->Match(a2);
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}
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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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std::string s1, s2;
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bool hascode1 = a1->getPropIfPresent(common_properties::_CIPCode, s1);
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bool hascode2 = a2->getPropIfPresent(common_properties::_CIPCode, s2);
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if(hascode1 || hascode2) {
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res = hascode1 && hascode2 && s1 == s2;
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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,bool useQueryQueryMatches){
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PRECONDITION(b1,"bad bond");
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PRECONDITION(b2,"bad bond");
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bool res;
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if(useQueryQueryMatches && b1->hasQuery() && b2->hasQuery()){
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res = static_cast<QueryBond *>(b1.get())->QueryMatch(static_cast<QueryBond *>(b2.get()));
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} else {
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res = b1->Match(b2);
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}
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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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