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https://github.com/rdkit/rdkit.git
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105 lines
3.8 KiB
C++
105 lines
3.8 KiB
C++
// $Id$
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//
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// Copyright (C) 2011 Greg Landrum
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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 <GraphMol/RDKitBase.h>
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#include <GraphMol/MolPickler.h>
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#include <GraphMol/Descriptors/MolDescriptors.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <boost/dynamic_bitset.hpp>
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#include <boost/foreach.hpp>
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#include <boost/flyweight.hpp>
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#include <boost/flyweight/key_value.hpp>
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#include <boost/flyweight/no_tracking.hpp>
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#include <vector>
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#include <string>
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namespace {
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class ss_matcher {
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public:
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ss_matcher(const std::string &pattern) : m_pattern(pattern){
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m_needCopies=(pattern.find_first_of("$")!=std::string::npos);
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RDKit::RWMol *p=RDKit::SmartsToMol(pattern);
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m_matcher=p;
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POSTCONDITION(m_matcher,"no matcher");
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};
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const RDKit::ROMol *getMatcher() const { return m_matcher; };
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unsigned int countMatches(const RDKit::ROMol &mol) const {
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PRECONDITION(m_matcher,"no matcher");
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std::vector<RDKit::MatchVectType> matches;
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unsigned int res=0;
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// This is an ugly one. Recursive queries aren't thread safe.
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// Unfortunately we have to take a performance hit here in order
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// to guarantee thread safety
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if(m_needCopies){
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const RDKit::ROMol nm(*(m_matcher),true);
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res=RDKit::SubstructMatch(mol,nm,matches);
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} else {
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const RDKit::ROMol &nm=*m_matcher;
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res=RDKit::SubstructMatch(mol,nm,matches);
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}
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return matches.size();
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}
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~ss_matcher() { delete m_matcher; };
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private:
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ss_matcher() : m_pattern(""), m_needCopies(false), m_matcher(0) {};
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std::string m_pattern;
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bool m_needCopies;
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const RDKit::ROMol *m_matcher;
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};
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}
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typedef boost::flyweight<boost::flyweights::key_value<std::string,ss_matcher>,boost::flyweights::no_tracking > pattern_flyweight;
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#define SMARTSCOUNTFUNC(nm,pattern,vers) \
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const std::string nm ## Version =vers; \
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unsigned int calc##nm(const RDKit::ROMol &mol){ \
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pattern_flyweight m(pattern); \
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return m.get().countMatches(mol); \
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} \
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extern int no_such_variable
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namespace RDKit{
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namespace Descriptors {
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unsigned int calcLipinskiHBA(const ROMol &mol){
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unsigned int res=0;
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for(ROMol::ConstAtomIterator iter=mol.beginAtoms();
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iter!=mol.endAtoms();++iter){
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if((*iter)->getAtomicNum()==7 || (*iter)->getAtomicNum()==8) ++res;
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}
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return res;
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}
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unsigned int calcLipinskiHBD(const ROMol &mol){
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unsigned int res=0;
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for(ROMol::ConstAtomIterator iter=mol.beginAtoms();
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iter!=mol.endAtoms();++iter){
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if( ((*iter)->getAtomicNum()==7 || (*iter)->getAtomicNum()==8) ) {
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res += (*iter)->getTotalNumHs(true);
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}
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}
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return res;
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}
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SMARTSCOUNTFUNC(NumRotatableBonds, "[!$(*#*)&!D1]-&!@[!$(*#*)&!D1]", "1.0.1" ) ;
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//SMARTSCOUNTFUNC(NumHBD, "[$([N;!H0;v3]),$([N;!H0;+1;v4]),$([O,S;H1;+0]),$([n;H1;+0])]","2.0.1" ) ;
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SMARTSCOUNTFUNC(NumHBD, "[N&!H0&v3,N&!H0&+1&v4,O&H1&+0,S&H1&+0,n&H1&+0]","2.0.1" ) ;
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SMARTSCOUNTFUNC(NumHBA, "[$([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),$([nH0,o,s;+0])]","2.0.1") ;
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SMARTSCOUNTFUNC(NumHeteroatoms,"[!#6;!#1]","1.0.1") ;
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SMARTSCOUNTFUNC(NumAmideBonds,"C(=[O;!R])N","1.0.0") ;
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const std::string NumRingsVersion="1.0.1";
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unsigned int calcNumRings(const ROMol &mol){
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return mol.getRingInfo()->numRings();
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}
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} // end of namespace Descriptors
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} // end of namespace RDKit
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