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https://github.com/rdkit/rdkit.git
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299 lines
11 KiB
C++
299 lines
11 KiB
C++
// $Id$
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//
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// Copyright (C) 2011-2013 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]-&!@[!$(*#*)&!D1]", "1.0.1" ) ;
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SMARTSCOUNTFUNC(NumStrictRotatableBonds, "[!$(*#*)&!D1&!$(C(F)(F)F)&!$(C(Cl)(Cl)Cl)&!$(C(Br)(Br)Br)&!$(C([CH3])([CH3])[CH3])&!$([CD3](=[N,O,S])-!@[#7,O,S!D1])&!$([#7,O,S!D1]-!@[CD3]=[N,O,S])&!$([CD3](=[N+])-!@[#7!D1])&!$([#7!D1]-!@[CD3]=[N+])]-!@[!$(*#*)&!D1&!$(C(F)(F)F)&!$(C(Cl)(Cl)Cl)&!$(C(Br)(Br)Br)&!$(C([CH3])([CH3])[CH3])]", "1.0.0" ) ;
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//SMARTSCOUNTFUNC(NumHBD, "[$([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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const std::string FractionCSP3Version="1.0.0";
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double calcFractionCSP3(const ROMol &mol){
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unsigned int nCSP3=0;
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unsigned int nC=0;
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ROMol::VERTEX_ITER atBegin,atEnd;
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boost::tie(atBegin,atEnd) = mol.getVertices();
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while(atBegin!=atEnd){
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ATOM_SPTR at=mol[*atBegin];
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if(at->getAtomicNum()==6){
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++nC;
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if(at->getTotalDegree()==4){
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++nCSP3;
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}
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}
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++atBegin;
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}
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if(!nC) return 0;
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return static_cast<double>(nCSP3)/nC;
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}
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const std::string NumAromaticRingsVersion="1.0.0";
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unsigned int calcNumAromaticRings(const ROMol &mol){
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unsigned int res=0;
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BOOST_FOREACH(const INT_VECT &iv,mol.getRingInfo()->bondRings()){
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++res;
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BOOST_FOREACH(int i,iv){
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if(!mol.getBondWithIdx(i)->getIsAromatic()){
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--res;
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break;
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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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const std::string NumSaturatedRingsVersion="1.0.0";
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unsigned int calcNumSaturatedRings(const ROMol &mol){
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unsigned int res=0;
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BOOST_FOREACH(const INT_VECT &iv,mol.getRingInfo()->bondRings()){
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++res;
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BOOST_FOREACH(int i,iv){
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if(mol.getBondWithIdx(i)->getBondType()!=Bond::SINGLE || mol.getBondWithIdx(i)->getIsAromatic()){
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--res;
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break;
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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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const std::string NumAliphaticRingsVersion="1.0.0";
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unsigned int calcNumAliphaticRings(const ROMol &mol){
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unsigned int res=0;
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BOOST_FOREACH(const INT_VECT &iv,mol.getRingInfo()->bondRings()){
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BOOST_FOREACH(int i,iv){
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if(!mol.getBondWithIdx(i)->getIsAromatic()){
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++res;
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break;
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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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const std::string NumAromaticHeterocyclesVersion="1.0.0";
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unsigned int calcNumAromaticHeterocycles(const ROMol &mol){
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unsigned int res=0;
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BOOST_FOREACH(const INT_VECT &iv,mol.getRingInfo()->bondRings()){
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bool countIt=false;
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BOOST_FOREACH(int i,iv){
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if(!mol.getBondWithIdx(i)->getIsAromatic()){
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countIt=false;
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break;
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}
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// we're checking each atom twice, which is kind of doofy, but this
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// function is hopefully not going to be a big time sink.
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if(!countIt &&
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(mol.getBondWithIdx(i)->getBeginAtom()->getAtomicNum()!=6 ||
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mol.getBondWithIdx(i)->getEndAtom()->getAtomicNum()!=6) ){
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countIt=true;
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}
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}
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if(countIt) ++res;
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}
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return res;
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}
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const std::string NumAromaticCarbocyclesVersion="1.0.0";
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unsigned int calcNumAromaticCarbocycles(const ROMol &mol){
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unsigned int res=0;
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BOOST_FOREACH(const INT_VECT &iv,mol.getRingInfo()->bondRings()){
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bool countIt=true;
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BOOST_FOREACH(int i,iv){
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if(!mol.getBondWithIdx(i)->getIsAromatic()){
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countIt=false;
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break;
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}
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// we're checking each atom twice, which is kind of doofy, but this
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// function is hopefully not going to be a big time sync.
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if(mol.getBondWithIdx(i)->getBeginAtom()->getAtomicNum()!=6 ||
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mol.getBondWithIdx(i)->getEndAtom()->getAtomicNum()!=6 ){
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countIt=false;
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break;
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}
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}
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if(countIt) ++res;
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}
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return res;
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}
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const std::string NumAliphaticHeterocyclesVersion="1.0.0";
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unsigned int calcNumAliphaticHeterocycles(const ROMol &mol){
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unsigned int res=0;
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BOOST_FOREACH(const INT_VECT &iv,mol.getRingInfo()->bondRings()){
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bool hasAliph=false;
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bool hasHetero=false;
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BOOST_FOREACH(int i,iv){
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if(!mol.getBondWithIdx(i)->getIsAromatic()){
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hasAliph=true;
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}
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// we're checking each atom twice, which is kind of doofy, but this
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// function is hopefully not going to be a big time sink.
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if(!hasHetero &&
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(mol.getBondWithIdx(i)->getBeginAtom()->getAtomicNum()!=6 ||
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mol.getBondWithIdx(i)->getEndAtom()->getAtomicNum()!=6) ){
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hasHetero=true;
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}
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}
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if(hasHetero&&hasAliph) ++res;
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}
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return res;
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}
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const std::string NumAliphaticCarbocyclesVersion="1.0.0";
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unsigned int calcNumAliphaticCarbocycles(const ROMol &mol){
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unsigned int res=0;
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BOOST_FOREACH(const INT_VECT &iv,mol.getRingInfo()->bondRings()){
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bool hasAliph=false;
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bool hasHetero=false;
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BOOST_FOREACH(int i,iv){
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if(!mol.getBondWithIdx(i)->getIsAromatic()){
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hasAliph=true;
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}
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// we're checking each atom twice, which is kind of doofy, but this
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// function is hopefully not going to be a big time sync.
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if(mol.getBondWithIdx(i)->getBeginAtom()->getAtomicNum()!=6 ||
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mol.getBondWithIdx(i)->getEndAtom()->getAtomicNum()!=6 ){
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hasHetero=true;
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break;
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}
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}
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if(hasAliph&&!hasHetero) ++res;
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}
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return res;
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}
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const std::string NumSaturatedHeterocyclesVersion="1.0.0";
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unsigned int calcNumSaturatedHeterocycles(const ROMol &mol){
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unsigned int res=0;
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BOOST_FOREACH(const INT_VECT &iv,mol.getRingInfo()->bondRings()){
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bool countIt=false;
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BOOST_FOREACH(int i,iv){
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if(mol.getBondWithIdx(i)->getBondType()!=Bond::SINGLE || mol.getBondWithIdx(i)->getIsAromatic()){
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countIt=false;
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break;
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}
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// we're checking each atom twice, which is kind of doofy, but this
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// function is hopefully not going to be a big time sync.
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if(!countIt &&
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(mol.getBondWithIdx(i)->getBeginAtom()->getAtomicNum()!=6 ||
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mol.getBondWithIdx(i)->getEndAtom()->getAtomicNum()!=6) ){
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countIt=true;
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}
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}
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if(countIt) ++res;
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}
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return res;
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}
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const std::string NumSaturatedCarbocyclesVersion="1.0.0";
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unsigned int calcNumSaturatedCarbocycles(const ROMol &mol){
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unsigned int res=0;
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BOOST_FOREACH(const INT_VECT &iv,mol.getRingInfo()->bondRings()){
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bool countIt=true;
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BOOST_FOREACH(int i,iv){
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if(mol.getBondWithIdx(i)->getBondType()!=Bond::SINGLE || mol.getBondWithIdx(i)->getIsAromatic()){
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countIt=false;
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break;
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}
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// we're checking each atom twice, which is kind of doofy, but this
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// function is hopefully not going to be a big time sync.
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if(mol.getBondWithIdx(i)->getBeginAtom()->getAtomicNum()!=6 ||
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mol.getBondWithIdx(i)->getEndAtom()->getAtomicNum()!=6 ){
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countIt=false;
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break;
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}
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}
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if(countIt) ++res;
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}
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return res;
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}
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} // end of namespace Descriptors
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} // end of namespace RDKit
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