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