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|
// $Id: rdMolDescriptors.cpp 2003 2012-03-26 03:08:02Z glandrum $
//
// Copyright (C) 2007-2011 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 <RDBoost/Wrap.h>
#include <GraphMol/Atom.h>
#include <GraphMol/GraphMol.h>
#include <numpy/arrayobject.h>
#include <boost/foreach.hpp>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/Fingerprints/AtomPairs.h>
#include <GraphMol/Fingerprints/MorganFingerprints.h>
#include <DataStructs/BitVects.h>
#include <vector>
namespace python = boost::python;
namespace {
std::vector<unsigned int> atomPairTypes(RDKit::AtomPairs::atomNumberTypes,
RDKit::AtomPairs::atomNumberTypes+sizeof(RDKit::AtomPairs::atomNumberTypes)/sizeof(unsigned int));
python::tuple computeASAContribs(const RDKit::ROMol &mol,bool includeHs=true,
bool force=false){
std::vector<double> contribs(mol.getNumAtoms());
double hContrib=0.0;
RDKit::Descriptors::getLabuteAtomContribs(mol,contribs,hContrib,includeHs,force);
python::tuple pycontribs(contribs);
return python::make_tuple(contribs,hContrib);
}
python::tuple computeTPSAContribs(const RDKit::ROMol &mol,
bool force=false){
std::vector<double> contribs(mol.getNumAtoms());
RDKit::Descriptors::getTPSAAtomContribs(mol,contribs,force);
python::tuple pycontribs(contribs);
return pycontribs;
}
python::list computeCrippenContribs(const RDKit::ROMol &mol,
bool force=false){
std::vector<double> logpContribs(mol.getNumAtoms());
std::vector<double> mrContribs(mol.getNumAtoms());
RDKit::Descriptors::getCrippenAtomContribs(mol,logpContribs,mrContribs,force);
python::list pycontribs;
for(unsigned int i=0;i<mol.getNumAtoms();++i){
pycontribs.append(python::make_tuple(logpContribs[i],mrContribs[i]));
}
return pycontribs;
}
python::tuple calcCrippenDescriptors(const RDKit::ROMol &mol,bool includeHs=true,
bool force=false){
double logp,mr;
RDKit::Descriptors::calcCrippenDescriptors(mol,logp,mr,includeHs,force);
return python::make_tuple(logp,mr);
}
RDKit::SparseIntVect<boost::int32_t> *GetAtomPairFingerprint(const RDKit::ROMol &mol,
unsigned int minLength,
unsigned int maxLength,
python::object fromAtoms,
python::object ignoreAtoms,
python::object atomInvariants){
std::vector<boost::uint32_t> *fvect=pythonObjectToVect(fromAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *ivect=pythonObjectToVect(ignoreAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *invvect=pythonObjectToVect(atomInvariants,mol.getNumAtoms());
RDKit::SparseIntVect<boost::int32_t> *res;
res = RDKit::AtomPairs::getAtomPairFingerprint(mol,minLength,maxLength,
fvect,ivect,invvect);
if(fvect) delete fvect;
if(ivect) delete ivect;
if(invvect) delete invvect;
return res;
}
RDKit::SparseIntVect<boost::int32_t> *GetHashedAtomPairFingerprint(const RDKit::ROMol &mol,
unsigned int nBits,
unsigned int minLength,
unsigned int maxLength,
python::object fromAtoms,
python::object ignoreAtoms,
python::object atomInvariants){
std::vector<boost::uint32_t> *fvect=pythonObjectToVect(fromAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *ivect=pythonObjectToVect(ignoreAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *invvect=pythonObjectToVect(atomInvariants,mol.getNumAtoms());
RDKit::SparseIntVect<boost::int32_t> *res;
res = RDKit::AtomPairs::getHashedAtomPairFingerprint(mol,nBits,minLength,maxLength,
fvect,ivect,invvect);
if(fvect) delete fvect;
if(ivect) delete ivect;
if(invvect) delete invvect;
return res;
}
RDKit::SparseIntVect<boost::int64_t> *GetTopologicalTorsionFingerprint(const RDKit::ROMol &mol,
unsigned int targetSize,
python::object fromAtoms,
python::object ignoreAtoms,
python::object atomInvariants){
std::vector<boost::uint32_t> *fvect=pythonObjectToVect(fromAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *ivect=pythonObjectToVect(ignoreAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *invvect=pythonObjectToVect(atomInvariants,mol.getNumAtoms());
if(targetSize*RDKit::AtomPairs::codeSize>64){
std::ostringstream errout;
errout << "Maximum supported topological torsion path length is " << 64/RDKit::AtomPairs::codeSize<<std::endl;
throw_value_error(errout.str());
}
RDKit::SparseIntVect<boost::int64_t> *res;
res = RDKit::AtomPairs::getTopologicalTorsionFingerprint(mol,targetSize,fvect,ivect,invvect);
if(fvect) delete fvect;
if(ivect) delete ivect;
if(invvect) delete invvect;
return res;
}
RDKit::SparseIntVect<boost::int64_t> *GetHashedTopologicalTorsionFingerprint(const RDKit::ROMol &mol,
unsigned int nBits,
unsigned int targetSize,
python::object fromAtoms,
python::object ignoreAtoms,
python::object atomInvariants){
std::vector<boost::uint32_t> *fvect=pythonObjectToVect(fromAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *ivect=pythonObjectToVect(ignoreAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *invvect=pythonObjectToVect(atomInvariants,mol.getNumAtoms());
RDKit::SparseIntVect<boost::int64_t> *res;
res = RDKit::AtomPairs::getHashedTopologicalTorsionFingerprint(mol,nBits,targetSize,fvect,ivect,
invvect);
if(fvect) delete fvect;
if(ivect) delete ivect;
if(invvect) delete invvect;
return res;
}
ExplicitBitVect *GetHashedTopologicalTorsionFingerprintAsBitVect(const RDKit::ROMol &mol,
unsigned int nBits,
unsigned int targetSize,
python::object fromAtoms,
python::object ignoreAtoms,
python::object atomInvariants,
unsigned int nBitsPerEntry
){
std::vector<boost::uint32_t> *fvect=pythonObjectToVect(fromAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *ivect=pythonObjectToVect(ignoreAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *invvect=pythonObjectToVect(atomInvariants,mol.getNumAtoms());
ExplicitBitVect *res;
res = RDKit::AtomPairs::getHashedTopologicalTorsionFingerprintAsBitVect(mol,nBits,targetSize,fvect,ivect,
invvect,
nBitsPerEntry);
if(fvect) delete fvect;
if(ivect) delete ivect;
if(invvect) delete invvect;
return res;
}
ExplicitBitVect *GetHashedAtomPairFingerprintAsBitVect(const RDKit::ROMol &mol,
unsigned int nBits,
unsigned int minLength,
unsigned int maxLength,
python::object fromAtoms,
python::object ignoreAtoms,
python::object atomInvariants,
unsigned int nBitsPerEntry
){
std::vector<boost::uint32_t> *fvect=pythonObjectToVect(fromAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *ivect=pythonObjectToVect(ignoreAtoms,mol.getNumAtoms());
std::vector<boost::uint32_t> *invvect=pythonObjectToVect(atomInvariants,mol.getNumAtoms());
ExplicitBitVect *res;
res = RDKit::AtomPairs::getHashedAtomPairFingerprintAsBitVect(mol,nBits,
minLength,maxLength,
fvect,ivect,invvect,
nBitsPerEntry);
if(fvect) delete fvect;
if(ivect) delete ivect;
if(invvect) delete invvect;
return res;
}
RDKit::SparseIntVect<boost::uint32_t> *GetMorganFingerprint(const RDKit::ROMol &mol,
int radius,
python::object invariants,
python::object fromAtoms,
bool useChirality,
bool useBondTypes,
bool useFeatures,
python::object bitInfo){
std::vector<boost::uint32_t> *invars=0;
if(invariants){
unsigned int nInvar=python::extract<unsigned int>(invariants.attr("__len__")());
if(nInvar){
if(nInvar!=mol.getNumAtoms()){
throw_value_error("length of invariant vector != number of atoms");
}
invars = new std::vector<boost::uint32_t>(mol.getNumAtoms());
for(unsigned int i=0;i<mol.getNumAtoms();++i){
(*invars)[i] = python::extract<boost::uint32_t>(invariants[i]);
}
}
} else if(useFeatures){
invars = new std::vector<boost::uint32_t>(mol.getNumAtoms());
RDKit::MorganFingerprints::getFeatureInvariants(mol,*invars);
}
std::vector<boost::uint32_t> *froms=0;
if(fromAtoms){
unsigned int nFrom=python::extract<unsigned int>(fromAtoms.attr("__len__")());
if(nFrom){
froms = new std::vector<boost::uint32_t>();
for(unsigned int i=0;i<nFrom;++i){
froms->push_back(python::extract<boost::uint32_t>(fromAtoms[i]));
}
}
}
RDKit::MorganFingerprints::BitInfoMap *bitInfoMap=0;
if(bitInfo!=python::object()){
// make sure the optional argument actually was a dictionary
python::dict typecheck=python::extract<python::dict>(bitInfo);
bitInfoMap=new RDKit::MorganFingerprints::BitInfoMap();
}
RDKit::SparseIntVect<boost::uint32_t> *res;
res = RDKit::MorganFingerprints::getFingerprint(mol,
static_cast<unsigned int>(radius),
invars,froms,useChirality,useBondTypes,
false,bitInfoMap);
if(bitInfoMap){
bitInfo.attr("clear")();
for(RDKit::MorganFingerprints::BitInfoMap::const_iterator iter=bitInfoMap->begin();
iter!=bitInfoMap->end();++iter){
const std::vector<std::pair<boost::uint32_t,boost::uint32_t> > &v=iter->second;
python::list localL;
for(std::vector<std::pair<boost::uint32_t,boost::uint32_t> >::const_iterator vIt=v.begin();
vIt!=v.end();++vIt){
localL.append(python::make_tuple(vIt->first,vIt->second));
}
bitInfo[iter->first]=python::tuple(localL);
}
delete bitInfoMap;
}
if(invars) delete invars;
if(froms) delete froms;
return res;
}
ExplicitBitVect *GetMorganFingerprintBV(const RDKit::ROMol &mol,
int radius,
unsigned int nBits,
python::object invariants,
python::object fromAtoms,
bool useChirality,
bool useBondTypes,
bool useFeatures,
python::object bitInfo){
std::vector<boost::uint32_t> *invars=0;
if(invariants){
unsigned int nInvar=python::extract<unsigned int>(invariants.attr("__len__")());
if(nInvar){
if(nInvar!=mol.getNumAtoms()){
throw_value_error("length of invariant vector != number of atoms");
}
invars = new std::vector<boost::uint32_t>(mol.getNumAtoms());
for(unsigned int i=0;i<mol.getNumAtoms();++i){
(*invars)[i] = python::extract<boost::uint32_t>(invariants[i]);
}
}
} else if(useFeatures){
invars = new std::vector<boost::uint32_t>(mol.getNumAtoms());
RDKit::MorganFingerprints::getFeatureInvariants(mol,*invars);
}
std::vector<boost::uint32_t> *froms=0;
if(fromAtoms){
unsigned int nFrom=python::extract<unsigned int>(fromAtoms.attr("__len__")());
if(nFrom){
froms = new std::vector<boost::uint32_t>();
for(unsigned int i=0;i<nFrom;++i){
froms->push_back(python::extract<boost::uint32_t>(fromAtoms[i]));
}
}
}
RDKit::MorganFingerprints::BitInfoMap *bitInfoMap=0;
if(bitInfo!=python::object()){
// make sure the optional argument actually was a dictionary
python::dict typecheck=python::extract<python::dict>(bitInfo);
bitInfoMap=new RDKit::MorganFingerprints::BitInfoMap();
}
ExplicitBitVect *res;
res = RDKit::MorganFingerprints::getFingerprintAsBitVect(mol,
static_cast<unsigned int>(radius),
nBits,
invars,froms,useChirality,
useBondTypes,
false,bitInfoMap);
if(bitInfoMap){
bitInfo.attr("clear")();
for(RDKit::MorganFingerprints::BitInfoMap::const_iterator iter=bitInfoMap->begin();
iter!=bitInfoMap->end();++iter){
const std::vector<std::pair<boost::uint32_t,boost::uint32_t> > &v=iter->second;
python::list localL;
for(std::vector<std::pair<boost::uint32_t,boost::uint32_t> >::const_iterator vIt=v.begin();
vIt!=v.end();++vIt){
localL.append(python::make_tuple(vIt->first,vIt->second));
}
bitInfo[iter->first]=python::tuple(localL);
}
delete bitInfoMap;
}
if(invars) delete invars;
if(froms) delete froms;
return res;
}
python::list GetConnectivityInvariants(const RDKit::ROMol &mol,bool includeRingMembership){
std::vector<boost::uint32_t> invars(mol.getNumAtoms());
RDKit::MorganFingerprints::getConnectivityInvariants(mol,invars,includeRingMembership);
python::list res;
for(std::vector<boost::uint32_t>::const_iterator iv=invars.begin();iv!=invars.end();++iv){
res.append(python::long_(*iv));
}
return res;
}
python::list GetFeatureInvariants(const RDKit::ROMol &mol){
std::vector<boost::uint32_t> invars(mol.getNumAtoms());
RDKit::MorganFingerprints::getFeatureInvariants(mol,invars);
python::list res;
for(std::vector<boost::uint32_t>::const_iterator iv=invars.begin();iv!=invars.end();++iv){
res.append(python::long_(*iv));
}
return res;
}
python::list CalcSlogPVSA(const RDKit::ROMol &mol,
python::object bins,
bool force){
std::vector<double> *lbins=0;
if(bins){
unsigned int nBins=python::extract<unsigned int>(bins.attr("__len__")());
if(nBins){
lbins = new std::vector<double>(nBins,0.0);
for(unsigned int i=0;i<nBins;++i){
(*lbins)[i] = python::extract<double>(bins[i]);
}
}
}
std::vector<double> res;
res=RDKit::Descriptors::calcSlogP_VSA(mol,lbins,force);
python::list pyres;
for(std::vector<double>::const_iterator iv=res.begin();iv!=res.end();++iv){
pyres.append(*iv);
}
return pyres;
}
python::list CalcSMRVSA(const RDKit::ROMol &mol,
python::object bins,
bool force){
std::vector<double> *lbins=0;
if(bins){
unsigned int nBins=python::extract<unsigned int>(bins.attr("__len__")());
if(nBins){
lbins = new std::vector<double>(nBins,0.0);
for(unsigned int i=0;i<nBins;++i){
(*lbins)[i] = python::extract<double>(bins[i]);
}
}
}
std::vector<double> res;
res=RDKit::Descriptors::calcSMR_VSA(mol,lbins,force);
python::list pyres;
for(std::vector<double>::const_iterator iv=res.begin();iv!=res.end();++iv){
pyres.append(*iv);
}
return pyres;
}
python::list CalcPEOEVSA(const RDKit::ROMol &mol,
python::object bins,
bool force){
std::vector<double> *lbins=0;
if(bins){
unsigned int nBins=python::extract<unsigned int>(bins.attr("__len__")());
if(nBins){
lbins = new std::vector<double>(nBins,0.0);
for(unsigned int i=0;i<nBins;++i){
(*lbins)[i] = python::extract<double>(bins[i]);
}
}
}
std::vector<double> res;
res=RDKit::Descriptors::calcPEOE_VSA(mol,lbins,force);
python::list pyres;
for(std::vector<double>::const_iterator iv=res.begin();iv!=res.end();++iv){
pyres.append(*iv);
}
return pyres;
}
}
BOOST_PYTHON_MODULE(rdMolDescriptors) {
python::scope().attr("__doc__") =
"Module containing functions to compute molecular descriptors"
;
python::register_exception_translator<IndexErrorException>(&translate_index_error);
python::register_exception_translator<ValueErrorException>(&translate_value_error);
std::string docString = "";
python::class_<python::object>("AtomPairsParameters")
.setattr("version",
RDKit::AtomPairs::atomPairsVersion)
.setattr("numTypeBits",
RDKit::AtomPairs::numTypeBits)
.setattr("numPiBits",
RDKit::AtomPairs::numPiBits)
.setattr("numBranchBits",
RDKit::AtomPairs::numBranchBits)
.setattr("codeSize",
RDKit::AtomPairs::codeSize)
.setattr("atomTypes",
atomPairTypes)
.setattr("numPathBits",
RDKit::AtomPairs::numPathBits)
.setattr("numAtomPairFingerprintBits",
RDKit::AtomPairs::numAtomPairFingerprintBits)
;
docString="Returns the atom code (hash) for an atom";
python::def("GetAtomPairAtomCode", RDKit::AtomPairs::getAtomCode,
(python::arg("atom"), python::arg("branchSubtract")=0),
docString.c_str());
docString="Returns the atom-pair fingerprint for a molecule as an IntSparseIntVect";
python::def("GetAtomPairFingerprint", GetAtomPairFingerprint,
(python::arg("mol"),
python::arg("minLength")=1,
python::arg("maxLength")=RDKit::AtomPairs::maxPathLen-1,
python::arg("fromAtoms")=0,
python::arg("ignoreAtoms")=0,
python::arg("atomInvariants")=0),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString="Returns the hashed atom-pair fingerprint for a molecule as an IntSparseIntVect";
python::def("GetHashedAtomPairFingerprint",
GetHashedAtomPairFingerprint,
(python::arg("mol"),
python::arg("nBits")=2048,
python::arg("minLength")=1,
python::arg("maxLength")=RDKit::AtomPairs::maxPathLen-1,
python::arg("fromAtoms")=0,
python::arg("ignoreAtoms")=0,
python::arg("atomInvariants")=0),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString="Returns the atom-pair fingerprint for a molecule as an ExplicitBitVect";
python::def("GetHashedAtomPairFingerprintAsBitVect",
GetHashedAtomPairFingerprintAsBitVect,
(python::arg("mol"),
python::arg("nBits")=2048,
python::arg("minLength")=1,
python::arg("maxLength")=RDKit::AtomPairs::maxPathLen-1,
python::arg("fromAtoms")=0,
python::arg("ignoreAtoms")=0,
python::arg("atomInvariants")=0,
python::arg("nBitsPerEntry")=4),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString="Returns the topological-torsion fingerprint for a molecule as a LongIntSparseIntVect";
python::def("GetTopologicalTorsionFingerprint",
GetTopologicalTorsionFingerprint,
(python::arg("mol"),python::arg("targetSize")=4,
python::arg("fromAtoms")=0,
python::arg("ignoreAtoms")=0,
python::arg("atomInvariants")=0),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString="Returns the hashed topological-torsion fingerprint for a molecule as a LongIntSparseIntVect";
python::def("GetHashedTopologicalTorsionFingerprint",
GetHashedTopologicalTorsionFingerprint,
(python::arg("mol"),
python::arg("nBits")=2048,
python::arg("targetSize")=4,
python::arg("fromAtoms")=0,
python::arg("ignoreAtoms")=0,
python::arg("atomInvariants")=0),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString="Returns the topological-torsion fingerprint for a molecule as an ExplicitBitVect";
python::def("GetHashedTopologicalTorsionFingerprintAsBitVect",
GetHashedTopologicalTorsionFingerprintAsBitVect,
(python::arg("mol"),
python::arg("nBits")=2048,
python::arg("targetSize")=4,
python::arg("fromAtoms")=0,
python::arg("ignoreAtoms")=0,
python::arg("atomInvariants")=0,
python::arg("nBitsPerEntry")=4),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString="Returns a Morgan fingerprint for a molecule";
python::def("GetMorganFingerprint", GetMorganFingerprint,
(python::arg("mol"),python::arg("radius"),
python::arg("invariants")=python::list(),
python::arg("fromAtoms")=python::list(),
python::arg("useChirality")=false,
python::arg("useBondTypes")=true,
python::arg("useFeatures")=false,
python::arg("bitInfo")=python::object()),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
docString="Returns a Morgan fingerprint for a molecule as a bit vector";
python::def("GetMorganFingerprintAsBitVect", GetMorganFingerprintBV,
(python::arg("mol"),python::arg("radius"),python::arg("nBits")=2048,
python::arg("invariants")=python::list(),
python::arg("fromAtoms")=python::list(),
python::arg("useChirality")=false,
python::arg("useBondTypes")=true,
python::arg("useFeatures")=false,
python::arg("bitInfo")=python::object()),
docString.c_str(),
python::return_value_policy<python::manage_new_object>());
python::scope().attr("_MorganFingerprint_version")=
RDKit::MorganFingerprints::morganFingerprintVersion;
docString="Returns connectivity invariants (ECFP-like) for a molecule.";
python::def("GetConnectivityInvariants", GetConnectivityInvariants,
(python::arg("mol"),python::arg("includeRingMembership")=true),
docString.c_str());
python::scope().attr("_ConnectivityInvariants_version")=
RDKit::MorganFingerprints::morganConnectivityInvariantVersion;
docString="Returns feature invariants (FCFP-like) for a molecule.";
python::def("GetFeatureInvariants", GetFeatureInvariants,
(python::arg("mol")),
docString.c_str());
python::scope().attr("_FeatureInvariants_version")=
RDKit::MorganFingerprints::morganFeatureInvariantVersion;
docString="returns (as a list of 2-tuples) the contributions of each atom to\n"
"the Wildman-Cripppen logp and mr value";
python::def("_CalcCrippenContribs",
computeCrippenContribs,
(python::arg("mol"),
python::arg("force")=false),
docString.c_str());
docString="returns a 2-tuple with the Wildman-Crippen logp,mr values";
python::def("CalcCrippenDescriptors",
calcCrippenDescriptors,
(python::arg("mol"),python::arg("includeHs")=true,
python::arg("force")=false),
docString.c_str());
python::scope().attr("_CalcCrippenDescriptors_version")=
RDKit::Descriptors::crippenVersion;
docString="returns the Labute ASA value for a molecule";
python::def("CalcLabuteASA",
RDKit::Descriptors::calcLabuteASA,
(python::arg("mol"),python::arg("includeHs")=true,
python::arg("force")=false),
docString.c_str());
python::scope().attr("_CalcLabuteASA_version")=RDKit::Descriptors::labuteASAVersion;
docString="returns a list of atomic contributions to the Labute ASA";
python::def("_CalcLabuteASAContribs",
computeASAContribs,
(python::arg("mol"),python::arg("includeHs")=true,
python::arg("force")=false),
docString.c_str());
docString="returns the TPSA value for a molecule";
python::def("CalcTPSA",
RDKit::Descriptors::calcTPSA,
(python::arg("mol"),
python::arg("force")=false),
docString.c_str());
python::scope().attr("_CalcTPSA_version")=RDKit::Descriptors::tpsaVersion;
docString="returns a list of atomic contributions to the TPSA";
python::def("_CalcTPSAContribs",
computeTPSAContribs,
(python::arg("mol"),
python::arg("force")=false),
docString.c_str());
docString="returns the molecule's molecular weight";
python::def("_CalcMolWt",
RDKit::Descriptors::calcAMW,
(python::arg("mol"),python::arg("onlyHeavy")=false),
docString.c_str());
python::scope().attr("_CalcMolWt_version")="1.0.0";
docString="returns the molecule's exact molecular weight";
python::def("CalcExactMolWt",
RDKit::Descriptors::calcExactMW,
(python::arg("mol"),python::arg("onlyHeavy")=false),
docString.c_str());
python::scope().attr("_CalcExactMolWt_version")="1.0.0";
docString="returns the molecule's formula";
python::def("CalcMolFormula",
RDKit::Descriptors::calcMolFormula,
(python::arg("mol")),
docString.c_str());
python::scope().attr("_CalcMolFormula_version")="1.0.0";
docString="returns the number of Lipinski H-bond donors for a molecule";
python::def("CalcNumLipinskiHBD",
RDKit::Descriptors::calcLipinskiHBD,
(python::arg("mol")),
docString.c_str());
python::scope().attr("_CalcNumLipinskiHBD_version")=RDKit::Descriptors::lipinskiHBDVersion;
docString="returns the number of Lipinski H-bond acceptors for a molecule";
python::def("CalcNumLipinskiHBA",
RDKit::Descriptors::calcLipinskiHBA,
(python::arg("mol")),
docString.c_str());
python::scope().attr("_CalcNumLipinskiHBA_version")=RDKit::Descriptors::lipinskiHBAVersion;
docString="returns the number of H-bond donors for a molecule";
python::def("CalcNumHBD",
RDKit::Descriptors::calcNumHBD,
(python::arg("mol")),
docString.c_str());
python::scope().attr("_CalcNumHBD_version")=RDKit::Descriptors::NumHBDVersion;
docString="returns the number of H-bond acceptors for a molecule";
python::def("CalcNumHBA",
RDKit::Descriptors::calcNumHBA,
(python::arg("mol")),
docString.c_str());
python::scope().attr("_CalcNumHBA_version")=RDKit::Descriptors::NumHBAVersion;
docString="returns the number of rotatable bonds for a molecule";
python::def("CalcNumRotatableBonds",
RDKit::Descriptors::calcNumRotatableBonds,
(python::arg("mol")),
docString.c_str());
python::scope().attr("_CalcNumRotatableBonds_version")=RDKit::Descriptors::NumRotatableBondsVersion;
docString="returns the number of rings for a molecule";
python::def("CalcNumRings",
RDKit::Descriptors::calcNumRings,
(python::arg("mol")),
docString.c_str());
python::scope().attr("_CalcNumRings_version")=RDKit::Descriptors::NumRingsVersion;
docString="returns the number of heteroatoms for a molecule";
python::def("CalcNumHeteroatoms",
RDKit::Descriptors::calcNumHeteroatoms,
(python::arg("mol")),
docString.c_str());
python::scope().attr("_CalcNumHeteroatoms_version")=RDKit::Descriptors::NumHeteroatomsVersion;
docString="returns the number of amide bonds in a molecule";
python::def("CalcNumAmideBonds",
RDKit::Descriptors::calcNumAmideBonds,
(python::arg("mol")),
docString.c_str());
python::scope().attr("_CalcNumAmideBonds_version")=RDKit::Descriptors::NumAmideBondsVersion;
docString="returns the SlogP VSA contributions for a molecule";
python::def("SlogP_VSA_",
CalcSlogPVSA,
(python::arg("mol"),
python::arg("bins")=python::list(),
python::arg("force")=false));
docString="returns the SMR VSA contributions for a molecule";
python::def("SMR_VSA_",
CalcSMRVSA,
(python::arg("mol"),
python::arg("bins")=python::list(),
python::arg("force")=false));
docString="returns the PEOE VSA contributions for a molecule";
python::def("PEOE_VSA_",
CalcPEOEVSA,
(python::arg("mol"),
python::arg("bins")=python::list(),
python::arg("force")=false));
}
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