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#include "RDMolImpl.h"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/Fileparsers.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/DistGeomHelpers/Embedder.h>
#include <ForceField/ForceField.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
#include <string>
#include <vector>
#include <nsMemory.h>
NS_IMPL_ISUPPORTS1(RDMolecule, IRDMolecule)
RDMolecule::~RDMolecule() {
if (this->dp_mol) {
delete dp_mol;
dp_mol = 0;
}
}
/* double GetMW (); */
NS_IMETHODIMP RDMolecule::GetMW(double *_retval) {
if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
RDKit::PeriodicTable *pt = RDKit::PeriodicTable::getTable();
*_retval = 0.0;
for (RDKit::ROMol::AtomIterator atIt = dp_mol->beginAtoms();
atIt != dp_mol->endAtoms(); atIt++) {
*_retval += (*atIt)->getMass() +
(*atIt)->getNumImplicitHs() * pt->getAtomicWeight(1);
}
return NS_OK;
}
/* string GetSmiles (); */
NS_IMETHODIMP RDMolecule::GetSmiles(char **_retval) {
if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
std::string smi = RDKit::MolToSmiles(*dp_mol);
*_retval =
(char *)nsMemory::Clone(smi.c_str(), sizeof(char) * (smi.size() + 1));
return *_retval ? NS_OK : NS_ERROR_OUT_OF_MEMORY;
}
/* unsigned long GetSmartsMatchCount (in string smarts); */
NS_IMETHODIMP RDMolecule::GetSmartsMatchCount(const char *smarts,
PRUint32 *_retval) {
if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
RDKit::ROMol *patt = RDKit::SmartsToMol(std::string(smarts));
if (!patt) return NS_ERROR_FAILURE;
std::vector<RDKit::MatchVectType> matches;
int res = RDKit::SubstructMatch(dp_mol, patt, matches);
*_retval = res;
return NS_OK;
}
/* double LogP (); */
NS_IMETHODIMP RDMolecule::LogP(double *_retval) {
if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
double logp;
if (dp_mol->hasProp(common_properties::_CrippenLogP)) {
dp_mol->getProp(common_properties::_CrippenLogP, logp);
} else {
double mr;
RDKit::Descriptors::CalcCrippenDescriptors(dp_mol, logp, mr);
dp_mol->setProp(common_properties::_CrippenLogP, logp, true);
dp_mol->setProp(common_properties::_CrippenMR, mr, true);
}
*_retval = logp;
return NS_OK;
}
/* double MR (); */
NS_IMETHODIMP RDMolecule::MR(double *_retval) {
if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
double mr;
if (dp_mol->hasProp(common_properties::_CrippenMR)) {
dp_mol->getProp(common_properties::_CrippenMR, mr);
} else {
double logp;
RDKit::Descriptors::CalcCrippenDescriptors(dp_mol, logp, mr);
dp_mol->setProp(common_properties::_CrippenLogP, logp, true);
dp_mol->setProp(common_properties::_CrippenMR, mr, true);
}
*_retval = mr;
return NS_OK;
}
/* string GetMolBlock (); */
NS_IMETHODIMP RDMolecule::GetMolBlock(char **_retval) {
if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
std::string molB = RDKit::MolToMolBlock(dp_mol);
*_retval =
(char *)nsMemory::Clone(molB.c_str(), sizeof(char) * (molB.size() + 1));
return *_retval ? NS_OK : NS_ERROR_OUT_OF_MEMORY;
}
/* void Generate3DCoords (); */
NS_IMETHODIMP RDMolecule::Generate3DCoords() {
if (!dp_mol) return NS_ERROR_NOT_INITIALIZED;
bool embedded = RDKit::DGeomHelpers::EmbedMolecule(*dp_mol);
if (!embedded) return NS_ERROR_FAILURE;
ForceFields::ForceField *ff = RDKit::UFF::constructForceField(dp_mol);
if (!ff) return NS_ERROR_FAILURE;
ff->initialize();
int needsMore = ff->minimize();
delete ff;
if (needsMore) return NS_ERROR_FAILURE;
return NS_OK;
}
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