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// $Id$
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ 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/SmilesParse/SmilesParse.h>
#include "MolChemicalFeature.h"
#include "MolChemicalFeatureDef.h"
namespace RDKit {
const std::string &MolChemicalFeature::getFamily() const {
return dp_def->getFamily(); // return d_family;
};
const std::string &MolChemicalFeature::getType() const {
return dp_def->getType(); // return d_type;
};
void MolChemicalFeature::setActiveConformer(int confId) {
PRECONDITION(dp_mol, "bad molecule");
d_activeConf = confId;
}
RDGeom::Point3D MolChemicalFeature::getPos() const {
return this->getPos(d_activeConf);
}
RDGeom::Point3D MolChemicalFeature::getPos(int confId) const {
PRECONDITION(dp_mol, "bad molecule");
PRECONDITION(dp_mol->getNumConformers(), "molecule has no conformers");
if (confId == -1) confId = (*dp_mol->beginConformers())->getId();
// -------------
// Check to see if we've got the value cached:
PointCacheType::const_iterator cacheIt = d_locs.find(confId);
if (cacheIt != d_locs.end()) {
return cacheIt->second;
}
// --------------
// Nope, we have to figure it out on our own:
RDGeom::Point3D res(0, 0, 0);
bool setNeg1 = false;
RDUNUSED_PARAM(setNeg1);
if (confId == -1) {
setNeg1 = true;
}
if (d_atoms.size() == 1) {
res = dp_mol->getConformer(confId).getAtomPos((*d_atoms.begin())->getIdx());
} else {
PRECONDITION(dp_def, "bad definition");
PRECONDITION(dp_def->getNumWeights() == this->getNumAtoms(),
"weight/atom mismatch");
auto weightIt = dp_def->beginWeights();
const Conformer &conf = dp_mol->getConformer(confId);
for (auto atomIt = d_atoms.begin(); atomIt != d_atoms.end();
atomIt++, weightIt++) {
const Atom *atom = *atomIt;
RDGeom::Point3D p = conf.getAtomPos(atom->getIdx());
p *= *weightIt;
res += p;
}
}
d_locs[confId] = res;
return res;
}
}
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