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// $Id$
//
// Copyright (C) 2003-2009 Greg Landrum and 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 "MolOps.h"
#include "RDKitBase.h"
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <boost/dynamic_bitset.hpp>
#include <iomanip>
namespace RDKit {
namespace MolOps {
double computeBalabanJ(double *distMat, int nb, int nAts) {
// NOTE that the distance matrix is modified here for the sake of
// efficiency
PRECONDITION(distMat, "bogus distance matrix")
double sum = 0.0;
int nActive = nAts;
int mu = nb - nActive + 1;
if (mu == -1) return 0.0;
for (int i = 0; i < nAts; i++) {
int iTab = i * nAts;
sum = 0.0;
for (int j = 0; j < nAts; j++) {
if (j != i) {
sum += distMat[iTab + j];
}
}
distMat[iTab + i] *= sum;
}
double accum = 0.0;
for (int i = 0; i < nAts; i++) {
int iTab = i * nAts + i;
for (int j = i + 1; j < nAts; j++) {
// NOTE: this isn't strictly the Balaban J value, because we
// aren't only adding in adjacent atoms. Since we're doing a
// discriminator, that shouldn't be a problem.
if (j != i) {
accum += (1.0 / sqrt(distMat[iTab] * distMat[j * nAts + j]));
}
}
}
return nActive / ((mu + 1) * accum);
}
double computeBalabanJ(const ROMol &mol, bool useBO, bool force,
const std::vector<int> *bondPath, bool cacheIt) {
RDUNUSED_PARAM(useBO);
double res = 0.0;
if (!force && mol.hasProp(common_properties::BalabanJ)) {
mol.getProp(common_properties::BalabanJ, res);
} else {
double *dMat;
int nb = 0, nAts = 0;
if (bondPath) {
boost::dynamic_bitset<> atomsUsed(mol.getNumAtoms());
boost::dynamic_bitset<> bondsUsed(mol.getNumBonds());
for (int ci : *bondPath) {
bondsUsed[ci] = 1;
}
std::vector<const Bond *> bonds;
bonds.reserve(bondPath->size());
std::vector<int> atomsInPath;
atomsInPath.reserve(bondPath->size() + 1);
ROMol::EDGE_ITER beg, end;
boost::tie(beg, end) = mol.getEdges();
while (beg != end) {
const Bond *bond = mol[*beg];
if (bondsUsed[bond->getIdx()]) {
int begIdx = bond->getBeginAtomIdx();
int endIdx = bond->getEndAtomIdx();
bonds.push_back(bond);
if (!atomsUsed[begIdx]) {
atomsInPath.push_back(begIdx);
atomsUsed[begIdx] = 1;
}
if (!atomsUsed[endIdx]) {
atomsInPath.push_back(endIdx);
atomsUsed[endIdx] = 1;
}
}
beg++;
}
nb = rdcast<int>(bondPath->size());
nAts = rdcast<int>(atomsInPath.size());
dMat = MolOps::getDistanceMat(mol, atomsInPath, bonds, true, true);
res = computeBalabanJ(dMat, nb, nAts);
delete[] dMat;
} else {
nb = mol.getNumBonds();
nAts = mol.getNumAtoms();
dMat = MolOps::getDistanceMat(mol, true, true, true, nullptr);
res = computeBalabanJ(dMat, nb, nAts);
delete[] dMat;
}
if (cacheIt) mol.setProp(common_properties::BalabanJ, res, true);
}
return res;
}
} // end of namespace MolOps
} // end of namespace RDKit
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