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https://github.com/rdkit/rdkit.git
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ba12d98ad0
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers * Actually delete atoms and bonds... * RWMol::clear now calls destroy to handle atom/bond deletion * Changes broken Atom lookup for windows/gcc * Adds tests for running with valgrind * Adds test designed for valgrind and molecule deletions * Removes RNG, actually tests bond deletions * update swig wrappers * deal with most recent changes on the main branch
114 lines
3.3 KiB
C++
114 lines
3.3 KiB
C++
// $Id$
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//
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// Copyright (C) 2003-2009 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "MolOps.h"
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#include "RDKitBase.h"
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#include <RDGeneral/Invariant.h>
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#include <RDGeneral/RDLog.h>
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#include <boost/dynamic_bitset.hpp>
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#include <iomanip>
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namespace RDKit {
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namespace MolOps {
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double computeBalabanJ(double *distMat, int nb, int nAts) {
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// NOTE that the distance matrix is modified here for the sake of
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// efficiency
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PRECONDITION(distMat, "bogus distance matrix")
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double sum = 0.0;
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int nActive = nAts;
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int mu = nb - nActive + 1;
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if (mu == -1) return 0.0;
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for (int i = 0; i < nAts; i++) {
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int iTab = i * nAts;
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sum = 0.0;
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for (int j = 0; j < nAts; j++) {
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if (j != i) {
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sum += distMat[iTab + j];
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}
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}
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distMat[iTab + i] *= sum;
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}
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double accum = 0.0;
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for (int i = 0; i < nAts; i++) {
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int iTab = i * nAts + i;
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for (int j = i + 1; j < nAts; j++) {
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// NOTE: this isn't strictly the Balaban J value, because we
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// aren't only adding in adjacent atoms. Since we're doing a
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// discriminator, that shouldn't be a problem.
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if (j != i) {
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accum += (1.0 / sqrt(distMat[iTab] * distMat[j * nAts + j]));
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}
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}
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}
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return nActive / ((mu + 1) * accum);
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}
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double computeBalabanJ(const ROMol &mol, bool useBO, bool force,
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const std::vector<int> *bondPath, bool cacheIt) {
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RDUNUSED_PARAM(useBO);
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double res = 0.0;
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if (!force && mol.hasProp(common_properties::BalabanJ)) {
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mol.getProp(common_properties::BalabanJ, res);
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} else {
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double *dMat;
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int nb = 0, nAts = 0;
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if (bondPath) {
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boost::dynamic_bitset<> atomsUsed(mol.getNumAtoms());
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boost::dynamic_bitset<> bondsUsed(mol.getNumBonds());
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for (int ci : *bondPath) {
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bondsUsed[ci] = 1;
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}
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std::vector<const Bond *> bonds;
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bonds.reserve(bondPath->size());
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std::vector<int> atomsInPath;
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atomsInPath.reserve(bondPath->size() + 1);
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ROMol::EDGE_ITER beg, end;
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boost::tie(beg, end) = mol.getEdges();
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while (beg != end) {
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const Bond *bond = mol[*beg];
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if (bondsUsed[bond->getIdx()]) {
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int begIdx = bond->getBeginAtomIdx();
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int endIdx = bond->getEndAtomIdx();
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bonds.push_back(bond);
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if (!atomsUsed[begIdx]) {
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atomsInPath.push_back(begIdx);
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atomsUsed[begIdx] = 1;
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}
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if (!atomsUsed[endIdx]) {
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atomsInPath.push_back(endIdx);
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atomsUsed[endIdx] = 1;
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}
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}
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beg++;
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}
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nb = rdcast<int>(bondPath->size());
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nAts = rdcast<int>(atomsInPath.size());
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dMat = MolOps::getDistanceMat(mol, atomsInPath, bonds, true, true);
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res = computeBalabanJ(dMat, nb, nAts);
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delete[] dMat;
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} else {
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nb = mol.getNumBonds();
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nAts = mol.getNumAtoms();
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dMat = MolOps::getDistanceMat(mol, true, true, true, nullptr);
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res = computeBalabanJ(dMat, nb, nAts);
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delete[] dMat;
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}
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if (cacheIt) mol.setProp(common_properties::BalabanJ, res, true);
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}
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return res;
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}
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} // end of namespace MolOps
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} // end of namespace RDKit
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