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95a92282d1
o rdkit gains a RDKit::common_properties namespace that contains common string value properties o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns true/false on success or failure. This is used to optimize access. o rdkit learns how to pass property keys by reference, not value. A new namespace has been added to RDKit, common_properties that contains the std::string values for commonly used properties. This helps to avoid typos in string values but also avoids a creation of std::strings from character values. All accessors (has/get/clear and getPropIfPresent) now pass the key by reference. Additionally, getPropIfPresent removes the double lookup of hasProp/getProp which can be a significant speedup in the smiles and smarts parsers (10-20%)
120 lines
3.7 KiB
C++
120 lines
3.7 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,
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bool useBO,
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bool force,
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const std::vector<int> *bondPath,
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bool cacheIt) {
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double res=0.0;
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if (!force && mol.hasProp(common_properties::BalanbanJ)) {
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mol.getProp(common_properties::BalabanJ, res);
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}
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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(std::vector<int>::const_iterator ci=bondPath->begin();
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ci!=bondPath->end();ci++){
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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].get();
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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 = bondPath->size();
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nAts = 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,0);
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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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