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https://github.com/rdkit/rdkit.git
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e05580e495
instead of using the property map interface. A nice side-effect is that the wart of having to use property maps to loop over bonds or atom neighbors is now gone. This potentially breaks lots of client C++ code.
391 lines
9.9 KiB
C++
Executable File
391 lines
9.9 KiB
C++
Executable File
// $Id$
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//
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// Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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//
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#include <GraphMol/ROMol.h>
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#include <GraphMol/Atom.h>
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#include <GraphMol/Bond.h>
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#include <GraphMol/BondIterators.h>
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#include <GraphMol/MolOps.h>
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#include <memory.h>
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#include <boost/shared_array.hpp>
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#include <algorithm>
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#include <cstring>
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namespace RDKit{
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const int LOCAL_INF=(int)1e8;
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// local utility namespace
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namespace {
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/* ----------------------------------------------
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This implements the Floyd-Warshall all-pairs-shortest-paths
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algorithm as described on pg 564 of the White Book (Cormen, Leiserson, Rivest)
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Arguments:
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adjMat: the adjacency matrix. This is overwritten with the shortest
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paths, should be dim x dim
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dim: the size of adjMat
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pathMat: the path matrix, should be dim x dim
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-----------------------------------------------*/
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template<class T> void
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FloydWarshall(int dim,T *adjMat,int *pathMat)
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{
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int k,i,j;
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T *currD,*lastD,*tTemp;
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int *currP,*lastP,*iTemp;
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currD = new T[dim*dim];
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currP = new int[dim*dim];
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lastD = new T[dim*dim];
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lastP = new int[dim*dim];
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memcpy(static_cast<void *>(lastD),static_cast<void *>(adjMat),dim*dim*sizeof(T));
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// initialize the paths
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for(i=0;i<dim;i++){
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int itab=i*dim;
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for(j=0;j<dim;j++){
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if(i==j || adjMat[itab+j]==LOCAL_INF){
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pathMat[itab+j] = -1;
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}else{
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pathMat[itab+j] = i;
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}
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}
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}
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memcpy(static_cast<void *>(lastP),static_cast<void *>(pathMat),dim*dim*sizeof(int));
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for(k=0;k<dim;k++){
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int ktab=k*dim;
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for(i=0;i<dim;i++){
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int itab=i*dim;
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for(j=0;j<dim;j++){
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T v1=lastD[itab+j];
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T v2=lastD[itab+k]+lastD[ktab+j];
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if(v1<=v2){
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currD[itab+j] = v1;
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currP[itab+j] = lastP[itab+j];
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}else{
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currD[itab+j] = v2;
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currP[itab+j] = lastP[ktab+j];
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}
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}
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}
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tTemp = currD;
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currD = lastD;
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lastD = tTemp;
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iTemp = currP;
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currP = lastP;
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lastP = iTemp;
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}
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memcpy(static_cast<void *>(adjMat),static_cast<void *>(lastD),dim*dim*sizeof(T));
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memcpy(static_cast<void *>(pathMat),static_cast<void *>(lastP),dim*dim*sizeof(int));
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delete [] currD;
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delete [] currP;
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delete [] lastD;
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delete [] lastP;
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}
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template<class T> void
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FloydWarshall(int dim,T *adjMat,int *pathMat,const std::vector<int> &activeAtoms)
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{
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T *currD,*lastD,*tTemp;
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int *currP,*lastP,*iTemp;
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currD = new T[dim*dim];
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currP = new int[dim*dim];
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lastD = new T[dim*dim];
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lastP = new int[dim*dim];
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memcpy(static_cast<void *>(lastD),static_cast<void *>(adjMat),dim*dim*sizeof(T));
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// initialize the paths
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for(std::vector<int>::const_iterator i=activeAtoms.begin();
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i!=activeAtoms.end();
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i++){
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int itab=(*i)*dim;
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for(std::vector<int>::const_iterator j=activeAtoms.begin();
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j!=activeAtoms.end();
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j++){
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if((*i)==(*j) || adjMat[itab+(*j)]==LOCAL_INF){
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pathMat[itab+(*j)] = -1;
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}else{
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pathMat[itab+(*j)] = (*i);
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}
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}
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}
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memcpy(static_cast<void *>(lastP),static_cast<void *>(pathMat),dim*dim*sizeof(int));
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for(std::vector<int>::const_iterator k=activeAtoms.begin();
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k!=activeAtoms.end();
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k++){
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int ktab=(*k)*dim;
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for(std::vector<int>::const_iterator i=activeAtoms.begin();
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i!=activeAtoms.end();
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i++){
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int itab=(*i)*dim;
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for(std::vector<int>::const_iterator j=activeAtoms.begin();
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j!=activeAtoms.end();
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j++){
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T v1=lastD[itab+(*j)];
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T v2=lastD[itab+(*k)]+lastD[ktab+(*j)];
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if(v1<=v2){
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currD[itab+(*j)] = v1;
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currP[itab+(*j)] = lastP[itab+(*j)];
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}else{
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currD[itab+(*j)] = v2;
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currP[itab+(*j)] = lastP[ktab+(*j)];
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}
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}
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}
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tTemp = currD;
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currD = lastD;
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lastD = tTemp;
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iTemp = currP;
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currP = lastP;
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lastP = iTemp;
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}
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memcpy(static_cast<void *>(adjMat),static_cast<void *>(lastD),dim*dim*sizeof(T));
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memcpy(static_cast<void *>(pathMat),static_cast<void *>(lastP),dim*dim*sizeof(int));
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delete [] currD;
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delete [] currP;
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delete [] lastD;
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delete [] lastP;
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}
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} // end of local utility namespace
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namespace MolOps {
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double *getDistanceMat(const ROMol &mol,bool useBO,
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bool useAtomWts,
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bool force,
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const char *propNamePrefix){
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std::string propName;
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boost::shared_array<double> sptr;
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if(propNamePrefix){
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propName = propNamePrefix;
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} else {
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propName = "";
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}
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propName+="DistanceMatrix";
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// make sure we don't use the nonBO cache for the BO matrix and vice versa:
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if(useBO) propName+="BO";
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if(!force && mol.hasProp(propName)){
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mol.getProp(propName,sptr);
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return sptr.get();
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}
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int nAts=mol.getNumAtoms();
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double *dMat = new double[nAts*nAts];
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int i,j;
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// initialize off diagonals to LOCAL_INF and diagonals to 0
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for(i=0;i<nAts*nAts;i++) dMat[i] = LOCAL_INF;
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for(i=0;i<nAts;i++) dMat[i*nAts+i]=0.0;
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ROMol::EDGE_ITER firstB,lastB;
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boost::tie(firstB,lastB) = mol.getEdges();
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while(firstB!=lastB){
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const BOND_SPTR bond = mol[*firstB];
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i = bond->getBeginAtomIdx();
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j = bond->getEndAtomIdx();
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double contrib;
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if(useBO){
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if(!bond->getIsAromatic()){
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contrib = 1./bond->getBondTypeAsDouble();
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} else {
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contrib = 2. / 3.;
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}
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} else {
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contrib = 1.0;
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}
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dMat[i*nAts+j]=contrib;
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dMat[j*nAts+i]=contrib;
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++firstB;
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}
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int *pathMat = new int[nAts*nAts];
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memset(static_cast<void *>(pathMat),0,nAts*nAts*sizeof(int));
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FloydWarshall(nAts,dMat,pathMat);
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if(useAtomWts){
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for (i = 0; i < nAts; i++) {
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int anum = mol.getAtomWithIdx(i)->getAtomicNum();
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dMat[i*nAts+i] = 6.0/anum;
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}
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}
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sptr.reset(dMat);
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mol.setProp(propName,sptr,true);
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boost::shared_array<int> iSptr(pathMat);
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mol.setProp(propName+"_Paths",iSptr,true);
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return dMat;
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};
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double *getDistanceMat(const ROMol &mol,
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const std::vector<int> &activeAtoms,
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const std::vector<const Bond *> &bonds,
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bool useBO,
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bool useAtomWts){
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const int nAts=activeAtoms.size();
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double *dMat = new double[nAts*nAts];
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int i,j;
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// initialize off diagonals to LOCAL_INF and diagonals to 0
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for(i=0;i<nAts*nAts;i++) dMat[i] = LOCAL_INF;
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for(i=0;i<nAts;i++) dMat[i*nAts+i]=0.0;
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for(std::vector<const Bond *>::const_iterator bi=bonds.begin();
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bi!=bonds.end();bi++){
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const Bond *bond=*bi;
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i=std::find(activeAtoms.begin(),activeAtoms.end(),
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static_cast<int>(bond->getBeginAtomIdx())) - activeAtoms.begin();
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j=std::find(activeAtoms.begin(),activeAtoms.end(),
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static_cast<int>(bond->getEndAtomIdx())) - activeAtoms.begin();
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double contrib;
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if(useBO){
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if(!bond->getIsAromatic()){
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contrib = 1./bond->getBondTypeAsDouble();
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} else {
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contrib = 2. / 3.;
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}
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} else {
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contrib = 1.0;
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}
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dMat[i*nAts+j]=contrib;
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dMat[j*nAts+i]=contrib;
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}
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int *pathMat = new int[nAts*nAts];
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memset(static_cast<void *>(pathMat),0,nAts*nAts*sizeof(int));
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FloydWarshall(nAts,dMat,pathMat);
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delete [] pathMat;
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if(useAtomWts){
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for(i=0;i<nAts;i++){
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int anum = mol.getAtomWithIdx(activeAtoms[i])->getAtomicNum();
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dMat[i*nAts+i] = 6.0/anum;
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}
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}
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return dMat;
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};
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// NOTE: do *not* delete results
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double *getAdjacencyMatrix(const ROMol &mol,
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bool useBO,
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int emptyVal,
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bool force,
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const char *propNamePrefix)
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{
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std::string propName;
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boost::shared_array<double> sptr;
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if(propNamePrefix){
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propName = propNamePrefix;
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} else {
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propName = "";
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}
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propName+="AdjacencyMatrix";
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if(!force && mol.hasProp(propName)){
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mol.getProp(propName,sptr);
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return sptr.get();
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}
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int nAts = mol.getNumAtoms();
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double *res = new double[nAts*nAts];
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memset(static_cast<void *>(res),emptyVal,nAts*nAts*sizeof(double));
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ROMol::ConstBondIterator bondIt;
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for(bondIt=mol.beginBonds();bondIt!=mol.endBonds();bondIt++){
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if(!useBO){
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int beg=(*bondIt)->getBeginAtomIdx();
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int end=(*bondIt)->getEndAtomIdx();
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res[beg*nAts+end] = 1;
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res[end*nAts+beg] = 1;
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}
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else {
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int begIdx=(*bondIt)->getBeginAtomIdx();
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int endIdx=(*bondIt)->getEndAtomIdx();
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Atom const *beg=mol.getAtomWithIdx(begIdx);
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Atom const *end=mol.getAtomWithIdx(endIdx);
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res[begIdx*nAts+endIdx] = (*bondIt)->getValenceContrib(beg);
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res[endIdx*nAts+begIdx] = (*bondIt)->getValenceContrib(end);
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}
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}
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sptr.reset(res);
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mol.setProp(propName,sptr,true);
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return res;
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};
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INT_LIST getShortestPath(const ROMol &mol, int aid1, int aid2) {
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int nats = mol.getNumAtoms();
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RANGE_CHECK(0,aid1,nats-1);
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RANGE_CHECK(0,aid2,nats-1);
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CHECK_INVARIANT(aid1 != aid2, "");
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INT_VECT pred, doneAtms;
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//pred.reserve(nats);
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//doneAtms.reserve(nats);
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pred.resize(nats);
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doneAtms.resize(nats);
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int ai;
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for (ai = 0; ai < nats; ++ai) {
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doneAtms[ai] = 0;
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}
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std::deque<int> bfsQ;
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bfsQ.push_back(aid1);
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bool done = false;
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ROMol::ADJ_ITER nbrIdx,endNbrs;
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while ((!done) && (bfsQ.size() > 0)) {
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int curAid = bfsQ.front();
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boost::tie(nbrIdx,endNbrs) = mol.getAtomNeighbors(mol.getAtomWithIdx(curAid));
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while (nbrIdx != endNbrs) {
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if (doneAtms[*nbrIdx] == 0) {
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pred[*nbrIdx] = curAid;
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if (static_cast<int>(*nbrIdx) == aid2) {
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done = true;
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break;
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}
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bfsQ.push_back(*nbrIdx);
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}
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nbrIdx++;
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}
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doneAtms[curAid] = 1;
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bfsQ.pop_front();
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}
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INT_LIST res;
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if(done){
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done = false;
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int prev = aid2;
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res.push_back(aid2);
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while (!done) {
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prev = pred[prev];
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if (prev != aid1) {
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res.push_front(prev);
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} else {
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done = true;
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}
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}
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res.push_front(aid1);
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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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