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// $Id$
//
// Copyright (C) 2001-2008 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 "AlignMolecules.h"
#include <Geometry/Transform3D.h>
#include <Numerics/Vector.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/Conformer.h>
#include <GraphMol/ROMol.h>
#include <Numerics/Alignment/AlignPoints.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
namespace RDKit {
namespace MolAlign {
double getAlignmentTransform(const ROMol &prbMol, const ROMol &refMol,
RDGeom::Transform3D &trans, int prbCid, int refCid,
const MatchVectType *atomMap,
const RDNumeric::DoubleVector *weights,
bool reflect, unsigned int maxIterations) {
RDGeom::Point3DConstPtrVect refPoints, prbPoints;
const Conformer &prbCnf = prbMol.getConformer(prbCid);
const Conformer &refCnf = refMol.getConformer(refCid);
if (atomMap == nullptr) {
// we have to figure out the mapping between the two molecule
MatchVectType match;
const bool recursionPossible = true;
const bool useChirality = false;
const bool useQueryQueryMatches = true;
if (SubstructMatch(refMol, prbMol, match, recursionPossible, useChirality, useQueryQueryMatches)) {
MatchVectType::const_iterator mi;
for (mi = match.begin(); mi != match.end(); mi++) {
prbPoints.push_back(&prbCnf.getAtomPos(mi->first));
refPoints.push_back(&refCnf.getAtomPos(mi->second));
}
} else {
throw MolAlignException(
"No sub-structure match found between the probe and query mol");
}
} else {
MatchVectType::const_iterator mi;
for (mi = atomMap->begin(); mi != atomMap->end(); mi++) {
prbPoints.push_back(&prbCnf.getAtomPos(mi->first));
refPoints.push_back(&refCnf.getAtomPos(mi->second));
}
}
double ssr = RDNumeric::Alignments::AlignPoints(
refPoints, prbPoints, trans, weights, reflect, maxIterations);
ssr /= (prbPoints.size());
return sqrt(ssr);
}
double alignMol(ROMol &prbMol, const ROMol &refMol, int prbCid, int refCid,
const MatchVectType *atomMap,
const RDNumeric::DoubleVector *weights, bool reflect,
unsigned int maxIterations) {
RDGeom::Transform3D trans;
double res = getAlignmentTransform(prbMol, refMol, trans, prbCid, refCid,
atomMap, weights, reflect, maxIterations);
// now transform the relevant conformation on prbMol
Conformer &conf = prbMol.getConformer(prbCid);
MolTransforms::transformConformer(conf, trans);
return res;
}
double getBestRMS(ROMol &probeMol, ROMol &refMol, int probeId, int refId,
const std::vector<MatchVectType> &map, int maxMatches) {
std::vector<MatchVectType> matches = map;
if (matches.empty()) {
bool uniquify = false;
bool recursionPossible = true;
bool useChirality = false;
bool useQueryQueryMatches = false;
SubstructMatch(refMol, probeMol, matches, uniquify, recursionPossible,
useChirality, useQueryQueryMatches, maxMatches);
if (matches.empty()) {
throw MolAlignException(
"No sub-structure match found between the reference and probe mol");
}
if (matches.size() > 1e6) {
std::string name;
probeMol.getPropIfPresent(common_properties::_Name, name);
std::cerr << "Warning in " << __FUNCTION__ << ": " << matches.size()
<< " matches detected for molecule " << name << ", this may "
<< "lead to a performance slowdown.\n";
}
}
double bestRMS = 1.e300;
MatchVectType &bestMatch = matches[0];
for (auto &matche : matches) {
double rms = alignMol(probeMol, refMol, probeId, refId, &matche);
if (rms < bestRMS) {
bestRMS = rms;
bestMatch = matche;
}
}
// Perform a final alignment to the best alignment...
if (&bestMatch != &matches.back())
alignMol(probeMol, refMol, probeId, refId, &bestMatch);
return bestRMS;
}
void _fillAtomPositions(RDGeom::Point3DConstPtrVect &pts, const Conformer &conf,
const std::vector<unsigned int> *atomIds = nullptr) {
unsigned int na = conf.getNumAtoms();
pts.clear();
if (atomIds == nullptr) {
unsigned int ai;
pts.reserve(na);
for (ai = 0; ai < na; ++ai) {
pts.push_back(&conf.getAtomPos(ai));
}
} else {
pts.reserve(atomIds->size());
std::vector<unsigned int>::const_iterator cai;
for (cai = atomIds->begin(); cai != atomIds->end(); cai++) {
pts.push_back(&conf.getAtomPos(*cai));
}
}
}
void alignMolConformers(ROMol &mol, const std::vector<unsigned int> *atomIds,
const std::vector<unsigned int> *confIds,
const RDNumeric::DoubleVector *weights, bool reflect,
unsigned int maxIters, std::vector<double> *RMSlist) {
if (mol.getNumConformers() == 0) {
// nothing to be done ;
return;
}
RDGeom::Point3DConstPtrVect refPoints, prbPoints;
int cid = -1;
if ((confIds != nullptr) && (confIds->size() > 0)) {
cid = confIds->front();
}
const Conformer &refCnf = mol.getConformer(cid);
_fillAtomPositions(refPoints, refCnf, atomIds);
// now loop throught the remaininf conformations and transform them
RDGeom::Transform3D trans;
double ssd;
if (confIds == nullptr) {
unsigned int i = 0;
ROMol::ConformerIterator cnfi;
// Conformer *conf;
for (cnfi = mol.beginConformers(); cnfi != mol.endConformers(); cnfi++) {
// conf = (*cnfi);
i += 1;
if (i == 1) {
continue;
}
_fillAtomPositions(prbPoints, *(*cnfi), atomIds);
ssd = RDNumeric::Alignments::AlignPoints(refPoints, prbPoints, trans,
weights, reflect, maxIters);
if (RMSlist) {
ssd /= (prbPoints.size());
RMSlist->push_back(sqrt(ssd));
}
MolTransforms::transformConformer(*(*cnfi), trans);
}
} else {
std::vector<unsigned int>::const_iterator cai;
unsigned int i = 0;
for (cai = confIds->begin(); cai != confIds->end(); cai++) {
i += 1;
if (i == 1) {
continue;
}
Conformer &conf = mol.getConformer(*cai);
_fillAtomPositions(prbPoints, conf, atomIds);
ssd = RDNumeric::Alignments::AlignPoints(refPoints, prbPoints, trans,
weights, reflect, maxIters);
if (RMSlist) {
ssd /= (prbPoints.size());
RMSlist->push_back(sqrt(ssd));
}
MolTransforms::transformConformer(conf, trans);
}
}
}
}
}
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