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// $Id: MolTransforms.cpp 1625 2011-01-13 04:22:56Z glandrum $
//
// Copyright (C) 2003-2006 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 "MolTransforms.h"
#include <GraphMol/RDKitBase.h>
#include <Numerics/EigenSolvers/PowerEigenSolver.h>
#include <Numerics/SymmMatrix.h>
#include <Numerics/Matrix.h>
#include <Geometry/Transform3D.h>
#define EIGEN_TOLERANCE 1.0e-2
namespace MolTransforms {
using namespace RDKit;
void transformAtom(Atom *atom,RDGeom::Transform3D &tform){
PRECONDITION(atom,"no atom");
ROMol &mol = atom->getOwningMol();
for (ROMol::ConstConformerIterator ci = mol.beginConformers();
ci != mol.endConformers(); ci++) {
RDGeom::Point3D &pos = (*ci)->getAtomPos(atom->getIdx());
tform.TransformPoint(pos);
}
//atom->setPos(pos);
}
void transformMolsAtoms(ROMol *mol,RDGeom::Transform3D &tform){
PRECONDITION(mol,"no molecule");
ROMol::AtomIterator atomIt;
for(atomIt=mol->beginAtoms();atomIt!=mol->endAtoms();atomIt++){
transformAtom(*atomIt,tform);
}
}
RDGeom::Point3D computeCentroid(const Conformer &conf, bool ignoreHs) {
RDGeom::Point3D res(0.0, 0.0, 0.0);
const ROMol &mol = conf.getOwningMol();
ROMol::ConstAtomIterator cai;
unsigned int nAtms = 0;
for (cai = mol.beginAtoms(); cai != mol.endAtoms(); cai++) {
if (((*cai)->getAtomicNum() == 1) && (ignoreHs)) {
continue;
}
res += conf.getAtomPos((*cai)->getIdx());
nAtms++;
}
res /= nAtms;
return res;
}
RDNumeric::DoubleSymmMatrix *computeCovarianceMatrix(const Conformer &conf,
const RDGeom::Point3D ¢er,
bool normalize, bool ignoreHs) {
double xx, xy, xz, yy, yz, zz;
xx = xy = xz = yy = yz = zz = 0.0;
const ROMol &mol = conf.getOwningMol();
ROMol::ConstAtomIterator cai;
unsigned int nAtms = 0;
for (cai = mol.beginAtoms(); cai != mol.endAtoms(); cai++) {
if (((*cai)->getAtomicNum() == 1) && (ignoreHs) ) {
continue;
}
RDGeom::Point3D loc = conf.getAtomPos((*cai)->getIdx());
loc -= center;
xx += loc.x*loc.x;
xy += loc.x*loc.y;
xz += loc.x*loc.z;
yy += loc.y*loc.y;
yz += loc.y*loc.z;
zz += loc.z*loc.z;
nAtms++;
}
if (normalize) {
xx /= nAtms;
xy /= nAtms;
xz /= nAtms;
yy /= nAtms;
yz /= nAtms;
zz /= nAtms;
}
RDNumeric::DoubleSymmMatrix *res = new RDNumeric::DoubleSymmMatrix(3,3);
res->setVal(0,0, xx);
res->setVal(0,1, xy);
res->setVal(0,2, xz);
res->setVal(1,1, yy);
res->setVal(1,2, yz);
res->setVal(2,2, zz);
return res;
}
RDGeom::Transform3D *computeCanonicalTransform(const Conformer &conf,
const RDGeom::Point3D *center,
bool normalizeCovar,
bool ignoreHs) {
RDGeom::Point3D origin;
if (!center) {
origin = computeCentroid(conf, ignoreHs);
} else {
origin = (*center);
}
RDNumeric::DoubleSymmMatrix *covMat = computeCovarianceMatrix(conf, origin,
normalizeCovar, ignoreHs);
// find the eigen values and eigen vectors for the covMat
RDNumeric::DoubleMatrix eigVecs(3,3);
RDNumeric::DoubleVector eigVals(3);
// if we have a single atom system we don't need to do anyhting other than setting translation
// translation
unsigned int nAtms = conf.getNumAtoms();
RDGeom::Transform3D *trans = new RDGeom::Transform3D;
// set the translation
origin *= -1.0;
//trans->SetTranslation(origin);
// if we have a single atom system we don't need to do anyhting setting translation is sufficient
if (nAtms > 1) {
RDNumeric::EigenSolvers::powerEigenSolver(3, *covMat, eigVals, eigVecs,
conf.getNumAtoms());
// deal with zero eigen value systems
unsigned int i, j, dim = 3;
for (i = 0; i < 3; ++i) {
if (fabs(eigVals.getVal(i)) < EIGEN_TOLERANCE) {
dim--;
}
}
CHECK_INVARIANT(dim >= 1, "");
if (dim < 3) {
RDGeom::Point3D first(eigVecs.getVal(0,0), eigVecs.getVal(0,1), eigVecs.getVal(0,2));
if (dim == 1) {
// pick an arbitrary eigen vector perpendicular to the first vector
RDGeom::Point3D second(first.getPerpendicular());
eigVecs.setVal(1,0, second.x);
eigVecs.setVal(1,1, second.y);
eigVecs.setVal(1,2, second.z);
if (eigVals.getVal(0) > 1.0) {
eigVals.setVal(1, 1.0);
} else {
eigVals.setVal(1, eigVals.getVal(0)/2.0);
}
}
RDGeom::Point3D second(eigVecs.getVal(1,0), eigVecs.getVal(1,1), eigVecs.getVal(1,2));
// pick the third eigen vector perpendicular to the first two
RDGeom::Point3D third = first.crossProduct(second);
eigVecs.setVal(2,0, third.x);
eigVecs.setVal(2,1, third.y);
eigVecs.setVal(2,2, third.z);
if (eigVals.getVal(1) > 1.0) {
eigVals.setVal(2, 1.0);
} else {
eigVals.setVal(2, eigVals.getVal(1)/2.0);
}
}
// now set the transformation
for (i = 0; i < 3; ++i) {
for (j = 0; j < 3; ++j) {
trans->setVal(i, j, eigVecs.getVal(i,j));
}
}
}// end of multiple atom system
trans->TransformPoint(origin);
trans->SetTranslation(origin);
delete covMat;
return trans;
}
void transformConformer(Conformer &conf, const RDGeom::Transform3D &trans) {
RDGeom::POINT3D_VECT &positions = conf.getPositions();
RDGeom::POINT3D_VECT_I pi;
for (pi = positions.begin(); pi != positions.end(); ++pi) {
trans.TransformPoint(*pi);
}
}
void canonicalizeConformer(Conformer &conf, const RDGeom::Point3D *center,
bool normalizeCovar, bool ignoreHs) {
RDGeom::Transform3D *trans = computeCanonicalTransform(conf, center,
normalizeCovar, ignoreHs);
transformConformer(conf, *trans);
delete trans;
}
void canonicalizeMol(RDKit::ROMol &mol, bool normalizeCovar, bool ignoreHs) {
ROMol::ConformerIterator ci;
for (ci = mol.beginConformers(); ci != mol.endConformers(); ci++) {
canonicalizeConformer(*(*ci), 0, normalizeCovar, ignoreHs);
}
}
}
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