com.actelion.research.chem.alignment3d.PheSAAlignmentOptimizer Maven / Gradle / Ivy
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package com.actelion.research.chem.alignment3d;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import java.util.stream.IntStream;
import com.actelion.research.calc.Matrix;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.Conformer;
import com.actelion.research.chem.phesa.MolecularVolume;
import com.actelion.research.chem.phesa.PheSAAlignment;
import com.actelion.research.chem.phesa.PheSAMolecule;
import com.actelion.research.chem.phesa.pharmacophore.PPGaussian;
import com.actelion.research.chem.phesa.pharmacophore.PPTriangle;
import com.actelion.research.chem.phesa.pharmacophore.PPTriangleCreator;
import com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher;
import com.actelion.research.chem.phesa.pharmacophore.PPTriangleMatcher.AlignmentResult;
import com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator;
public class PheSAAlignmentOptimizer {
private static int OPTIMIZATIONS = 20;
private static double EXIT_VECTOR_WEIGHT = 10.0;
private PheSAAlignmentOptimizer() {}
public static double alignTwoMolsInPlace(StereoMolecule refMol, StereoMolecule fitMol) {
return alignTwoMolsInPlace(refMol,fitMol,0.5);
}
public static double alignTwoMolsInPlace(StereoMolecule refMol, StereoMolecule fitMol, double ppWeight) {
double similarity = 0.0;
MolecularVolume refVol = new MolecularVolume(refMol);
MolecularVolume fitVol = new MolecularVolume(fitMol);
Coordinates origCOM = new Coordinates(refVol.getCOM());
Conformer refConf = new Conformer(refMol);
Conformer fitConf = new Conformer(fitMol);
Matrix rotation = PheSAAlignment.preProcess(refConf, refVol);
rotation = rotation.getTranspose();
PheSAAlignment.preProcess(fitConf, fitVol);
Map> refTriangles = PPTriangleCreator.create(refVol.getPPGaussians(), refVol.getCOM());
Map> fitTriangles = PPTriangleCreator.create(fitVol.getPPGaussians(), fitVol.getCOM());
List results = PPTriangleMatcher.getMatchingTransforms(refTriangles, fitTriangles,0,0);
double[] bestTransformTriangle = new double[7];
double[] bestTransformPMI = new double[7];
StereoMolecule bestMatch = fitMol;
double bestScoreTriangle = 0.0;
if(results.size()!=0) { // found triangle alignments
results.sort((c1,c2) -> {
return Double.compare(c1.getSimilarity(),c2.getSimilarity());
});
AlignmentResult[] bestAlignments = new AlignmentResult[Math.min(results.size(),OPTIMIZATIONS)];
for(int i=1;ibestScoreTriangle) {
bestScoreTriangle = r[0];
bestTransformTriangle[0] = r[4];
bestTransformTriangle[1] = r[5];
bestTransformTriangle[2] = r[6];
bestTransformTriangle[3] = r[7];
bestTransformTriangle[4] = r[8];
bestTransformTriangle[5] = r[9];
bestTransformTriangle[6] = r[10];
bestMatch = fitMol2;
}
}
}
PheSAAlignment shapeAlignment = new PheSAAlignment(refVol,fitVol, ppWeight);
double[] r = shapeAlignment.findAlignment(PheSAAlignment.initialTransform(2),true);
if(r[0]>bestScoreTriangle) { //alignment found by PMI initial alignment is better
similarity = r[0];
bestTransformPMI = new double[] {r[4],r[5], r[6], r[7], r[8], r[9], r[10]};
bestMatch = fitConf.toMolecule();
PheSAAlignment.rotateMol(bestMatch, bestTransformPMI);
for(int a=0;a0.0) {
similarity = bestScoreTriangle;
result[0] = similarity;
result[1] = triangleRes[1];
result[2] = triangleRes[2];
bestAlignment[0] = bestPairTriangle[0];
bestAlignment[1] = bestPairTriangle[1];
}
else {
for(int i=0;i=bestScorePMI) {
bestScorePMI = r[0];
bestTransformPMI = new double[] {r[4],r[5], r[6], r[7], r[8], r[9], r[10]};
bestPairPMI[0] = refVol;
bestPairPMI[1] = fitVol;
}
}
}
//optimize best PMI alignment
PheSAAlignment shapeAlignment = new PheSAAlignment(bestPairPMI[0],bestPairPMI[1],ppWeight);
double[] r = shapeAlignment.findAlignment(new double[][] {bestTransformPMI},true);
if(r[0]>bestScoreTriangle) { //alignment found by PMI initial alignment is better
similarity = r[0];
result[0] = similarity;
result[1] = r[1];
result[2] = r[2];
result[3] = r[3];
bestAlignment[0] = refShape.getConformer(bestPairPMI[0]);
bestAlignment[1] = fitShape.getConformer(bestPairPMI[1]);
PheSAAlignment.rotateMol(bestAlignment[1], bestTransformPMI);
}
else {
bestAlignment[0] = bestPairTriangle[0];
bestAlignment[1] = bestPairTriangle[1];
}
}
int n1 = refShape.getVolumes().get(0).getExitVectorGaussians().size();
int n2 = fitShape.getVolumes().get(0).getExitVectorGaussians().size();
if(refShape.getVolumes().get(0).getExitVectorGaussians().size()!=0 ||
refShape.getVolumes().get(0).getExitVectorGaussians().size()!=0) {
// there are exit vectors
if(n1!=n2) { //different number of exit vectors --> no match
result[0] = 0.0;
result[1] = 0.0;
result[2] = 0.0;
result[3] = 0.0;
}
}
return result;
}
public static double align(PheSAMolecule fitShape, MolecularVolume refVol, MolecularVolume fitVol, StereoMolecule aligned, double ppWeight) {
Coordinates[] origCoords = new Coordinates[aligned.getAllAtoms()];
IntStream.range(0,aligned.getAllAtoms()).forEach(i -> origCoords[i] = new Coordinates(aligned.getCoordinates(i)));
double[] bestTransformTriangle = new double[7];
double bestScoreTriangle = getTriangleAlignment(fitShape,new MolecularVolume(refVol),new MolecularVolume(fitVol),bestTransformTriangle,aligned,ppWeight);
double bestScorePMI = 0.0;
double[] bestTransformPMI = new double[7];
PheSAAlignment shapeAlignment = new PheSAAlignment(new MolecularVolume(refVol),new MolecularVolume(fitVol), ppWeight);
double[] r = shapeAlignment.findAlignment(PheSAAlignment.initialTransform(2),true);
bestScorePMI = r[0];
bestTransformPMI = new double[] {r[4],r[5], r[6], r[7], r[8], r[9], r[10]};
double similarity = 0.0;
if(bestScorePMI>bestScoreTriangle) { //alignment found by PMI initial alignment is better
IntStream.range(0,aligned.getAllAtoms()).forEach(i -> {
aligned.setAtomX(i, origCoords[i].x);
aligned.setAtomY(i, origCoords[i].y);
aligned.setAtomZ(i, origCoords[i].z);
});
similarity = r[0];
PheSAAlignment.rotateMol(aligned, bestTransformPMI);
}
else {
similarity = bestScoreTriangle;
}
return similarity;
}
private static double[] getBestTriangleAlignment(PheSAMolecule refShape, PheSAMolecule fitShape, StereoMolecule[] bestPairTriangle,
double[] bestTransformTriangle, double ppWeight, boolean optimize) {
List results = new ArrayList();
double[] res = new double[3];
for(int i=0;i> refTriangles = PPTriangleCreator.create(refVol.getPPGaussians(), refVol.getCOM());
for(int j=0;j> fitTriangles = PPTriangleCreator.create(fitVol.getPPGaussians(),fitVol.getCOM());
results.addAll(PPTriangleMatcher.getMatchingTransforms(refTriangles, fitTriangles,i,j));
}
}
double bestScoreTriangle = 0.0;
if(results.size()!=0) { // found triangle alignments
results.sort((c1,c2) -> {
return Double.compare(c1.getSimilarity(),c2.getSimilarity());
});
AlignmentResult[] bestAlignments = new AlignmentResult[Math.min(results.size(),OPTIMIZATIONS)];
for(int i=1;ibestScoreTriangle) {
bestScoreTriangle = r[0];
res = new double[] {r[0],r[1],r[2], r[3]};
bestTransformTriangle[0] = r[4];
bestTransformTriangle[1] = r[5];
bestTransformTriangle[2] = r[6];
bestTransformTriangle[3] = r[7];
bestTransformTriangle[4] = r[8];
bestTransformTriangle[5] = r[9];
bestTransformTriangle[6] = r[10];
bestPairTriangle[1] = fitShape.getConformer(fitVol);
bestPairTriangle[0] = refShape.getConformer(refVol);
}
}
}
if(bestScoreTriangle>0.0)
PheSAAlignment.rotateMol(bestPairTriangle[1], bestTransformTriangle);
return res;
}
private static double getTriangleAlignment(PheSAMolecule fitShape,MolecularVolume refVol_, MolecularVolume fitVol_, double[] bestTransformTriangle, StereoMolecule aligned, double ppWeight) {
MolecularVolume refVol = new MolecularVolume(refVol_);
MolecularVolume fitVol = new MolecularVolume(fitVol_);
List results = new ArrayList();
Map> refTriangles = PPTriangleCreator.create(refVol.getPPGaussians(), refVol.getCOM());
Map> fitTriangles = PPTriangleCreator.create(fitVol.getPPGaussians(),fitVol.getCOM());
results.addAll(PPTriangleMatcher.getMatchingTransforms(refTriangles, fitTriangles,0,0));
double bestScoreTriangle = 0.0;
if(results.size()!=0) { // found triangle alignments
results.sort((c1,c2) -> {
return Double.compare(c1.getSimilarity(),c2.getSimilarity());
});
AlignmentResult[] bestAlignments = new AlignmentResult[Math.min(results.size(),OPTIMIZATIONS)];
for(int i=1;ibestScoreTriangle) {
bestTransform = transform;
bestScoreTriangle = r[0];
bestTransformTriangle[0] = r[4];
bestTransformTriangle[1] = r[5];
bestTransformTriangle[2] = r[6];
bestTransformTriangle[3] = r[7];
bestTransformTriangle[4] = r[8];
bestTransformTriangle[5] = r[9];
bestTransformTriangle[6] = r[10];
}
}
if(bestScoreTriangle>0.0) {
rotate[0] = bestTransform[0];
rotate[1] = bestTransform[1];
rotate[2] = bestTransform[2];
PheSAAlignment.translateMol(aligned, bestTransform[3]);
PheSAAlignment.rotateMol(aligned, rotate);
PheSAAlignment.translateMol(aligned, bestTransform[4]);
PheSAAlignment.rotateMol(aligned, bestTransformTriangle);
}
}
return bestScoreTriangle;
}
}
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