com.actelion.research.chem.phesa.MolecularVolume Maven / Gradle / Ivy
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Open Source Chemistry Library
package com.actelion.research.chem.phesa;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.Conformer;
import com.actelion.research.chem.phesa.pharmacophore.IPharmacophorePoint;
import com.actelion.research.chem.phesa.pharmacophore.IonizableGroupDetector;
import com.actelion.research.chem.phesa.pharmacophore.PPGaussian;
import com.actelion.research.chem.phesa.pharmacophore.PharmacophoreCalculator;
import java.util.ArrayList;
import java.util.List;
import com.actelion.research.util.EncoderFloatingPointNumbers;
/**
* @version: 1.0, February 2018
* Author: J. Wahl
* class to approximate the volume of a molecule as a sum of atom-centered Gaussians, as introduced by Grant and Pickup, J. Phys. Chem. 1995, 99, 3503-3510
* no higher order terms (atom-atom overlaps) are calculated to reduce computational costs
*/
public class MolecularVolume {
static public final double p = 2.82842712475; // height of Atomic Gaussian, 2*sqrt(2), commonly used in the literature: Haque and Pande, DOI 10.1002/jcc.11307
static public final double alpha_pref = 2.41798793102; // taken from DOI 10.1002/jcc.11307
private double volume;
private Coordinates com;
private ArrayList atomicGaussians;
private ArrayList ppGaussians;
private ArrayList volumeGaussians; //exclusion and inclusion spheres
private ArrayList hydrogens;
public MolecularVolume(List atomicGaussiansInp,List ppGaussiansInp,List volGaussians,
List hydrogenCoords) {
this.volume = 0.0;
this.atomicGaussians = new ArrayList();
for(AtomicGaussian ag : atomicGaussiansInp) {
atomicGaussians.add(new AtomicGaussian(ag));
}
this.ppGaussians = new ArrayList();
for(PPGaussian pg : ppGaussiansInp) {
ppGaussians.add(new PPGaussian(pg));
}
this.hydrogens = new ArrayList();
for(Coordinates hydrogen : hydrogenCoords) {
this.hydrogens.add(hydrogen);
}
this.volumeGaussians = new ArrayList();
for(VolumeGaussian eg : volGaussians) {
this.volumeGaussians.add(new VolumeGaussian(eg));
}
this.calcCOM();
}
public void updateCOM() {
this.calcCOM();
}
private void updateAtomIndeces(List gaussians,int[] map) {
for(Gaussian3D gaussian:gaussians)
gaussian.updateAtomIndeces(map);
}
public void updateAtomIndeces(int[] map) {
updateAtomIndeces(ppGaussians,map);
updateAtomIndeces(atomicGaussians,map);
updateAtomIndeces(volumeGaussians,map);
}
public MolecularVolume(StereoMolecule mol) {
this.volume = 0.0;
this.hydrogens = new ArrayList();
this.volumeGaussians = new ArrayList();
this.calc(mol);
this.calcPPVolume(mol);
this.calcCOM();
}
public MolecularVolume(MolecularVolume original, Conformer conf) {
this(original);
update(conf);
}
public MolecularVolume(MolecularVolume original) {
this.volume = new Double(original.volume);
this.atomicGaussians = new ArrayList();
this.ppGaussians = new ArrayList();
this.volumeGaussians = new ArrayList();
for(AtomicGaussian ag : original.getAtomicGaussians()) {
this.atomicGaussians.add(new AtomicGaussian(ag));
}
for(PPGaussian pg : original.getPPGaussians()) {
this.ppGaussians.add(new PPGaussian(pg));
}
this.hydrogens = new ArrayList();
for(Coordinates hydrogen : original.hydrogens) {
this.hydrogens.add(new Coordinates(hydrogen));
}
for(VolumeGaussian eg : original.volumeGaussians) {
this.volumeGaussians.add(new VolumeGaussian(eg));
}
this.com = new Coordinates(original.com);
}
/**
* calculates the molecular Volume for a StereoMolecule with 3D coordinates
* @param mol
*/
private void calc(StereoMolecule mol) {
this.atomicGaussians = new ArrayList();
int nrOfAtoms = mol.getAllAtoms();
for (int i=0;i();
List ppPoints = new ArrayList();
IonizableGroupDetector detector = new IonizableGroupDetector(mol);
ppPoints.addAll(detector.detect());
ppPoints.addAll(PharmacophoreCalculator.getPharmacophorePoints(mol));
for(IPharmacophorePoint ppPoint : ppPoints )
ppGaussians.add(new PPGaussian(6,ppPoint));
}
/**
* calculates volume weighted center of mass of the molecular Volume
*/
private void calcCOM(){
double volume = 0.0;
double comX = 0.0;
double comY = 0.0;
double comZ = 0.0;
for(AtomicGaussian atGauss : this.atomicGaussians){
volume += atGauss.getVolume();
comX += atGauss.getCenter().x*atGauss.getVolume();
comY += atGauss.getCenter().y*atGauss.getVolume();
comZ += atGauss.getCenter().z*atGauss.getVolume();
}
for(VolumeGaussian volGauss : this.volumeGaussians){
volume += volGauss.getRole()*volGauss.getVolume();
comX += volGauss.getRole()*volGauss.getCenter().x*volGauss.getVolume();
comY += volGauss.getRole()*volGauss.getCenter().y*volGauss.getVolume();
comZ += volGauss.getRole()*volGauss.getCenter().z*volGauss.getVolume();
}
comX = comX/volume;
comY = comY/volume;
comZ = comZ/volume;
this.volume = volume;
this.com = new Coordinates(comX,comY,comZ);
}
public Coordinates getCOM() {
this.calcCOM();
return this.com;
}
public ArrayList getAtomicGaussians() {
return this.atomicGaussians;
}
public ArrayList getPPGaussians() {
return this.ppGaussians;
}
public ArrayList getVolumeGaussians() {
return this.volumeGaussians;
}
public ArrayList getHydrogens() {
return this.hydrogens;
}
private void updateHydrogens(StereoMolecule mol) {
int h = 0;
for(int i = mol.getAtoms();i gaussians, StereoMolecule mol) {
for(Gaussian3D gaussian : gaussians) {
gaussian.updateCoordinates(mol);
}
}
private void updateCoordinates(ArrayList gaussians, Conformer conf) {
for(Gaussian3D gaussian : gaussians) {
gaussian.updateCoordinates(conf);
}
}
public void translateToCOM(Coordinates com) {
for (AtomicGaussian ag : getAtomicGaussians()){
ag.getCenter().sub(com); //translate atomicGaussians. Moves center of mass to the origin.
}
for (PPGaussian pg : getPPGaussians()){
pg.getCenter().sub(com); //translate atomicGaussians. Moves center of mass to the origin.
}
for (VolumeGaussian vg : getVolumeGaussians()){
vg.translateRef(com.scaleC(-1.0)); //translate atomicGaussians. Moves center of mass to the origin.
}
for (Coordinates hydrogen : getHydrogens()){
hydrogen.sub(com); //translate atomicGaussians. Moves center of mass to the origin.
}
}
public String encodeFull() {
StringBuilder molVolString = new StringBuilder();
molVolString.append(Integer.toString(atomicGaussians.size()));
molVolString.append(" ");
for(AtomicGaussian ag : atomicGaussians) {
molVolString.append(ag.encode());
molVolString.append(" ");
}
molVolString.append(Integer.toString(ppGaussians.size()));
molVolString.append(" ");
for(PPGaussian pg : ppGaussians) {
molVolString.append(pg.encode().trim());
molVolString.append(" ");
}
molVolString.append(Integer.toString(volumeGaussians.size()));
molVolString.append(" ");
for(VolumeGaussian vg : volumeGaussians) {
molVolString.append(vg.encode());
molVolString.append(" ");
}
double[] hydrogenCoords = new double[3*hydrogens.size()];
for(int i=0;i referenceAtomicGaussians = reference.getAtomicGaussians();
ArrayList referencePPGaussians = reference.getPPGaussians();
ArrayList referenceVolGaussians = reference.getVolumeGaussians();
String[] splitString = string.split(" ");
double[] atomicGaussiansCoords = EncoderFloatingPointNumbers.decode(splitString[0]);
double[] ppGaussiansCoords = EncoderFloatingPointNumbers.decode(splitString[1]);
double[] ppGaussiansDirectionalities = EncoderFloatingPointNumbers.decode(splitString[2]);
double[] volumeGaussiansRefCoords = EncoderFloatingPointNumbers.decode(splitString[3]);
double[] volumeGaussiansShiftCoords = EncoderFloatingPointNumbers.decode(splitString[4]);
double[] hydrogensCoords = EncoderFloatingPointNumbers.decode(splitString[5]);
ArrayList atomicGaussians = new ArrayList();
ArrayList ppGaussians = new ArrayList();
ArrayList volumeGaussians = new ArrayList();
ArrayList hydrogens = new ArrayList();
int nrOfAtomicGaussians = atomicGaussiansCoords.length/3;
int nrOfHydrogens = hydrogensCoords.length/3;
int nrOfPPGaussians = ppGaussiansCoords.length/3;
int nrOfVolumeGaussians = volumeGaussiansRefCoords.length/3;
for(int i=0;i atomicGaussians = new ArrayList();
List ppGaussians = new ArrayList();
List volumeGaussians = new ArrayList();
List hydrogens = new ArrayList();
for(int i=firstIndex;i © 2015 - 2025 Weber Informatics LLC | Privacy Policy