com.actelion.research.chem.phesa.pharmacophore.AcceptorPoint Maven / Gradle / Ivy
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package com.actelion.research.chem.phesa.pharmacophore;
import java.util.ArrayList;
import java.util.List;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.Conformer;
import com.actelion.research.chem.interactionstatistics.InteractionSimilarityTable;
import com.actelion.research.chem.phesaflex.MathHelper;
public class AcceptorPoint implements IPharmacophorePoint {
private int acceptorAtom;
private List neighbours;
private Coordinates directionality;
private int interactionClass;
private Coordinates center;
private int acceptorID; //necessary to assign different directionalities to two acceptor points in sp2 oxygen
public AcceptorPoint(StereoMolecule mol, int a, List neighbours, int interactionClass) {
this(mol, a, neighbours, interactionClass, 0);
}
public AcceptorPoint(AcceptorPoint aP) {
acceptorAtom = aP.acceptorAtom;
neighbours = new ArrayList();
for(int neighbour : aP.neighbours) {
neighbours.add(neighbour);
}
directionality = new Coordinates(aP.directionality);
interactionClass = aP.interactionClass;
center = new Coordinates(aP.center);
acceptorID = aP.acceptorID;
}
public AcceptorPoint(StereoMolecule mol, int a, List neighbours, int interactionClass, int acceptorID) {
acceptorAtom = a;
this.neighbours = neighbours;
this.interactionClass = interactionClass;
this.acceptorID = acceptorID;
updateCoordinates(mol);
}
private AcceptorPoint(String ppString, StereoMolecule mol) {
decode(ppString,mol);
}
public static AcceptorPoint fromString(String ppString, StereoMolecule mol) {
return new AcceptorPoint(ppString,mol);
}
@Override
public void updateCoordinates(StereoMolecule mol) {
center = new Coordinates(mol.getAtomX(acceptorAtom),mol.getAtomY(acceptorAtom),mol.getAtomZ(acceptorAtom));
if(neighbours.size()==1) {
int aa1 = neighbours.get(0);
directionality = center.subC(mol.getCoordinates(aa1));
}
else if(neighbours.size()==2 && acceptorID!=0) {
int aa1 = neighbours.get(0);
Coordinates v1 = center.subC(mol.getCoordinates(aa1));
int aa2 = neighbours.get(1);
Coordinates v2 = mol.getCoordinates(aa2).subC(center);
Coordinates rotAxis = v1.cross(v2).unit();
double theta = acceptorID == 1 ? 45.0/180.0*Math.PI : -45.0/180.0*Math.PI;
directionality = v1.rotate(rotAxis, theta);
}
else if(neighbours.size()==3) {
int aa1 = neighbours.get(0);
int aa2 = neighbours.get(1);
int aa3 = neighbours.get(2);
Coordinates v1 = center.subC(mol.getCoordinates(aa1)).unit();
Coordinates v2 = center.subC(mol.getCoordinates(aa2)).unit();
Coordinates v3 = center.subC(mol.getCoordinates(aa3)).unit();
directionality = v3.add(v2).add(v1);
}
else {
int aa1 = neighbours.get(0);
int aa2 = neighbours.get(1);
Coordinates v1 = center.subC(mol.getCoordinates(aa1)).unit();
Coordinates v2 = center.subC(mol.getCoordinates(aa2)).unit();
directionality = v1.addC(v2);
}
directionality.unit();
// TODO Auto-generated method stub
}
@Override
public void updateCoordinates(Conformer conf) {
center = new Coordinates(conf.getX(acceptorAtom),conf.getY(acceptorAtom),conf.getZ(acceptorAtom));
if(neighbours.size()==1) {
int aa1 = neighbours.get(0);
directionality = center.subC(conf.getCoordinates(aa1));
}
else if(neighbours.size()==2 && acceptorID!=0) {
int aa1 = neighbours.get(0);
Coordinates v1 = center.subC(conf.getCoordinates(aa1));
int aa2 = neighbours.get(1);
Coordinates v2 = conf.getCoordinates(aa2).subC(center);
Coordinates rotAxis = v1.cross(v2).unit();
double theta = acceptorID == 1 ? 45.0/180.0*Math.PI : -45.0/180.0*Math.PI;
directionality = v1.rotate(rotAxis, theta);
}
else if(neighbours.size()==3) {
int aa1 = neighbours.get(0);
int aa2 = neighbours.get(1);
int aa3 = neighbours.get(2);
Coordinates v1 = center.subC(conf.getCoordinates(aa1)).unit();
Coordinates v2 = center.subC(conf.getCoordinates(aa2)).unit();
Coordinates v3 = center.subC(conf.getCoordinates(aa3)).unit();
directionality = v3.add(v2).add(v1);
}
else {
int aa1 = neighbours.get(0);
int aa2 = neighbours.get(1);
Coordinates v1 = center.subC(conf.getCoordinates(aa1)).unit();
Coordinates v2 = center.subC(conf.getCoordinates(aa2)).unit();
directionality = v1.addC(v2);
}
directionality.unit();
// TODO Auto-generated method stub
}
@Override
public Coordinates getCenter() {
return center;
}
@Override
public Coordinates getDirectionality() {
return directionality;
}
@Override
public String encode() {
StringBuilder molVolString = new StringBuilder();
molVolString.append("a");
molVolString.append(" ");
molVolString.append(Integer.toString(acceptorAtom));
molVolString.append(" ");
molVolString.append(Integer.toString(interactionClass));
molVolString.append(" ");
molVolString.append(Integer.toString(acceptorID));
molVolString.append(" ");
//molVolString.append(Integer.toString(neighbours.size()));
//molVolString.append(" ");
for(Integer neighbour : neighbours) {
molVolString.append(neighbour);
molVolString.append(" ");
}
return molVolString.toString().trim();
}
private void decode(String ppString, StereoMolecule mol) {
String[] strings = ppString.split(" ");
acceptorAtom = Integer.decode(strings[1]);
interactionClass = Integer.decode(strings[2]);
acceptorID = Integer.decode(strings[3]);
neighbours = new ArrayList();
for(int i=4;id
*
* d = A-AA1
*
*
*
*
*/
if(neighbours.size()==1) {
int aa1 = neighbours.get(0);
grad[3*acceptorAtom] = sim*di.x/3.0;
grad[3*acceptorAtom+1] = sim*di.y/3.0;
grad[3*acceptorAtom+2] = sim*di.z/3.0;
grad[3*aa1] = sim*-di.x/3.0;
grad[3*aa1+1] = sim*-di.y/3.0;
grad[3*aa1+2] = sim*-di.z/3.0;
}
/*
* d: directionality vector of lone pair
C1 v2: C1-C2
\ / v1: A-C2
\ v2 d / d is constructed by rotating v1 by the mount theta around the axis u that
\ / is perpendicular to v2 and v1 -> u = v1xv2
C2=======A d depends on C1,C2,A -> d(C1,C2,A)
/ v1 we therefore need to calculate the derivatives dd/dC1, dd/dC2, dd/dA
/ d = R(u,theta)*v1 theta is constant
/ * dd/dC1 = dR/du*du/dC1*v1+R*d(O4-O2)/dC1
C3 dd/dC1 = dR/du*du/dC2*v1 (since v1= A-C2 is not a function of C1
u = v1xv2
du/dC1 = dv2/dC1 x v1
*/
else if(neighbours.size()==2 && acceptorID!=0) { //sp2 oxygen
Coordinates centerCoords = new Coordinates(v[3*acceptorAtom],v[3*acceptorAtom+1],v[3*acceptorAtom+2]);
int c2 = neighbours.get(0);
Coordinates c2Coords = new Coordinates(v[3*c2],v[3*c2+1],v[3*c2+2]);
Coordinates v1 = centerCoords.subC(c2Coords);
int c1 = neighbours.get(1);
Coordinates c1Coords = new Coordinates(v[3*c1],v[3*c1+1],v[3*c1+2]);
Coordinates v2 = c1Coords.subC(centerCoords);
Coordinates u = v1.cross(v2).unit();
double theta = acceptorID == 1 ? 45.0/180.0*Math.PI : -45.0/180.0*Math.PI;
double[][] r = new double[3][3];
Coordinates[][] drdu = new Coordinates[3][3];
double[][] drdc1 = new double[3][3];
MathHelper.getRotMatrix(u, theta, r);
MathHelper.getRotMatrixDerivative(u, theta, drdu);
Coordinates dv2dc1 = new Coordinates(1,1,1);
Coordinates dudc1 = dv2dc1.cross(v1);
drdc1[0][0] = drdu[0][0].dot(dudc1);
drdc1[0][1] = drdu[0][1].dot(dudc1);
drdc1[0][2] = drdu[0][2].dot(dudc1);
drdc1[1][0] = drdu[1][0].dot(dudc1);
drdc1[1][1] = drdu[1][1].dot(dudc1);
drdc1[1][2] = drdu[1][2].dot(dudc1);
drdc1[2][0] = drdu[2][0].dot(dudc1);
drdc1[2][1] = drdu[2][2].dot(dudc1);
drdc1[2][2] = drdu[2][2].dot(dudc1);
Coordinates dddc1 = new Coordinates(drdc1[0][0]*v1.x+drdc1[0][1]*v1.y + drdc1[0][2]*v1.z, // dd/dc1
drdc1[1][0]*v1.x+drdc1[1][1]*v1.y + drdc1[2][1]*v1.z,
drdc1[2][0]*v1.x+drdc1[2][1]*v1.y + drdc1[2][2]*v1.z);
grad[3*c1] += sim*dddc1.x/3.0;
grad[3*c1+1] += sim*dddc1.y/3.0;
grad[3*c1+2] += sim*dddc1.z/3.0;
Coordinates dv1dc2 = new Coordinates(-1,-1,-1);
Coordinates dv2dc2 = dv1dc2;
Coordinates dudc2 = dv1dc2.cross(v2).add(dv2dc2.cross(v1));
double [][]drdc2 = drdc1;
drdc2[0][0] = drdu[0][0].dot(dudc2);
drdc2[0][1] = drdu[0][1].dot(dudc2);
drdc2[0][2] = drdu[0][2].dot(dudc2);
drdc2[1][0] = drdu[1][0].dot(dudc2);
drdc2[1][1] = drdu[1][1].dot(dudc2);
drdc2[1][2] = drdu[1][2].dot(dudc2);
drdc2[2][0] = drdu[2][0].dot(dudc2);
drdc2[2][1] = drdu[2][2].dot(dudc2);
drdc2[2][2] = drdu[2][2].dot(dudc2);
Coordinates dddc2 = new Coordinates(drdc1[0][0]*v1.x+drdc1[0][1]*v1.y + drdc1[0][2]*v1.z +
r[0][0]*dv1dc2.x + r[0][1]*dv1dc2.y + r[0][2]*dv1dc2.z,
drdc1[1][0]*v1.x+drdc1[1][1]*v1.y + drdc1[1][2]*v1.z +
r[1][0]*dv1dc2.x + r[1][1]*dv1dc2.y + r[1][2]*dv1dc2.z,
drdc1[2][0]*v1.x+drdc1[2][1]*v1.y + drdc1[2][2]*v1.z +
r[2][0]*dv1dc2.x + r[2][1]*dv1dc2.y + r[2][2]*dv1dc2.z);
grad[3*c2] += sim*dddc2.x/3.0; //directionality is scaled by 1/3
grad[3*c2+1] += sim*dddc2.y/3.0;
grad[3*c2+2] += sim*dddc2.z/3.0;
Coordinates dv1da = dv2dc1;
Coordinates duda = dv1da.cross(v2);
double [][]drda = drdc1;
drda[0][0] = drdu[0][0].dot(duda);
drda[0][1] = drdu[0][1].dot(duda);
drda[0][2] = drdu[0][2].dot(duda);
drda[1][0] = drdu[1][0].dot(duda);
drda[1][1] = drdu[1][1].dot(duda);
drda[1][2] = drdu[1][2].dot(duda);
drda[2][0] = drdu[2][0].dot(duda);
drda[2][1] = drdu[2][2].dot(duda);
drda[2][2] = drdu[2][2].dot(duda);
Coordinates ddda = new Coordinates(drda[0][0]*v1.x+drda[0][1]*v1.y + drda[0][2]*v1.z +
r[0][0]*dv1da.x + r[0][1]*dv1da.y + r[0][2]*dv1da.z,
drda[1][0]*v1.x+drda[1][1]*v1.y + drda[1][2]*v1.z +
r[1][0]*dv1da.x + r[1][1]*dv1da.y + r[1][2]*dv1da.z,
drda[2][0]*v1.x+drda[2][1]*v1.y + drda[2][2]*v1.z +
r[2][0]*dv1da.x + r[2][1]*dv1da.y + r[2][2]*dv1da.z);
grad[3*acceptorAtom] += sim*ddda.x/3.0;
grad[3*acceptorAtom+1] += sim*ddda.y/3.0;
grad[3*acceptorAtom+2] += sim*ddda.z/3.0;
}
else if(neighbours.size()==3) {
int aa1 = neighbours.get(0);
int aa2 = neighbours.get(1);
int aa3 = neighbours.get(2);
grad[3*acceptorAtom] += sim*3*di.x/3.0;
grad[3*acceptorAtom+1] += sim*3*di.y/3.0;
grad[3*acceptorAtom+2] += sim*3*di.z/3.0;
grad[3*aa1] += sim*-di.x/3.0;
grad[3*aa1+1] += sim*-di.y/3.0;
grad[3*aa1+2] += sim*-di.z/3.0;
grad[3*aa2] += sim*-di.x/3.0;
grad[3*aa2+1] += sim*-di.y/3.0;
grad[3*aa2+2] += sim*-di.z/3.0;
grad[3*aa3] += sim*-di.x/3.0;
grad[3*aa3+1] += sim*-di.y/3.0;
grad[3*aa3+2] += sim*-di.z/3.0;
}
else { //two neighbours, sp3 acceptor
int aa1 = neighbours.get(0);
int aa2 = neighbours.get(1);
grad[3*acceptorAtom] += sim*2*di.x/3.0;
grad[3*acceptorAtom+1] += sim*2*di.y/3.0;
grad[3*acceptorAtom+2] += sim*2*di.z/3.0;
grad[3*aa1] += sim*-di.x/3.0;
grad[3*aa1+1] += sim*-di.y/3.0;
grad[3*aa1+2] += sim*-di.z/3.0;
grad[3*aa2] += sim*-di.x/3.0;
grad[3*aa2+1] += sim*-di.y/3.0;
grad[3*aa2+2] += sim*-di.z/3.0;
}
}
@Override
public void updateAtomIndeces(int[] map) {
acceptorAtom = map[acceptorAtom];
for(int i=0;i © 2015 - 2025 Weber Informatics LLC | Privacy Policy