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/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
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package com.actelion.research.chem.conf.torsionstrain;
import java.text.DecimalFormat;
import java.util.Arrays;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.Conformer;
import com.actelion.research.chem.forcefield.mmff.Vector3;
import com.actelion.research.chem.interactionstatistics.SplineFunction;
import com.actelion.research.chem.potentialenergy.PotentialEnergyTerm;
/**
* Represents a torsion potential as a function of the angle, derived from statistical torsion distributions from the COD/CSD
* The dihedral angle is defined by a atom sequence of 4 atoms. If a core atom is sp3 hybridized and has two neighbours of the same symmetry rank,
* then the torsion angle has to be defined by a virtual atom, occupying the position of the hypothetical third atom
*
*/
public class StatisticalTorsionTerm implements PotentialEnergyTerm {
private static final double EPS = 0.00001;
public double rik2;
private Conformer conf;
private int atoms[];
private int rearAtoms[][]; //to define virtual torsion atoms
//Statistics
private final SplineFunction f;
private StatisticalTorsionTerm(Conformer conf, int[] atoms, SplineFunction f) {
this.conf = conf;
this.f = f;
this.atoms = atoms;
assessRearAtoms();
}
private void assessRearAtoms() {
StereoMolecule mol = conf.getMolecule();
rearAtoms = new int[2][];
if(atoms[0]==-1) {
rearAtoms[0] = new int[2];
int index = 0;
for(int i=0;i 0.0) ? Math.sqrt(sinPhiSq) : 0.0);
double sinTerm = -dEdPhi * (Math.abs(sinPhi) < 0.00001
? (1.0 / cosPhi) : (1.0 / sinPhi));
double[] dCos_dT = new double[]{
1.0 / d[0] * (t[1].x - cosPhi * t[0].x),
1.0 / d[0] * (t[1].y - cosPhi * t[0].y),
1.0 / d[0] * (t[1].z - cosPhi * t[0].z),
1.0 / d[1] * (t[0].x - cosPhi * t[1].x),
1.0 / d[1] * (t[0].y - cosPhi * t[1].y),
1.0 / d[1] * (t[0].z - cosPhi * t[1].z)
};
if(rearAtoms!=null) {
if(rearAtoms[0]!=null) { // chain rule, take into account derivate of virtual atom wrt rear atoms
double derX = sinTerm * (dCos_dT[2] * r[1].y - dCos_dT[1] * r[1].z);
double derY = sinTerm * (dCos_dT[0] * r[1].z - dCos_dT[2] * r[1].x);
double derZ = sinTerm * (dCos_dT[1] * r[1].x - dCos_dT[0] * r[1].y);
gradient[3*rearAtoms[0][0]] -= derX;
gradient[3*rearAtoms[0][0]+1] -= derY;
gradient[3*rearAtoms[0][0]+2] -= derZ;
gradient[3*rearAtoms[0][1]] -= derX;
gradient[3*rearAtoms[0][1]+1] -= derY;
gradient[3*rearAtoms[0][1]+2] -= derZ;
}
else {
gradient[3*a1+0] += sinTerm * (dCos_dT[2] * r[1].y - dCos_dT[1] * r[1].z);
gradient[3*a1+1] += sinTerm * (dCos_dT[0] * r[1].z - dCos_dT[2] * r[1].x);
gradient[3*a1+2] += sinTerm * (dCos_dT[1] * r[1].x - dCos_dT[0] * r[1].y);
}
}
gradient[3*a2+0] += sinTerm * (dCos_dT[1] * (r[1].z - r[0].z)
+ dCos_dT[2] * (r[0].y - r[1].y)
+ dCos_dT[4] * (-r[3].z)
+ dCos_dT[5] * (r[3].y));
gradient[3*a2+1] += sinTerm * (dCos_dT[0] * (r[0].z - r[1].z)
+ dCos_dT[2] * (r[1].x - r[0].x)
+ dCos_dT[3] * (r[3].z)
+ dCos_dT[5] * (-r[3].x));
gradient[3*a2+2] += sinTerm * (dCos_dT[0] * (r[1].y - r[0].y)
+ dCos_dT[1] * (r[0].x - r[1].x)
+ dCos_dT[3] * (-r[3].y)
+ dCos_dT[4] * (r[3].x));
gradient[3*a3+0] += sinTerm * (dCos_dT[1] * (r[0].z)
+ dCos_dT[2] * (-r[0].y)
+ dCos_dT[4] * (r[3].z - r[2].z)
+ dCos_dT[5] * (r[2].y - r[3].y));
gradient[3*a3+1] += sinTerm * (dCos_dT[0] * (-r[0].z)
+ dCos_dT[2] * (r[0].x)
+ dCos_dT[3] * (r[2].z - r[3].z)
+ dCos_dT[5] * (r[3].x - r[2].x));
gradient[3*a3+2] += sinTerm * (dCos_dT[0] * (r[0].y)
+ dCos_dT[1] * (-r[0].x)
+ dCos_dT[3] * (r[3].y - r[2].y)
+ dCos_dT[4] * (r[2].x - r[3].x));
if(rearAtoms!=null) {
if(rearAtoms[1]!=null) {
double derX = sinTerm * (dCos_dT[4] * r[2].z - dCos_dT[5] * r[2].y);
double derY = sinTerm * (dCos_dT[5] * r[2].x - dCos_dT[3] * r[2].z);
double derZ = sinTerm * (dCos_dT[3] * r[2].y - dCos_dT[4] * r[2].x);
gradient[3*rearAtoms[1][0]] -= derX;
gradient[3*rearAtoms[1][0]+1] -= derY;
gradient[3*rearAtoms[1][0]+2] -= derZ;
gradient[3*rearAtoms[1][1]] -= derX;
gradient[3*rearAtoms[1][1]+1] -= derY;
gradient[3*rearAtoms[1][1]+2] -= derZ;
}
else {
gradient[3*a4+0] += sinTerm * (dCos_dT[4] * r[2].z - dCos_dT[5] * r[2].y);
gradient[3*a4+1] += sinTerm * (dCos_dT[5] * r[2].x - dCos_dT[3] * r[2].z);
gradient[3*a4+2] += sinTerm * (dCos_dT[3] * r[2].y - dCos_dT[4] * r[2].x);
}
}
}
@Override
public final double getFGValue(final double[] gradient) {
Coordinates c1,c2,c3,c4;
int a1 = atoms[0];
int a2 = atoms[1];
int a3 = atoms[2];
int a4 = atoms[3];
if(a1==-1) {
Coordinates c = conf.getCoordinates(a2);
Coordinates c1a = conf.getCoordinates(rearAtoms[0][0]);
Coordinates c2a = conf.getCoordinates(rearAtoms[0][1]);
Coordinates v1 = c1a.subC(c);
Coordinates v2 = c2a.subC(c);
c1 = v1.addC(v2);
c1.scale(-1.0);
}
else {
c1 = conf.getCoordinates(a1);
}
if(a4==-1) {
Coordinates c = conf.getCoordinates(a3);
Coordinates c1a = conf.getCoordinates(rearAtoms[1][0]);
Coordinates c2a = conf.getCoordinates(rearAtoms[1][1]);
Coordinates v1 = c1a.subC(c);
Coordinates v2 = c2a.subC(c);
c4 = v1.addC(v2);
c4.scale(-1.0);
}
else {
c4 = conf.getCoordinates(a4);
}
c2 = conf.getCoordinates(atoms[1]);
c3 = conf.getCoordinates(atoms[2]);
double dihedral = Coordinates.getDihedral(c1, c2, c3, c4);
if(dihedral<0.0)
dihedral+=2*Math.PI;
double[] res = f.getFGValue(360.0*dihedral/2*Math.PI);
double e = res[0];
double dEdPhi = res[1];
getCartesianTorsionGradient(atoms, conf,gradient, dEdPhi,new Coordinates[] {c1,c2,c3,c4}, rearAtoms);
return e;
}
}
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