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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
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* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
package com.actelion.research.chem.forcefield.mmff;
import java.util.ArrayList;
import java.util.List;
/**
* Out of plane energy term class. This energy term represents the
* out of plane energy associated with four atoms:
*
* A1
* /
* A2--AC
* \
* A3
*
* Where AC is the central atom and A1, A2 and A3 are each connected to
* AC.
*/
public class OutOfPlane implements EnergyTerm {
int ac;
int a1;
int a2;
int a3;
double koop;
/**
* Construct a new out of plane energy term.
* @param table The tables parameter object.
* @param mol The molecule.
* @param a1 Index of atom 1 in mol.
* @param a2 Index of atom 2 (the central atom) in mol.
* @param a3 Index of atom 3 in mol.
*/
public OutOfPlane(Tables table, MMFFMolecule mol, int ac, int a1,
int a2, int a3) {
this.ac = ac; // j
this.a1 = a1; // i
this.a2 = a2; // k
this.a3 = a3; // l
koop = table.oop.getKoop(mol, ac, a1, a2, a3);
}
public double getKoop() {
return koop;
}
/**
* Calculates the out of plane energy.
* @param pos The atoms current positions array.
* @return The energy.
*/
@Override
public double getEnergy(double[] pos) {
Vector3 rji = new Vector3(pos, ac, a1).normalise();
Vector3 rjk = new Vector3(pos, ac, a2).normalise();
Vector3 rjl = new Vector3(pos, ac, a3).normalise();
Vector3 n = rji.cross(rjk).normalise();
double chi = Constants.RAD2DEG * Math.asin(n.dot(rjl));
double c2 = Constants.MDYNE_A_TO_KCAL_MOL * Constants.DEG2RAD
* Constants.DEG2RAD;
return 0.5 * c2 * koop * chi * chi;
}
/**
* Calculates the gradient and adds it to the gradients array.
* @param pos The atoms current positions array.
* @param grad the atoms current gradients array.
*/
@Override
public void getGradient(double[] pos, double[] grad) {
Vector3 rji = new Vector3(pos, ac, a1);
Vector3 rjk = new Vector3(pos, ac, a2);
Vector3 rjl = new Vector3(pos, ac, a3);
final double dji = rji.length();
final double djk = rjk.length();
final double djl = rjl.length();
rji = rji.normalise();
rjk = rjk.normalise();
rjl = rjl.normalise();
Vector3 n = rji.negate().cross(rjk).normalise();
final double c2 = Constants.MDYNE_A_TO_KCAL_MOL * Constants.DEG2RAD
* Constants.DEG2RAD;
double sinChi = rjl.dot(n);
double cosChiSq = 1.0 - sinChi*sinChi;
double cosChi = Math.max(cosChiSq > 0.0
? Math.sqrt(cosChiSq) : 0.0, 1.0e-8);
double chi = Constants.RAD2DEG * Math.asin(sinChi);
double cosTheta = rji.dot(rjk);
double sinThetaSq = Math.max(1.0 - cosTheta * cosTheta, 1.0e-8);
double sinTheta = Math.max(sinThetaSq > 0.0
? Math.sqrt(sinThetaSq) : 0.0, 1.0e-8);
double dE_dChi = Constants.RAD2DEG * c2 * koop * chi;
Vector3 t1 = rjl.cross(rjk);
Vector3 t2 = rji.cross(rjl);
Vector3 t3 = rjk.cross(rji);
double term1 = cosChi * sinTheta;
double term2 = sinChi / (cosChi * sinThetaSq);
double[] tg1 = new double[]{
(t1.x/term1 - (rji.x - rjk.x*cosTheta) * term2) / dji,
(t1.y/term1 - (rji.y - rjk.y*cosTheta) * term2) / dji,
(t1.z/term1 - (rji.z - rjk.z*cosTheta) * term2) / dji};
double[] tg3 = new double[]{
(t2.x/term1 - (rjk.x - rji.x*cosTheta) * term2) / djk,
(t2.y/term1 - (rjk.y - rji.y*cosTheta) * term2) / djk,
(t2.z/term1 - (rjk.z - rji.z*cosTheta) * term2) / djk};
double[] tg4 = new double[]{
(t3.x/term1 - rjl.x*sinChi/cosChi) / djl,
(t3.y/term1 - rjl.y*sinChi/cosChi) / djl,
(t3.z/term1 - rjl.z*sinChi/cosChi) / djl};
for (int i=0; i<3; i++) {
grad[3*a1 + i] += dE_dChi * tg1[i];
grad[3*ac + i] += -dE_dChi * (tg1[i] + tg3[i] + tg4[i]);
grad[3*a2 + i] += dE_dChi * tg3[i];
grad[3*a3 + i] += dE_dChi * tg4[i];
}
}
/**
* Checks if this OutOfPlane's atoms are the same as a given set of 4
* atoms, it checks all possible permutations of a1, a2 and a3.
* @param ac The central atom.
* @param a1 Neighbouring atom 1.
* @param a2 Neighbouring atom 2.
* @param a3 Neighbouring atom 3.
* @return True if this OutOfPlane has the same permutation of
* neighbouring atoms as those provided.
*/
public boolean equals(int ac, int a1, int a2, int a3) {
return this.ac == ac
&& (this.a1 == a1 && this.a2 == a2 && this.a3 == a3
|| this.a1 == a1 && this.a2 == a3 && this.a3 == a2
|| this.a1 == a2 && this.a2 == a1 && this.a3 == a3
|| this.a1 == a2 && this.a2 == a3 && this.a3 == a1
|| this.a1 == a3 && this.a2 == a1 && this.a3 == a2
|| this.a1 == a3 && this.a2 == a2 && this.a3 == a1);
}
/**
* Checks if this OutOfPlane term is exactly equal to a given set of
* four atoms.
* @param ac The central atom.
* @param a1 Neighbouring atom 1.
* @param a2 Neighbouring atom 2.
* @param a3 Neighbouring atom 3.
* @return True if the out of plane atoms are the same as the
* provided atoms.
*/
public boolean exactly(int ac, int a1, int a2, int a3) {
return this.ac == ac
&& this.a1 == a1 && this.a2 == a2 && this.a3 == a3;
}
/**
* Finds all out of plane angles in the current molecule.
* @param t The tables parameter object.
* @param mol The molecule to search in.
* @return An array of OutOfPlane angles.
*/
public static List findIn(Tables t, MMFFMolecule mol) {
ArrayList oops = new ArrayList();
for (int ac=0; ac findIn(MMFFMolecule mol) {
return findIn(ForceFieldMMFF94.table(ForceFieldMMFF94.MMFF94), mol);
}
}