/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2005-2007 Violeta Labarta <vlabarta@users.sf.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.modeling.forcefield;
import java.util.Map;
import javax.vecmath.GMatrix;
import javax.vecmath.GVector;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.descriptors.atomic.BondsToAtomDescriptor;
import org.openscience.cdk.qsar.result.IntegerResult;
/**
* MMFF94 Electrostatic Interactions energy. Include function and derivatives.
*
*@author vlabarta
*@cdk.created May 13, 2005
*@cdk.module forcefield
* @cdk.githash
*/
public class ElectrostaticInteractions {
String functionShape = " Electrostatic Interactions ";
double mmff94SumEQ = 0;
GVector gradientMMFF94SumEQ = null;
GVector order2ndErrorApproximateGradientMMFF94SumEQ = null;
GVector order5thErrorApproximateGradientMMFF94SumEQ = null;
GMatrix hessianMMFF94SumEQ = null;
double[] forHessian = null;
double[][] dR = null; // internuclear separation first order derivative respect to atoms coordinates
double[][][] ddR = null; // internuclear separation second order derivative respect to atoms coordinates
IAtomicDescriptor shortestPathBetweenTwoAtoms = new BondsToAtomDescriptor();
Object[] params = {Integer.valueOf(0)};
int electrostaticInteractionNumber;
int[][] electrostaticInteractionAtomPosition = null;
double[] r = null; // internuclear separation in Angstroms.
double[] qi = null;
double[] qj = null;
double delta = 0.05; //electrostatic buffering constant.
double n = 1;
double D = 1.0;
double[] iQ = null;
double electrostatic14interactionsScale = 0.75; // Scale factor for 1-4 interactions. To take in the future from mmff94.prm files.
/**
* Constructor for the ElectrostaticInteractions object
*/
public ElectrostaticInteractions() {}
/**
* Set CCG Electrostatic parameters for the molecule.
*
*
*@param molecule The molecule like an AtomContainer object.
*@param parameterSet MMFF94 parameters set
*@exception Exception Description of the Exception
*/
public void setMMFF94ElectrostaticParameters(IAtomContainer molecule, Map parameterSet) throws Exception {
//distances = wnd.getShortestPathLengthBetweenAtoms((AtomContainer) molecule);
//logger.debug("molecule.getAtomCount() : " + molecule.getAtomCount());
//logger.debug("molecule.getBondCount() : " + molecule.getBondCount());
if (molecule.getAtomCount() == 12 & molecule.getBondCount() == 11) {
molecule.getAtom(3).setCharge(Double.valueOf(1.0));
molecule.getAtom(8).setCharge(Double.valueOf(1.0));
}
electrostaticInteractionNumber = 0;
for (int i=0; i<molecule.getAtomCount(); i++) {
for (int j=i+1; j<molecule.getAtomCount(); j++) {
params[0] = Integer.valueOf(j);
shortestPathBetweenTwoAtoms.setParameters(params);
//if (distances[molecule.getAtomNumber(molecule.getAtomAt(i))][molecule.getAtomNumber(molecule.getAtomAt(j))]>2) {
if (((IntegerResult)shortestPathBetweenTwoAtoms.calculate(molecule.getAtom(i),molecule).getValue()).intValue()>2){
electrostaticInteractionNumber += 1;
}
}
}
//logger.debug("electrostaticInteractionNumber : " + electrostaticInteractionNumber);
qi = new double[electrostaticInteractionNumber];
qj = new double[electrostaticInteractionNumber];
r = new double[electrostaticInteractionNumber];
iQ = new double[electrostaticInteractionNumber];
electrostaticInteractionAtomPosition = new int[electrostaticInteractionNumber][];
int l = -1;
for (int i=0; i<molecule.getAtomCount(); i++) {
for (int j=i+1; j<molecule.getAtomCount(); j++) {
params[0] = Integer.valueOf(j);
shortestPathBetweenTwoAtoms.setParameters(params);
//if (distances[molecule.getAtomNumber(molecule.getAtomAt(i))][molecule.getAtomNumber(molecule.getAtomAt(j))]>2) {
if (((IntegerResult)shortestPathBetweenTwoAtoms.calculate(molecule.getAtom(i),molecule).getValue()).intValue()>2){
l += 1;
qi[l]= molecule.getAtom(i).getCharge();
qj[l]= molecule.getAtom(j).getCharge();
//logger.debug("qi[" + l + "] = " + qi[l] + ", qj[" + l + "] = " + qj[l]);
if (((IntegerResult)shortestPathBetweenTwoAtoms.calculate(molecule.getAtom(i),molecule).getValue()).intValue()==3){
iQ[l] = electrostatic14interactionsScale;
} else {
iQ[l] = 1;
}
electrostaticInteractionAtomPosition[l] = new int[2];
electrostaticInteractionAtomPosition[l][0] = i;
electrostaticInteractionAtomPosition[l][1] = j;
//logger.debug("electrostaticInteractionAtomPosition " + l + " : " + electrostaticInteractionAtomPosition[l][0] + ", " + electrostaticInteractionAtomPosition[l][1]);
}
}
}
}
/**
* Calculate the internuclear separation Rij
*
*@param coords3d Current molecule coordinates.
*/
public void setInternuclearSeparation(GVector coords3d) {
for (int l = 0; l < electrostaticInteractionNumber; l++) {
r[l] = ForceFieldTools.distanceBetweenTwoAtomsFrom3xNCoordinates(coords3d, electrostaticInteractionAtomPosition[l][0], electrostaticInteractionAtomPosition[l][1]);
//logger.debug("r[" + l + "]= " + r[l]);
}
}
/**
* Get the internuclear separation values (Rij).
*
*@return Internuclear separation values.
*/
public double[] getInternuclearSeparation() {
return r;
}
/**
* Evaluate the MMFF94 Electrostatic interaction energy.
*
*@param coords3d Current molecule coordinates.
*@return MMFF94 Electrostatic interaction term value.
*/
public double functionMMFF94SumEQ(GVector coords3d) {
setInternuclearSeparation(coords3d);
mmff94SumEQ = 0;
for (int l = 0; l < electrostaticInteractionNumber; l++) {
mmff94SumEQ = mmff94SumEQ + iQ[l] * 332.0716 * qi[l] * qj[l] / (D * Math.pow(r[l] + delta, n));
//logger.debug("mmff94SumEQ = " + mmff94SumEQ);
}
//logger.debug("mmff94SumEQ = " + mmff94SumEQ);
return mmff94SumEQ;
}
/**
* Calculate the internuclear separation (Rij) first derivative respect to the cartesian coordinates of the atoms.
*
*@param coord3d Current molecule coordinates.
*/
public void setInternuclearSeparationFirstOrderDerivative(GVector coord3d) {
dR = new double[coord3d.getSize()][];
setInternuclearSeparation(coord3d);
Double forAtomNumber = null;
int atomNumber = 0;
int coordinate;
for (int i = 0; i < dR.length; i++) {
dR[i] = new double[electrostaticInteractionNumber];
forAtomNumber = new Double(i/3);
coordinate = i % 3;
//logger.debug("coordinate = " + coordinate);
atomNumber = forAtomNumber.intValue();
//logger.debug("atomNumber = " + atomNumber);
for (int j = 0; j < electrostaticInteractionNumber; j++) {
if ((electrostaticInteractionAtomPosition[j][0] == atomNumber) | (electrostaticInteractionAtomPosition[j][1] == atomNumber)) {
//logger.debug("atomNumber, r[" + j + "] = " + r[j]);
switch (coordinate) {
//x-coordinate
case 0: dR[i][j] = (coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][0]) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][1])) / r[j];
//logger.debug("xi-xj = " + (coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][0]) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][1])));
break;
//y-coordinate
case 1: dR[i][j] = (coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][0] + 1) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][1] + 1)) / r[j];
//logger.debug("xi-xj = " + (coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][0]) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][1])));
break;
//z-coordinate
case 2: dR[i][j] = (coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][0] + 2) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][1] + 2)) / r[j];
//logger.debug("xi-xj = " + (coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][0]) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[j][1])));
break;
}
if (electrostaticInteractionAtomPosition[j][1] == atomNumber) {
dR[i][j] = (-1) * dR[i][j];
}
} else {
dR[i][j] = 0;
}
//logger.debug("electrostaticInteraction " + j + " : " + "dR[" + i + "][" + j + "] = " + dR[i][j]);
}
}
}
/**
* Get the internuclear separation first order derivative respect to the cartesian coordinates of the atoms.
*
*@return Internuclear separation first order derivative value [dimension(3xN)] [vdW interaction number]
*/
public double[][] getInternuclearSeparationFirstDerivative() {
return dR;
}
/**
* Set the gradient of the MMFF94 Electrostatic interaction term.
*
*
*@param coords3d Current molecule coordinates.
*/
public void setGradientMMFF94SumEQ(GVector coords3d) {
gradientMMFF94SumEQ = new GVector(coords3d.getSize());
setInternuclearSeparation(coords3d);
setInternuclearSeparationFirstOrderDerivative(coords3d);
double sumGradientEQ;
for (int i = 0; i < gradientMMFF94SumEQ.getSize(); i++) {
sumGradientEQ = 0;
for (int l = 0; l < electrostaticInteractionNumber; l++) {
sumGradientEQ = sumGradientEQ + ((-332.0716 * qi[l] * qj[l] * n)/(D * Math.pow(r[l] + delta, n+1))) * dR[i][l];
}
gradientMMFF94SumEQ.setElement(i, sumGradientEQ);
}
//logger.debug("gradientMMFF94SumEQ = " + gradientMMFF94SumEQ);
}
/**
* Get the gradient of the MMFF94 Electrostatic interaction term.
*
*
*@return MMFF94 Electrostatic interaction gradient value.
*/
public GVector getGradientMMFF94SumEQ() {
return gradientMMFF94SumEQ;
}
/**
* Evaluate a 2nd order error approximation of the gradient, for the Electrostatic interaction term, given the atoms
* coordinates
*
*@param coord3d Current molecule coordinates.
*/
/* public void set2ndOrderErrorApproximateGradientMMFF94SumEQ(GVector coord3d) {
order2ndErrorApproximateGradientMMFF94SumEQ = new GVector(coord3d.getSize());
double sigma = Math.pow(0.000000000000001,0.33);
GVector xplusSigma = new GVector(coord3d.getSize());
GVector xminusSigma = new GVector(coord3d.getSize());
for (int m = 0; m < order2ndErrorApproximateGradientMMFF94SumEQ.getSize(); m++) {
xplusSigma.set(coord3d);
xplusSigma.setElement(m,coord3d.getElement(m) + sigma);
xminusSigma.set(coord3d);
xminusSigma.setElement(m,coord3d.getElement(m) - sigma);
order2ndErrorApproximateGradientMMFF94SumEQ.setElement(m,(functionMMFF94SumEQ(xplusSigma) - functionMMFF94SumEQ(xminusSigma)) / (2 * sigma));
}
//logger.debug("order2ndErrorApproximateGradientMMFF94SumEQ : " + order2ndErrorApproximateGradientMMFF94SumEQ);
}
*/
/**
* Get the 2nd order error approximate gradient for the Electrostatic interaction term.
*
*
*@return Electrostatic interaction 2nd order error approximate gradient value
*/
/* public GVector get2ndOrderErrorApproximateGradientMMFF94SumEQ() {
return order2ndErrorApproximateGradientMMFF94SumEQ;
}
*/
/**
* Evaluate a 5th order error approximation of the gradient, for the Electrostatic interaction term, given the atoms
* coordinates
*
*@param coords3d Current molecule coordinates.
*/
/* public void set5thOrderErrorApproximateGradientMMFF94SumEQ(GVector coord3d) {
order5thErrorApproximateGradientMMFF94SumEQ = new GVector(coord3d.getSize());
double sigma = Math.pow(0.000000000000001,0.2);
GVector xplusSigma = new GVector(coord3d.getSize());
GVector xminusSigma = new GVector(coord3d.getSize());
GVector xplus2Sigma = new GVector(coord3d.getSize());
GVector xminus2Sigma = new GVector(coord3d.getSize());
for (int m=0; m < order5thErrorApproximateGradientMMFF94SumEQ.getSize(); m++) {
xplusSigma.set(coord3d);
xplusSigma.setElement(m,coord3d.getElement(m) + sigma);
xminusSigma.set(coord3d);
xminusSigma.setElement(m,coord3d.getElement(m) - sigma);
xplus2Sigma.set(coord3d);
xplus2Sigma.setElement(m,coord3d.getElement(m) + 2 * sigma);
xminus2Sigma.set(coord3d);
xminus2Sigma.setElement(m,coord3d.getElement(m) - 2 * sigma);
order5thErrorApproximateGradientMMFF94SumEQ.setElement(m, (8 * (functionMMFF94SumEQ(xplusSigma) - functionMMFF94SumEQ(xminusSigma)) - (functionMMFF94SumEQ(xplus2Sigma) - functionMMFF94SumEQ(xminus2Sigma))) / (12 * sigma));
}
//logger.debug("order5thErrorApproximateGradientMMFF94SumEQ : " + order5thErrorApproximateGradientMMFF94SumEQ);
}
*/
/**
* Get the 5th order error approximate gradient for the Electrostatic interaction term.
*
*@return Electrostatic interaction 5th order error approximate gradient value.
*/
/* public GVector get5OrderApproximateGradientMMFF94SumEQ() {
return order5thErrorApproximateGradientMMFF94SumEQ;
}
*/
/**
* Calculate the internuclear separation second derivative respect to the cartesian coordinates of the atoms.
*
*@param coord3d Current molecule coordinates.
*/
public void setInternuclearSeparationSecondDerivative(GVector coord3d) {
ddR = new double[coord3d.getSize()][][];
Double forAtomNumber = null;
int atomNumberi;
int atomNumberj;
int coordinatei;
int coordinatej;
double ddR1=0; // ddR[i][j][k] = ddR1 - ddR2
double ddR2=0;
setInternuclearSeparationFirstOrderDerivative(coord3d);
for (int i=0; i<coord3d.getSize(); i++) {
ddR[i] = new double[coord3d.getSize()][];
forAtomNumber = new Double(i/3);
atomNumberi = forAtomNumber.intValue();
//logger.debug("atomNumberi = " + atomNumberi);
coordinatei = i % 3;
//logger.debug("coordinatei = " + coordinatei);
for (int j=0; j<coord3d.getSize(); j++) {
ddR[i][j] = new double[electrostaticInteractionNumber];
forAtomNumber = new Double(j/3);
atomNumberj = forAtomNumber.intValue();
//logger.debug("atomNumberj = " + atomNumberj);
coordinatej = j % 3;
//logger.debug("coordinatej = " + coordinatej);
//logger.debug("atomj : " + molecule.getAtomAt(atomNumberj));
for (int k=0; k < electrostaticInteractionNumber; k++) {
if ((electrostaticInteractionAtomPosition[k][0] == atomNumberj) | (electrostaticInteractionAtomPosition[k][1] == atomNumberj)) {
if ((electrostaticInteractionAtomPosition[k][0] == atomNumberi) | (electrostaticInteractionAtomPosition[k][1] == atomNumberi)) {
// ddR1
if (electrostaticInteractionAtomPosition[k][0] == atomNumberj) {
ddR1 = 1;
}
if (electrostaticInteractionAtomPosition[k][1] == atomNumberj) {
ddR1 = -1;
}
if (electrostaticInteractionAtomPosition[k][0] == atomNumberi) {
ddR1 = ddR1 * 1;
}
if (electrostaticInteractionAtomPosition[k][1] == atomNumberi) {
ddR1 = ddR1 * (-1);
}
ddR1 = ddR1 / r[k];
// ddR2
switch (coordinatej) {
case 0: ddR2 = (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0]) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1]));
//logger.debug("OK: d1 x");
break;
case 1: ddR2 = (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0] + 1) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1] + 1));
//logger.debug("OK: d1 y");
break;
case 2: ddR2 = (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0] + 2) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1] + 2));
//logger.debug("OK: d1 z");
break;
}
if (electrostaticInteractionAtomPosition[k][1] == atomNumberj) {
ddR2 = (-1) * ddR2;
//logger.debug("OK: bond 1");
}
switch (coordinatei) {
case 0: ddR2 = ddR2 * (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0]) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1]));
//logger.debug("OK: have d2 x");
break;
case 1: ddR2 = ddR2 * (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0] + 1) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1] + 1));
//logger.debug("OK: have d2 y");
break;
case 2: ddR2 = ddR2 * (coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][0] + 2) - coord3d.getElement(3 * electrostaticInteractionAtomPosition[k][1] + 2));
//logger.debug("OK: have d2 z");
break;
}
if (electrostaticInteractionAtomPosition[k][1] == atomNumberi) {
ddR2 = (-1) * ddR2;
//logger.debug("OK: d2 bond 1");
}
ddR2 = ddR2 / Math.pow(r[k],2);
// ddR[i][j][k]
ddR[i][j][k] = ddR1 - ddR2;
} else {
ddR[i][j][k] = 0;
//logger.debug("OK: 0");
}
} else {
ddR[i][j][k] = 0;
//logger.debug("OK: 0");
}
//logger.debug("Electrostatic interactionn " + k + " : " + "ddR[" + i + "][" + j + "][" + k + "] = " + ddR[i][j][k]);
}
}
}
}
/**
* Get the internuclear separation second derivative respect to the cartesian coordinates of the atoms.
*
*@return Bond lengths second derivative value [dimension(3xN)] [bonds Number]
*/
public double[][][] getInternuclearSeparationSecondDerivative() {
return ddR;
}
/**
* Evaluate the second order partial derivative (hessian) for the Electrostatic interaction energy given the atoms coordinates
*
*@param coord3d Current molecule coordinates.
*/
public void setHessianMMFF94SumEQ(GVector coord3d) {
forHessian = new double[coord3d.getSize() * coord3d.getSize()];
setInternuclearSeparationSecondDerivative(coord3d);
double sumHessianEQ;
int forHessianIndex;
for (int i = 0; i < coord3d.getSize(); i++) {
for (int j = 0; j < coord3d.getSize(); j++) {
sumHessianEQ = 0;
for (int k = 0; k < electrostaticInteractionNumber; k++) {
sumHessianEQ = sumHessianEQ + (((332.0716 * qi[k] * qj[k] * n * (n+1) / D*Math.pow(r[k]+delta,n+2)) * dR[i][k]) * dR[j][k]
+ (-332.0716 * qi[k] * qj[k] * n / D * Math.pow(r[k]+delta,n+1)) * ddR[i][j][k]);
}
forHessianIndex = i*coord3d.getSize()+j;
forHessian[forHessianIndex] = sumHessianEQ;
//logger.debug("forHessian[forHessianIndex] : " + forHessian[forHessianIndex]);
}
}
hessianMMFF94SumEQ = new GMatrix(coord3d.getSize(), coord3d.getSize(), forHessian);
//logger.debug("hessianMMFF94SumEQ : " + hessianMMFF94SumEQ);
}
/**
* Get the hessian for the Electrostatic interaction energy.
*
*@return Hessian value of the Electrostatic interaction term.
*/
public GMatrix getHessianMMFF94SumEQ() {
return hessianMMFF94SumEQ;
}
/**
* Get the hessian for the Electrostatic interaction energy.
*
*@return Hessian value of the Electrostatic interaction term.
*/
public double[] getForHessianMMFF94SumEQ() {
return forHessian;
}
}