electrostaticinteractions.java

化学图形处理软件

package org.openscience.cdk.modeling.forcefield;

import java.util.Hashtable;

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;
//import org.openscience.cdk.tools.LoggingTool;


/**			
 *  MMFF94 Electrostatic Interactions energy. Include function and derivatives.
 *
 *@author     vlabarta
 *@cdk.created    May 13, 2005
 *@cdk.module     forcefield
 */
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 = {new Integer(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.
	
	//private LoggingTool logger;
	
	/**
	 *  Constructor for the ElectrostaticInteractions object
	 */
	public ElectrostaticInteractions() {        
		//logger = new LoggingTool(this);
	}


	/**
	 *  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, Hashtable 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(1);
		    molecule.getAtom(8).setCharge(1);
		}
		
		electrostaticInteractionNumber = 0;
		for (int i=0; i<molecule.getAtomCount(); i++) {
			for (int j=i+1; j<molecule.getAtomCount(); j++) {
				params[0] = new Integer(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] = new Integer(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.
	 *
	 *