/* Copyright (C) 2007  Federico
 *
 * 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.qsar.descriptors.molecular;

import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.matrix.TopologicalMatrix;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.qsar.AbstractMolecularDescriptor;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleArrayResultType;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

/**
 * This class calculates ATS autocorrelation descriptor, where the weight equal
 * to the charges.
 *
 * @author      Federico
 * @cdk.created 2007-02-27
 * @cdk.module  qsarmolecular
 * @cdk.githash
 */

public class AutocorrelationDescriptorCharge extends AbstractMolecularDescriptor implements IMolecularDescriptor {

    private static final String[] NAMES = {"ATSc1", "ATSc2", "ATSc3", "ATSc4", "ATSc5"};

    private static double[] listcharges(IAtomContainer container) throws CDKException {
        int natom = container.getAtomCount();
        double[] charges = new double[natom];
        try {
            IAtomContainer mol = container.getBuilder().newInstance(IAtomContainer.class,
                    ((IAtomContainer) container.clone()));
            GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges();
            peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true);
            for (int i = 0; i < natom; i++) {
                IAtom atom = mol.getAtom(i);
                charges[i] = atom.getCharge();
            }
        } catch (Exception ex1) {
            throw new CDKException("Problems with assignGasteigerMarsiliPartialCharges due to " + ex1.toString(), ex1);
        }

        return charges;
    }

    @Override
    public DescriptorValue calculate(IAtomContainer atomContainer) {
        IAtomContainer container;
        try {
            container = (IAtomContainer) atomContainer.clone();
            container = AtomContainerManipulator.removeHydrogens(container);
        } catch (CloneNotSupportedException e) {
            DoubleArrayResult result = new DoubleArrayResult(5);
            for (int i = 0; i < 5; i++)
                result.add(Double.NaN);
            return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), result,
                    getDescriptorNames(), new CDKException("Error during cloner: " + e.getMessage(), e));
        }

        try {
            double[] w = listcharges(container);
            int natom = container.getAtomCount();
            int[][] distancematrix = TopologicalMatrix.getMatrix(container);

            double[] chargeSum = new double[5];

            for (int k = 0; k < 5; k++) {
                for (int i = 0; i < natom; i++) {
                    for (int j = 0; j < natom; j++) {
                        if (distancematrix[i][j] == k) {
                            chargeSum[k] += w[i] * w[j];
                        } else
                            chargeSum[k] += 0.0;
                    }
                }
                if (k > 0) chargeSum[k] = chargeSum[k] / 2;

            }
            DoubleArrayResult result = new DoubleArrayResult(5);
            for (double aChargeSum : chargeSum) {
                result.add(aChargeSum);
            }
            return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), result, NAMES);

        } catch (Exception ex) {
            DoubleArrayResult result = new DoubleArrayResult(5);
            for (int i = 0; i < 5; i++)
                result.add(Double.NaN);
            return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), result, NAMES,
                    new CDKException("Error while calculating the ATS_charge descriptor: " + ex.getMessage(), ex));
        }
    }

    @Override
    public String[] getParameterNames() {
        return new String[0];
    }

    @Override
    public Object getParameterType(String name) {
        return null;
    }

    @Override
    public Object[] getParameters() {
        return null;
    }

    @Override
    public String[] getDescriptorNames() {
        return NAMES;
    }

    @Override
    public DescriptorSpecification getSpecification() {
        return new DescriptorSpecification(
                "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#autoCorrelationCharge", this
                        .getClass().getName(), "The Chemistry Development Kit");
    }

    @Override
    public IDescriptorResult getDescriptorResultType() {
        return new DoubleArrayResultType(5);
    }

    @Override
    public void setParameters(Object[] params) throws CDKException {

    }

}
