Examples with Polarizability org.openscience.cdk.charges.Polarizability used on opensource projects

Example 1 with Polarizability

use of org.openscience.cdk.charges.Polarizability in project cdk by cdk.

the class BCUTDescriptor method calculate.

/**
 * Calculates the three classes of BCUT descriptors.
 *
 * @param container Parameter is the atom container.
 * @return An ArrayList containing the descriptors. The default is to return
 *         all calculated eigenvalues of the Burden matrices in the order described
 *         above. If a parameter list was supplied, then only the specified number
 *         of highest and lowest eigenvalues (for each class of BCUT) will be returned.
 */
@Override
public DescriptorValue calculate(IAtomContainer container) {
    int counter;
    IAtomContainer molecule;
    try {
        molecule = container.clone();
    } catch (CloneNotSupportedException e) {
        logger.debug("Error during clone");
        return getDummyDescriptorValue(new CDKException("Error occurred during clone " + e));
    }
    // add H's in case they're not present
    try {
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
        CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(molecule.getBuilder());
        hAdder.addImplicitHydrogens(molecule);
        AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
    } catch (Exception e) {
        return getDummyDescriptorValue(new CDKException("Could not add hydrogens: " + e.getMessage(), e));
    }
    // do aromaticity detecttion for calculating polarizability later on
    if (this.checkAromaticity) {
        try {
            AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
        } catch (CDKException e) {
            return getDummyDescriptorValue(new CDKException("Error in atom typing: " + e.getMessage(), e));
        }
        try {
            Aromaticity.cdkLegacy().apply(molecule);
        } catch (CDKException e) {
            return getDummyDescriptorValue(new CDKException("Error in aromaticity perception: " + e.getMessage()));
        }
    }
    // find number of heavy atoms
    int nheavy = 0;
    for (int i = 0; i < molecule.getAtomCount(); i++) {
        if (molecule.getAtom(i).getAtomicNumber() != IElement.H)
            nheavy++;
    }
    if (nheavy == 0)
        return getDummyDescriptorValue(new CDKException("No heavy atoms in the molecule"));
    double[] diagvalue = new double[nheavy];
    // get atomic mass weighted BCUT
    counter = 0;
    try {
        for (int i = 0; i < molecule.getAtomCount(); i++) {
            if (molecule.getAtom(i).getAtomicNumber() == IElement.H)
                continue;
            diagvalue[counter] = Isotopes.getInstance().getMajorIsotope(molecule.getAtom(i).getSymbol()).getExactMass();
            counter++;
        }
    } catch (Exception e) {
        return getDummyDescriptorValue(new CDKException("Could not calculate weight: " + e.getMessage(), e));
    }
    double[][] burdenMatrix = BurdenMatrix.evalMatrix(molecule, diagvalue);
    if (hasUndefined(burdenMatrix))
        return getDummyDescriptorValue(new CDKException("Burden matrix has undefined values"));
    Matrix matrix = new Matrix(burdenMatrix);
    EigenvalueDecomposition eigenDecomposition = new EigenvalueDecomposition(matrix);
    double[] eval1 = eigenDecomposition.getRealEigenvalues();
    // get charge weighted BCUT
    LonePairElectronChecker lpcheck = new LonePairElectronChecker();
    GasteigerMarsiliPartialCharges peoe;
    try {
        lpcheck.saturate(molecule);
        double[] charges = new double[molecule.getAtomCount()];
        // pepe = new GasteigerPEPEPartialCharges();
        // pepe.calculateCharges(molecule);
        // for (int i = 0; i < molecule.getAtomCount(); i++) charges[i] = molecule.getAtom(i).getCharge();
        peoe = new GasteigerMarsiliPartialCharges();
        peoe.assignGasteigerMarsiliSigmaPartialCharges(molecule, true);
        for (int i = 0; i < molecule.getAtomCount(); i++) charges[i] += molecule.getAtom(i).getCharge();
        for (int i = 0; i < molecule.getAtomCount(); i++) {
            molecule.getAtom(i).setCharge(charges[i]);
        }
    } catch (Exception e) {
        return getDummyDescriptorValue(new CDKException("Could not calculate partial charges: " + e.getMessage(), e));
    }
    counter = 0;
    for (int i = 0; i < molecule.getAtomCount(); i++) {
        if (molecule.getAtom(i).getAtomicNumber() == IElement.H)
            continue;
        diagvalue[counter] = molecule.getAtom(i).getCharge();
        counter++;
    }
    burdenMatrix = BurdenMatrix.evalMatrix(molecule, diagvalue);
    if (hasUndefined(burdenMatrix))
        return getDummyDescriptorValue(new CDKException("Burden matrix has undefined values"));
    matrix = new Matrix(burdenMatrix);
    eigenDecomposition = new EigenvalueDecomposition(matrix);
    double[] eval2 = eigenDecomposition.getRealEigenvalues();
    int[][] topoDistance = PathTools.computeFloydAPSP(AdjacencyMatrix.getMatrix(molecule));
    // get polarizability weighted BCUT
    Polarizability pol = new Polarizability();
    counter = 0;
    for (int i = 0; i < molecule.getAtomCount(); i++) {
        if (molecule.getAtom(i).getAtomicNumber() == IElement.H)
            continue;
        diagvalue[counter] = pol.calculateGHEffectiveAtomPolarizability(molecule, molecule.getAtom(i), false, topoDistance);
        counter++;
    }
    burdenMatrix = BurdenMatrix.evalMatrix(molecule, diagvalue);
    if (hasUndefined(burdenMatrix))
        return getDummyDescriptorValue(new CDKException("Burden matrix has undefined values"));
    matrix = new Matrix(burdenMatrix);
    eigenDecomposition = new EigenvalueDecomposition(matrix);
    double[] eval3 = eigenDecomposition.getRealEigenvalues();
    // return only the n highest & lowest eigenvalues
    int lnlow, lnhigh, enlow, enhigh;
    if (nlow > nheavy) {
        lnlow = nheavy;
        enlow = nlow - nheavy;
    } else {
        lnlow = nlow;
        enlow = 0;
    }
    if (nhigh > nheavy) {
        lnhigh = nheavy;
        enhigh = nhigh - nheavy;
    } else {
        lnhigh = nhigh;
        enhigh = 0;
    }
    DoubleArrayResult retval = new DoubleArrayResult((lnlow + enlow + lnhigh + enhigh) * 3);
    for (int i = 0; i < lnlow; i++) retval.add(eval1[i]);
    for (int i = 0; i < enlow; i++) retval.add(Double.NaN);
    for (int i = 0; i < lnhigh; i++) retval.add(eval1[eval1.length - i - 1]);
    for (int i = 0; i < enhigh; i++) retval.add(Double.NaN);
    for (int i = 0; i < lnlow; i++) retval.add(eval2[i]);
    for (int i = 0; i < enlow; i++) retval.add(Double.NaN);
    for (int i = 0; i < lnhigh; i++) retval.add(eval2[eval2.length - i - 1]);
    for (int i = 0; i < enhigh; i++) retval.add(Double.NaN);
    for (int i = 0; i < lnlow; i++) retval.add(eval3[i]);
    for (int i = 0; i < enlow; i++) retval.add(Double.NaN);
    for (int i = 0; i < lnhigh; i++) retval.add(eval3[eval3.length - i - 1]);
    for (int i = 0; i < enhigh; i++) retval.add(Double.NaN);
    return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), retval, getDescriptorNames());
}

Example 2 with Polarizability

use of org.openscience.cdk.charges.Polarizability in project cdk by cdk.

the class IonizationPotentialTool method getQSARs.

/**
 * Get the results of 7 qsar descriptors been applied. They are:
 * Electronegativity,
 * GasteigerMarsiliPartialCharges,
 * GasteigerPEPEPartialCharges,
 * Polarizability,
 * StabilizationCharge,
 * Number of Atom in resonance
 * if the container in resonance is aromatic.
 *
 * @param container  The IAtomContainer which contain the IAtom
 * @param atom       The IAtom to calculate
 * @return           An Array containing the results
 */
public static double[] getQSARs(IAtomContainer container, IAtom atom) throws CDKException {
    Electronegativity electronegativity = new Electronegativity();
    PiElectronegativity pielectronegativity = new PiElectronegativity();
    GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges();
    GasteigerPEPEPartialCharges pepe = new GasteigerPEPEPartialCharges();
    Polarizability pol = new Polarizability();
    StabilizationCharges stabil = new StabilizationCharges();
    StructureResonanceGenerator gRI = new StructureResonanceGenerator();
    IAtomContainer product = initiateIonization(container, atom);
    double[] results = new double[8];
    // sigmaElectronegativity
    results[0] = electronegativity.calculateSigmaElectronegativity(container, atom);
    // piElectronegativity
    results[1] = pielectronegativity.calculatePiElectronegativity(container, atom);
    // partialSigmaCharge
    try {
        peoe.assignGasteigerMarsiliSigmaPartialCharges(container, true);
    } catch (Exception e) {
    // ignored, underlying classes are logging this and this class
    // is deprecated
    }
    results[2] = atom.getCharge();
    // partialPiCharge
    for (int i = 0; i < container.getAtomCount(); i++) container.getAtom(i).setCharge(0.0);
    try {
        pepe.assignGasteigerPiPartialCharges(container, true);
    } catch (Exception e) {
        LoggingToolFactory.createLoggingTool(IonizationPotentialTool.class).warn("Unexpected Error:", e);
    }
    results[3] = atom.getCharge();
    // effectiveAtomicPolarizability
    results[4] = pol.calculateGHEffectiveAtomPolarizability(container, atom, 100, true);
    int position = container.indexOf(atom);
    if (product != null)
        results[5] = stabil.calculatePositive(product, product.getAtom(position));
    else
        results[5] = 0.0;
    // numberResonance
    IAtomContainer acR = gRI.getContainer(container, atom);
    if (acR != null) {
        results[6] = acR.getAtomCount();
        // numberAromaticAtoms
        // boolean isAromatic = Aromaticity.cdkLegacy().apply(container);
        IRingSet ringSet = Cycles.sssr(container).toRingSet();
        RingSetManipulator.markAromaticRings(ringSet);
        int aromRingCount = 0;
        for (IAtomContainer ring : ringSet.atomContainers()) {
            if (ring.getFlag(CDKConstants.ISAROMATIC))
                aromRingCount++;
        }
        results[7] = aromRingCount;
    } else {
        results[6] = 0;
        results[7] = 0;
    }
    return results;
}

Example 3 with Polarizability

use of org.openscience.cdk.charges.Polarizability in project cdk by cdk.

the class IonizationPotentialTool method getQSARs.

/**
 * Get the results of 7 qsar descriptors been applied. They are:
 * Electronegativity,
 * GasteigerMarsiliPartialCharges,
 * GasteigerPEPEPartialCharges,
 * Polarizability,
 * StabilizationCharge,
 * Number of Atom in resonance
 * if the container in resonance is aromatic.
 *
 * @param container  The IAtomContainer which contain the IAtom
 * @param bond       The IBond to calculate
 * @return           An Array containing the results
 */
public static double[] getQSARs(IAtomContainer container, IBond bond) throws CDKException {
    Electronegativity electronegativity = new Electronegativity();
    PiElectronegativity pielectronegativity = new PiElectronegativity();
    GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges();
    GasteigerPEPEPartialCharges pepe = new GasteigerPEPEPartialCharges();
    Polarizability pol = new Polarizability();
    StabilizationCharges stabil = new StabilizationCharges();
    StructureResonanceGenerator gRI = new StructureResonanceGenerator();
    double[] results = new double[7];
    for (int ia = 0; ia < 2; ia++) {
        IAtom atom = bond.getAtom(ia);
        IAtomContainer product = initiateIonization(container, atom);
        // sigmaElectronegativity
        results[0] += electronegativity.calculateSigmaElectronegativity(container, atom);
        // piElectronegativity
        results[1] += pielectronegativity.calculatePiElectronegativity(container, atom);
        // partialSigmaCharge
        try {
            peoe.assignGasteigerMarsiliSigmaPartialCharges(container, true);
        } catch (Exception e) {
            LoggingToolFactory.createLoggingTool(IonizationPotentialTool.class).warn("Unexpected Error:", e);
        }
        results[2] += atom.getCharge();
        // partialPiCharge
        for (int i = 0; i < container.getAtomCount(); i++) container.getAtom(i).setCharge(0.0);
        try {
            pepe.assignGasteigerPiPartialCharges(container, true);
        } catch (Exception e) {
            LoggingToolFactory.createLoggingTool(IonizationPotentialTool.class).warn("Unexpected Error:", e);
        }
        results[3] += atom.getCharge();
        // effectiveAtomicPolarizability
        results[4] += pol.calculateGHEffectiveAtomPolarizability(container, atom, 100, true);
        int position = container.indexOf(atom);
        if (product != null)
            results[5] += stabil.calculatePositive(product, product.getAtom(position));
        else
            results[5] += 0.0;
        // numberResonance
        IAtomContainer acR = gRI.getContainer(container, atom);
        if (acR != null) {
            results[6] += acR.getAtomCount();
        // numberAromaticAtoms
        // boolean isAromatic = Aromaticity.cdkLegacy().apply(container);
        // if(isAromatic)
        // results[7] += 0.1;
        } else {
            results[6] += 0;
        // results[7] += 0;
        }
    }
    for (int i = 0; i < results.length; i++) results[i] = results[i] / 2;
    return results;
}

Example 4 with Polarizability

use of org.openscience.cdk.charges.Polarizability in project cdk by cdk.

the class AutocorrelationDescriptorPolarizability method listpolarizability.

private static double[] listpolarizability(IAtomContainer container, int[][] dmat) throws CDKException {
    int natom = container.getAtomCount();
    double[] polars = new double[natom];
    Polarizability polar = new Polarizability();
    for (int i = 0; i < natom; i++) {
        IAtom atom = container.getAtom(i);
        try {
            polars[i] = polar.calculateGHEffectiveAtomPolarizability(container, atom, false, dmat);
        } catch (Exception ex1) {
            throw new CDKException("Problems with assign Polarizability due to " + ex1, ex1);
        }
    }
    return polars;
}