Examples with TorsionTorsionType ffx.potential.parameters.TorsionTorsionType used on opensource projects

Example 1 with TorsionTorsionType

use of ffx.potential.parameters.TorsionTorsionType in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method addTorsionTorsionForce.

private void addTorsionTorsionForce() {
    TorsionTorsion[] torsionTorsions = super.getTorsionTorsions();
    if (torsionTorsions == null || torsionTorsions.length < 1) {
        return;
    }
    /**
     * Load the torsion-torsions.
     */
    int nTypes = 0;
    LinkedHashMap<String, TorsionTorsionType> torTorTypes = new LinkedHashMap<>();
    int nTorsionTorsions = torsionTorsions.length;
    amoebaTorsionTorsionForce = OpenMM_AmoebaTorsionTorsionForce_create();
    for (int i = 0; i < nTorsionTorsions; i++) {
        TorsionTorsion torsionTorsion = torsionTorsions[i];
        int ia = torsionTorsion.getAtom(0).getXyzIndex() - 1;
        int ib = torsionTorsion.getAtom(1).getXyzIndex() - 1;
        int ic = torsionTorsion.getAtom(2).getXyzIndex() - 1;
        int id = torsionTorsion.getAtom(3).getXyzIndex() - 1;
        int ie = torsionTorsion.getAtom(4).getXyzIndex() - 1;
        TorsionTorsionType torsionTorsionType = torsionTorsion.torsionTorsionType;
        String key = torsionTorsionType.getKey();
        /**
         * Check if the TorTor parameters have already been added to the
         * Hash.
         */
        int gridIndex = 0;
        if (torTorTypes.containsKey(key)) {
            /**
             * If the TorTor has been added, get its (ordered) index in the
             * Hash.
             */
            int index = 0;
            for (String entry : torTorTypes.keySet()) {
                if (entry.equalsIgnoreCase(key)) {
                    gridIndex = index;
                    break;
                } else {
                    index++;
                }
            }
        } else {
            /**
             * Add the new TorTor.
             */
            torTorTypes.put(key, torsionTorsionType);
            gridIndex = nTypes;
            nTypes++;
        }
        Atom atom = torsionTorsion.getChiralAtom();
        int iChiral = -1;
        if (atom != null) {
            iChiral = atom.getXyzIndex() - 1;
        }
        OpenMM_AmoebaTorsionTorsionForce_addTorsionTorsion(amoebaTorsionTorsionForce, ia, ib, ic, id, ie, iChiral, gridIndex);
    }
    /**
     * Load the Torsion-Torsion parameters.
     */
    PointerByReference values = OpenMM_DoubleArray_create(6);
    int gridIndex = 0;
    for (String key : torTorTypes.keySet()) {
        TorsionTorsionType torTorType = torTorTypes.get(key);
        int nx = torTorType.nx;
        int ny = torTorType.ny;
        double[] tx = torTorType.tx;
        double[] ty = torTorType.ty;
        double[] f = torTorType.energy;
        double[] dx = torTorType.dx;
        double[] dy = torTorType.dy;
        double[] dxy = torTorType.dxy;
        /**
         * Create the 3D grid.
         */
        PointerByReference grid3D = OpenMM_3D_DoubleArray_create(nx, ny, 6);
        int xIndex = 0;
        int yIndex = 0;
        for (int j = 0; j < nx * ny; j++) {
            int addIndex = 0;
            OpenMM_DoubleArray_set(values, addIndex++, tx[xIndex]);
            OpenMM_DoubleArray_set(values, addIndex++, ty[yIndex]);
            OpenMM_DoubleArray_set(values, addIndex++, OpenMM_KJPerKcal * f[j]);
            OpenMM_DoubleArray_set(values, addIndex++, OpenMM_KJPerKcal * dx[j]);
            OpenMM_DoubleArray_set(values, addIndex++, OpenMM_KJPerKcal * dy[j]);
            OpenMM_DoubleArray_set(values, addIndex++, OpenMM_KJPerKcal * dxy[j]);
            OpenMM_3D_DoubleArray_set(grid3D, yIndex, xIndex, values);
            xIndex++;
            if (xIndex == nx) {
                xIndex = 0;
                yIndex++;
            }
        }
        OpenMM_AmoebaTorsionTorsionForce_setTorsionTorsionGrid(amoebaTorsionTorsionForce, gridIndex++, grid3D);
        OpenMM_3D_DoubleArray_destroy(grid3D);
    }
    OpenMM_DoubleArray_destroy(values);
    OpenMM_System_addForce(system, amoebaTorsionTorsionForce);
    logger.log(Level.INFO, " Added Torsion-Torsions ({0})", nTorsionTorsions);
}

Example 2 with TorsionTorsionType

use of ffx.potential.parameters.TorsionTorsionType in project ffx by mjschnie.

the class ForceFieldFilter method parseTorsionTorsion.

private void parseTorsionTorsion(String input, String[] tokens, BufferedReader br) {
    if (tokens.length < 8) {
        logger.log(Level.WARNING, "Invalid TORTORS type:\n{0}", input);
        return;
    }
    try {
        int[] atomClasses = new int[5];
        for (int i = 0; i < 5; i++) {
            atomClasses[i] = Integer.parseInt(tokens[i + 1]);
        }
        int[] gridPoints = new int[2];
        gridPoints[0] = Integer.parseInt(tokens[6]);
        gridPoints[1] = Integer.parseInt(tokens[7]);
        int points = gridPoints[0] * gridPoints[1];
        double[] torsion1 = new double[points];
        double[] torsion2 = new double[points];
        double[] energy = new double[points];
        for (int i = 0; i < points; i++) {
            input = br.readLine();
            tokens = input.trim().split(" +");
            if (tokens.length != 3) {
                logger.log(Level.WARNING, "Invalid TORTORS type:\n{0}", input);
                return;
            }
            torsion1[i] = Double.parseDouble(tokens[0]);
            torsion2[i] = Double.parseDouble(tokens[1]);
            energy[i] = Double.parseDouble(tokens[2]);
        }
        TorsionTorsionType torsionTorsionType = new TorsionTorsionType(atomClasses, gridPoints, torsion1, torsion2, energy);
        forceField.addForceFieldType(torsionTorsionType);
    } catch (NumberFormatException | IOException e) {
        String message = "Exception parsing TORTORS type:\n" + input + "\n";
        logger.log(Level.SEVERE, message, e);
    }
}

Example 3 with TorsionTorsionType

use of ffx.potential.parameters.TorsionTorsionType in project ffx by mjschnie.

the class TorsionTorsion method torsionTorsionFactory.

/**
 * @param firstBond the first Bond.
 * @param angle the Angle.
 * @param lastBond the last Bond.
 * @param forceField the ForceField parameters to apply.
 * @return the new TorsionTorsion, or null.
 */
public static TorsionTorsion torsionTorsionFactory(Bond firstBond, Angle angle, Bond lastBond, ForceField forceField) {
    int[] c5 = new int[5];
    Atom atom1 = angle.atoms[0];
    Atom atom3 = angle.atoms[2];
    c5[0] = firstBond.get1_2(atom1).getAtomType().atomClass;
    c5[1] = atom1.getAtomType().atomClass;
    c5[2] = angle.atoms[1].getAtomType().atomClass;
    c5[3] = atom3.getAtomType().atomClass;
    c5[4] = lastBond.get1_2(atom3).getAtomType().atomClass;
    String key = TorsionTorsionType.sortKey(c5);
    boolean reversed = false;
    TorsionTorsionType torsionTorsionType = forceField.getTorsionTorsionType(key);
    if (torsionTorsionType == null) {
        key = TorsionTorsionType.reverseKey(c5);
        torsionTorsionType = forceField.getTorsionTorsionType(key);
        reversed = true;
    }
    if (torsionTorsionType == null) {
        return null;
    }
    TorsionTorsion torsionTorsion = new TorsionTorsion(firstBond, angle, lastBond, reversed);
    torsionTorsion.torsionTorsionType = torsionTorsionType;
    return torsionTorsion;
}

Example 4 with TorsionTorsionType

use of ffx.potential.parameters.TorsionTorsionType in project ffx by mjschnie.

the class ForceFieldFilter method parseTorsionTorsion.

private void parseTorsionTorsion(String input, String[] tokens) {
    if (tokens.length < 8) {
        logger.log(Level.WARNING, "Invalid TORTORS type:\n{0}", input);
        return;
    }
    try {
        int[] atomClasses = new int[5];
        for (int i = 0; i < 5; i++) {
            atomClasses[i] = Integer.parseInt(tokens[i + 1]);
        }
        int[] gridPoints = new int[2];
        gridPoints[0] = new Integer(tokens[6]);
        gridPoints[1] = new Integer(tokens[7]);
        int points = gridPoints[0] * gridPoints[1];
        int numTokens = points * 3 + 8;
        if (tokens.length < numTokens) {
            logger.log(Level.WARNING, "Invalid TORTORS type:\n{0}", input);
            return;
        }
        double[] torsion1 = new double[points];
        double[] torsion2 = new double[points];
        double[] energy = new double[points];
        int index = 8;
        for (int i = 0; i < points; i++) {
            torsion1[i] = new Double(tokens[index++]);
            torsion2[i] = new Double(tokens[index++]);
            energy[i] = new Double(tokens[index++]);
        }
        TorsionTorsionType torsionTorsionType = new TorsionTorsionType(atomClasses, gridPoints, torsion1, torsion2, energy);
        forceField.addForceFieldType(torsionTorsionType);
    } catch (NumberFormatException e) {
        String message = "Exception parsing TORTORS type:\n" + input + "\n";
        logger.log(Level.SEVERE, message, e);
    }
}