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

Example 1 with ImproperTorsionType

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

the class ImproperTorsion method improperTorsionFactory.

/**
 * ImproperTorsion factory method.
 *
 * @param atom Create the improper torsion around this atom.
 * @param forceField retrieve parameters from this ForceField.
 * @return the ImproperTorsion if created, or null otherwise.
 */
public static ArrayList<ImproperTorsion> improperTorsionFactory(Atom atom, ForceField forceField) {
    if (atom == null) {
        return null;
    }
    Atom[] atoms = new Atom[4];
    atoms[2] = atom;
    ArrayList<Bond> bonds = atom.getBonds();
    if (bonds == null || bonds.size() != 3) {
        return null;
    }
    for (int i = 0; i < 3; i++) {
        Bond bond = bonds.get(i);
        Atom atom2 = bond.get1_2(atom);
        if (i == 2) {
            atoms[3] = atom2;
        } else {
            atoms[i] = atom2;
        }
    }
    ArrayList<ImproperTorsion> improperTorsions = new ArrayList<>();
    Collection<ImproperTorsionType> types = forceField.getImproperTypes();
    double units = forceField.getDouble(ForceField.ForceFieldDouble.IMPTORUNIT, 0.5);
    for (ImproperTorsionType type : types) {
        int[] classes = new int[4];
        classes[0] = atoms[0].getAtomType().atomClass;
        classes[1] = atoms[1].getAtomType().atomClass;
        classes[2] = atoms[2].getAtomType().atomClass;
        classes[3] = atoms[3].getAtomType().atomClass;
        boolean assigned = type.assigned(classes);
        if (assigned) {
            // Finalize atom ordering.
            if (classes[3] == atoms[3].getAtomType().atomClass || type.atomClasses[3] == 0) {
            // do nothing.
            } else if (classes[3] == atoms[1].getAtomType().atomClass) {
                Atom temp = atoms[3];
                atoms[3] = atoms[1];
                atoms[1] = temp;
            } else {
                Atom temp = atoms[0];
                atoms[0] = atoms[3];
                atoms[3] = temp;
            }
            if (classes[1] == atoms[1].getAtomType().atomClass || type.atomClasses[1] == 0) {
            // do nothing.
            } else if (classes[1] == atoms[0].getAtomType().atomClass) {
                Atom temp = atoms[1];
                atoms[1] = atoms[0];
                atoms[0] = temp;
            }
            ImproperTorsion improperTorsion = new ImproperTorsion(atoms[0], atoms[1], atoms[2], atoms[3]);
            improperTorsion.setImproperType(type);
            improperTorsion.units = units;
            improperTorsions.add(improperTorsion);
            int c0 = type.atomClasses[0];
            int c1 = type.atomClasses[1];
            int c3 = type.atomClasses[3];
            if (c0 == c1 && c1 == c3) {
                improperTorsion.scaleFactor = 1.0 / 6.0;
                improperTorsion = new ImproperTorsion(atoms[0], atoms[3], atoms[2], atoms[1]);
                improperTorsion.setImproperType(type);
                improperTorsion.units = units;
                improperTorsion.scaleFactor = 1.0 / 6.0;
                improperTorsions.add(improperTorsion);
                improperTorsion = new ImproperTorsion(atoms[1], atoms[0], atoms[2], atoms[3]);
                improperTorsion.setImproperType(type);
                improperTorsion.units = units;
                improperTorsion.scaleFactor = 1.0 / 6.0;
                improperTorsions.add(improperTorsion);
                improperTorsion = new ImproperTorsion(atoms[1], atoms[3], atoms[2], atoms[0]);
                improperTorsion.setImproperType(type);
                improperTorsion.units = units;
                improperTorsion.scaleFactor = 1.0 / 6.0;
                improperTorsions.add(improperTorsion);
                improperTorsion = new ImproperTorsion(atoms[3], atoms[0], atoms[2], atoms[1]);
                improperTorsion.setImproperType(type);
                improperTorsion.units = units;
                improperTorsion.scaleFactor = 1.0 / 6.0;
                improperTorsions.add(improperTorsion);
                improperTorsion = new ImproperTorsion(atoms[3], atoms[1], atoms[2], atoms[0]);
                improperTorsion.setImproperType(type);
                improperTorsion.units = units;
                improperTorsion.scaleFactor = 1.0 / 6.0;
                improperTorsions.add(improperTorsion);
            } else if (c0 == c1) {
                improperTorsion.scaleFactor = 0.5;
                improperTorsion = new ImproperTorsion(atoms[1], atoms[0], atoms[2], atoms[3]);
                improperTorsion.setImproperType(type);
                improperTorsion.units = units;
                improperTorsion.scaleFactor = 0.5;
                improperTorsions.add(improperTorsion);
            } else if (c0 == c3) {
                improperTorsion.scaleFactor = 0.5;
                improperTorsion = new ImproperTorsion(atoms[3], atoms[1], atoms[2], atoms[0]);
                improperTorsion.setImproperType(type);
                improperTorsion.units = units;
                improperTorsion.scaleFactor = 0.5;
                improperTorsions.add(improperTorsion);
            } else if (c1 == c3) {
                improperTorsion.scaleFactor = 0.5;
                improperTorsion = new ImproperTorsion(atoms[0], atoms[3], atoms[2], atoms[1]);
                improperTorsion.setImproperType(type);
                improperTorsion.units = units;
                improperTorsion.scaleFactor = 0.5;
                improperTorsions.add(improperTorsion);
            }
        }
    }
    if (improperTorsions.isEmpty()) {
        return null;
    }
    return improperTorsions;
}

Example 2 with ImproperTorsionType

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

the class ForceFieldFilter method parseImproper.

private void parseImproper(String input, String[] tokens) {
    if (tokens.length < 8) {
        logger.log(Level.WARNING, "Invalid IMPTORS type:\n{0}", input);
        return;
    }
    try {
        int[] atomClasses = new int[4];
        atomClasses[0] = Integer.parseInt(tokens[1]);
        atomClasses[1] = Integer.parseInt(tokens[2]);
        atomClasses[2] = Integer.parseInt(tokens[3]);
        atomClasses[3] = Integer.parseInt(tokens[4]);
        double k = Double.parseDouble(tokens[5]);
        double phase = Double.parseDouble(tokens[6]);
        int period = Integer.parseInt(tokens[7]);
        if (improperTorsionScale > 0.0) {
            k = k * improperTorsionScale;
        }
        ImproperTorsionType improperType = new ImproperTorsionType(atomClasses, k, phase, period);
        forceField.addForceFieldType(improperType);
    } catch (NumberFormatException e) {
        String message = "Exception parsing IMPTORS type:\n" + input + "\n";
        logger.log(Level.SEVERE, message, e);
    }
}

Example 3 with ImproperTorsionType

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

the class ForceFieldEnergyOpenMM method addImproperTorsionForce.

private void addImproperTorsionForce() {
    ImproperTorsion[] impropers = super.getImproperTorsions();
    if (impropers == null || impropers.length < 1) {
        return;
    }
    int nImpropers = impropers.length;
    amoebaImproperTorsionForce = OpenMM_PeriodicTorsionForce_create();
    for (int i = 0; i < nImpropers; i++) {
        ImproperTorsion improperTorsion = impropers[i];
        int a1 = improperTorsion.getAtom(0).getXyzIndex() - 1;
        int a2 = improperTorsion.getAtom(1).getXyzIndex() - 1;
        int a3 = improperTorsion.getAtom(2).getXyzIndex() - 1;
        int a4 = improperTorsion.getAtom(3).getXyzIndex() - 1;
        ImproperTorsionType improperTorsionType = improperTorsion.improperType;
        OpenMM_PeriodicTorsionForce_addTorsion(amoebaImproperTorsionForce, a1, a2, a3, a4, improperTorsionType.periodicity, improperTorsionType.phase * OpenMM_RadiansPerDegree, OpenMM_KJPerKcal * improperTorsion.units * improperTorsion.scaleFactor * improperTorsionType.k);
    }
    OpenMM_System_addForce(system, amoebaImproperTorsionForce);
    logger.log(Level.INFO, " Added improper torsions ({0})", nImpropers);
}