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

Example 1 with BondType

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

the class ForceFieldEnergyOpenMM method setUpHydrogenConstraints.

public void setUpHydrogenConstraints(PointerByReference system) {
    int i;
    int iAtom1;
    int iAtom2;
    // Atom[] atoms = molecularAssembly.getAtomArray();
    Bond[] bonds = super.getBonds();
    logger.info(String.format(" Setting up Hydrogen constraints"));
    if (bonds == null || bonds.length < 1) {
        return;
    }
    int nBonds = bonds.length;
    Atom atom1;
    Atom atom2;
    Atom parentAtom;
    Bond bondForBondLength;
    BondType bondType;
    for (i = 0; i < nBonds; i++) {
        Bond bond = bonds[i];
        atom1 = bond.getAtom(0);
        atom2 = bond.getAtom(1);
        if (atom1.isHydrogen()) {
            parentAtom = atom1.getBonds().get(0).get1_2(atom1);
            bondForBondLength = atom1.getBonds().get(0);
            bondType = bondForBondLength.bondType;
            iAtom1 = atom1.getXyzIndex() - 1;
            iAtom2 = parentAtom.getXyzIndex() - 1;
            OpenMM_System_addConstraint(system, iAtom1, iAtom2, bondForBondLength.bondType.distance * OpenMM_NmPerAngstrom);
        } else if (atom2.isHydrogen()) {
            parentAtom = atom2.getBonds().get(0).get1_2(atom2);
            bondForBondLength = atom2.getBonds().get(0);
            bondType = bondForBondLength.bondType;
            iAtom1 = atom2.getXyzIndex() - 1;
            iAtom2 = parentAtom.getXyzIndex() - 1;
            OpenMM_System_addConstraint(system, iAtom1, iAtom2, bondForBondLength.bondType.distance * OpenMM_NmPerAngstrom);
        }
    }
}

Example 2 with BondType

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

the class ForceFieldEnergyOpenMM method addBondForce.

private void addBondForce() {
    Bond[] bonds = super.getBonds();
    if (bonds == null || bonds.length < 1) {
        return;
    }
    int nBonds = bonds.length;
    amoebaBondForce = OpenMM_AmoebaBondForce_create();
    double kParameterConversion = OpenMM_KJPerKcal / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom);
    for (int i = 0; i < nBonds; i++) {
        Bond bond = bonds[i];
        int i1 = bond.getAtom(0).getXyzIndex() - 1;
        int i2 = bond.getAtom(1).getXyzIndex() - 1;
        BondType bondType = bond.bondType;
        OpenMM_AmoebaBondForce_addBond(amoebaBondForce, i1, i2, bond.bondType.distance * OpenMM_NmPerAngstrom, kParameterConversion * bondType.forceConstant * BondType.units);
    }
    if (bonds[0].bondType.bondFunction == BondFunction.QUARTIC) {
        OpenMM_AmoebaBondForce_setAmoebaGlobalBondCubic(amoebaBondForce, BondType.cubic / OpenMM_NmPerAngstrom);
        OpenMM_AmoebaBondForce_setAmoebaGlobalBondQuartic(amoebaBondForce, BondType.quartic / (OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom));
    }
    OpenMM_System_addForce(system, amoebaBondForce);
    logger.log(Level.INFO, " Added bonds ({0})", nBonds);
}

Example 3 with BondType

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

the class BondedUtils method buildBond.

public static Bond buildBond(Atom a1, Atom a2, ForceField forceField, ArrayList<Bond> bondList) {
    Bond bond = new Bond(a1, a2);
    int[] c = new int[2];
    c[0] = a1.getAtomType().atomClass;
    c[1] = a2.getAtomType().atomClass;
    String key = BondType.sortKey(c);
    BondType bondType = forceField.getBondType(key);
    if (bondType == null) {
        logger.severe(format("No BondType for key: %s\n %s\n %s\n %s\n %s", key, a1.toString(), a1.getAtomType().toString(), a2.toString(), a2.getAtomType().toString()));
    } else {
        bond.setBondType(bondType);
    }
    if (bondList != null) {
        bondList.add(bond);
    }
    return bond;
}

Example 4 with BondType

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

the class MultiTerminus method updateBondedTerms.

private void updateBondedTerms() {
    StringBuilder sb = new StringBuilder();
    sb.append(String.format("Updating bonded terms: \n"));
    List<ROLS> bonds = getBondList();
    for (int i = 0; i < bonds.size(); i++) {
        Bond bond = (Bond) bonds.get(i);
        BondType oldType = bond.bondType;
        int[] c = new int[2];
        c[0] = bond.atoms[0].getAtomType().atomClass;
        c[1] = bond.atoms[1].getAtomType().atomClass;
        String key = BondType.sortKey(c);
        BondType newType = forceField.getBondType(key);
        if (oldType != newType) {
            sb.append(String.format(" Bond: %s --> %s \n", bond.bondType, newType));
            bond.setBondType(newType);
            if (newType.distance < 0.9 * oldType.distance || newType.distance > 1.1 * oldType.distance) {
                logger.info(String.format(" Large bond distance change: %s %s,  %.2f --> %.2f ", bond.atoms[0].describe(Atom.Descriptions.XyzIndex_Name), bond.atoms[1].describe(Atom.Descriptions.XyzIndex_Name), oldType.distance, newType.distance));
            }
        }
    }
    List<ROLS> angles = getAngleList();
    for (int i = 0; i < angles.size(); i++) {
        Angle angle = (Angle) angles.get(i);
        AngleType oldType = angle.angleType;
        if (DEBUG) {
            logger.info(String.format(" %d ( %s %s %s ) ( %d %d %d )", i, angle.atoms[0].describe(Atom.Descriptions.XyzIndex_Name), angle.atoms[1].describe(Atom.Descriptions.XyzIndex_Name), angle.atoms[2].describe(Atom.Descriptions.XyzIndex_Name), angle.atoms[0].getAtomType().atomClass, angle.atoms[1].getAtomType().atomClass, angle.atoms[2].getAtomType().atomClass));
        }
        Angle dummy = Angle.angleFactory(angle.bonds[0], angle.bonds[1], forceField);
        AngleType newType = dummy.angleType;
        if (oldType != newType) {
            sb.append(String.format(" Angle: %s --> %s \n", angle.angleType, dummy.angleType));
            angle.setAngleType(dummy.angleType);
            if (newType.angle[0] < 0.9 * oldType.angle[0] || newType.angle[0] > 1.1 * oldType.angle[0]) {
                logger.info(String.format(" Large angle change: %s %s %s,  %.2f --> %.2f ", angle.atoms[0].describe(Atom.Descriptions.XyzIndex_Name), angle.atoms[1].describe(Atom.Descriptions.XyzIndex_Name), angle.atoms[2].describe(Atom.Descriptions.XyzIndex_Name), oldType.angle[0], newType.angle[0]));
            }
        }
    }
    List<ROLS> torsions = getTorsionList();
    for (int i = 0; i < torsions.size(); i++) {
        Torsion tors = (Torsion) torsions.get(i);
        TorsionType oldType = tors.torsionType;
        Torsion dummy = Torsion.torsionFactory(tors.bonds[0], tors.bonds[1], tors.bonds[2], forceField);
        TorsionType newType = dummy.torsionType;
        if (oldType != newType) {
            sb.append(String.format(" Torsion: %s --> %s \n", tors.torsionType, dummy.torsionType));
            tors.torsionType = dummy.torsionType;
        }
    }
    if (DEBUG) {
        logger.info(sb.toString());
    }
}

Example 5 with BondType

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

the class ForceFieldEnergy method setRestraintBond.

/**
 * <p>
 * setRestraintBond</p>
 *
 * @param a1 a {@link ffx.potential.bonded.Atom} object.
 * @param a2 a {@link ffx.potential.bonded.Atom} object.
 * @param distance a double.
 * @param forceConstant the force constant in kcal/mole.
 * @param flatBottom Radius of a flat-bottom potential in Angstroms.
 */
public void setRestraintBond(Atom a1, Atom a2, double distance, double forceConstant, double flatBottom) {
    restraintBondTerm = true;
    RestraintBond rb = new RestraintBond(a1, a2, crystal);
    int[] classes = { a1.getAtomType().atomClass, a2.getAtomType().atomClass };
    if (flatBottom != 0) {
        rb.setBondType(new BondType(classes, forceConstant, distance, BondType.BondFunction.FLAT_BOTTOM_HARMONIC, flatBottom));
    } else {
        rb.setBondType((new BondType(classes, forceConstant, distance, BondType.BondFunction.HARMONIC)));
    }
    // As long as we continue to add elements one-at-a-time to an array, this code will continue to be ugly.
    RestraintBond[] newRbs = new RestraintBond[++nRestraintBonds];
    if (restraintBonds != null && restraintBonds.length != 0) {
        System.arraycopy(restraintBonds, 0, newRbs, 0, (nRestraintBonds - 1));
    }
    newRbs[nRestraintBonds - 1] = rb;
    restraintBonds = newRbs;
    rb.energy(false);
    rb.log();
}