Examples with Bond ffx.potential.bonded.Bond used on opensource projects

Example 1 with Bond

use of ffx.potential.bonded.Bond in project ffx by mjschnie.

the class SimulationFilter method readFile.

/**
 * {@inheritDoc}
 */
@Override
public boolean readFile() {
    // information
    for (int i = 0; i < system.numatoms; i++) {
        AtomType atomType = atomTypes.get(system.types[i]);
        if (atomType == null) {
            atomType = new AtomType(system.types[i], -1, system.name[i], system.story[i], system.atomic[i], system.mass[i], 0);
            atomTypes.put(system.types[i], atomType);
        }
    }
    atomList = new ArrayList<Atom>();
    Vector<Integer> bonds1 = new Vector<Integer>();
    Vector<Integer> bonds2 = new Vector<Integer>();
    double[] d = new double[3];
    int[] b = new int[4];
    for (int i = 0; i < system.numatoms; i++) {
        d[0] = system.coordinates[0][i];
        d[1] = system.coordinates[1][i];
        d[2] = system.coordinates[2][i];
        String s = new String("" + system.types[i]);
        AtomType atomType = atomTypes.get(s);
        Atom a = new Atom(i + 1, new String("" + atomType.type), atomType, d);
        atomList.add(a);
        int b1 = i + 1;
        b[0] = system.connectivity[0][i];
        b[1] = system.connectivity[1][i];
        b[2] = system.connectivity[2][i];
        b[3] = system.connectivity[3][i];
        int j = 0;
        while (j < 4 && b[j] != 0) {
            int b2 = b[j];
            bonds1.add(b1);
            bonds2.add(b2);
            j++;
        }
    }
    bondList = new ArrayList<Bond>();
    for (int i = 0; i < bonds1.size(); i++) {
        int a1 = bonds1.get(i);
        int a2 = bonds2.get(i);
        if (a1 < a2) {
            Atom atom1 = atomList.get(a1 - 1);
            Atom atom2 = atomList.get(a2 - 1);
            bondList.add(new Bond(atom1, atom2));
        }
    }
    setFileRead(true);
    return true;
}

Example 2 with Bond

use of ffx.potential.bonded.Bond 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 3 with Bond

use of ffx.potential.bonded.Bond 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 4 with Bond

use of ffx.potential.bonded.Bond in project ffx by mjschnie.

the class Utilities method addPhosphate.

/**
 * Add a phosphate and its bonded oxygens that are not bonded to a carbon to
 * the specified residue.
 *
 * @param phosphate Atom
 * @param residue Residue
 */
public static void addPhosphate(Atom phosphate, Residue residue) {
    if (phosphate == null) {
        return;
    }
    residue.addMSNode(phosphate);
    for (Bond b : phosphate.getBonds()) {
        Atom oxygen = b.get1_2(phosphate);
        // Add oxygens not bonded to a Carbon
        if (numberOfBondsWith(oxygen, 6) == 0) {
            residue.addMSNode(oxygen);
            // Add hydrogens atoms for protonated oxygen groups
            Atom hydrogen = findBondWith(oxygen, 1);
            if (hydrogen != null) {
                residue.addMSNode(hydrogen);
            }
        }
    }
}

Example 5 with Bond

use of ffx.potential.bonded.Bond in project ffx by mjschnie.

the class Utilities method biochemistry.

/**
 * This routine sub-divides a system into groups of ions, water, hetero
 * molecules, and polynucleotides/polypeptides.
 *
 * @param molecularAssembly a {@link ffx.potential.MolecularAssembly}
 * object.
 * @param atoms a {@link java.util.List} object.
 */
public static void biochemistry(MolecularAssembly molecularAssembly, List<Atom> atoms) {
    Atom atom, seed = null;
    int num = 0;
    int waterNum = 0;
    int ionNum = 0;
    int moleculeNum = 0;
    List<String> segIDs = new ArrayList<>();
    while (atoms.size() > 0) {
        /**
         * Nitrogen is used to "seed" a backbone search because carbon can
         * be separated from the backbone by a sulfur (ie. MET).
         */
        for (Atom a : atoms) {
            seed = a;
            if (seed.getAtomicNumber() == 7) {
                break;
            }
        }
        /**
         * If no nitrogen atoms remain, there are no nucleic or amino acids.
         */
        if (seed.getAtomicNumber() != 7) {
            List<Atom> moleculeAtoms;
            while (atoms.size() > 0) {
                atom = atoms.get(0);
                // Check for a metal ion or noble gas
                if (atom.getNumBonds() == 0) {
                    ionNum++;
                    Molecule ion = new Molecule(atom.getName() + "-" + ionNum);
                    ion.addMSNode(atom);
                    atoms.remove(0);
                    molecularAssembly.addMSNode(ion);
                    continue;
                } else // Check for water
                if (atom.getAtomicNumber() == 8 && isWaterOxygen(atom)) {
                    waterNum++;
                    Molecule water = new Molecule("Water-" + waterNum);
                    water.addMSNode(atom);
                    atoms.remove(0);
                    List<Bond> bonds = atom.getBonds();
                    for (Bond b : bonds) {
                        Atom hydrogen = b.get1_2(atom);
                        water.addMSNode(hydrogen);
                        atoms.remove(hydrogen);
                    }
                    molecularAssembly.addMSNode(water);
                    continue;
                }
                // Otherwise classify the molecule as a hetero
                moleculeNum++;
                Molecule molecule = new Molecule("Molecule-" + moleculeNum);
                moleculeAtoms = getAtomListFromPool();
                collectAtoms(atoms.get(0), moleculeAtoms);
                while (moleculeAtoms.size() > 0) {
                    atom = moleculeAtoms.get(0);
                    moleculeAtoms.remove(0);
                    molecule.addMSNode(atom);
                    atoms.remove(atom);
                }
                molecularAssembly.addMSNode(molecule);
            }
            seed = null;
            break;
        }
        List<Atom> backbone = findPolymer(atoms, seed, null);
        if (backbone.size() > 0) {
            for (ListIterator li = backbone.listIterator(backbone.size()); li.hasPrevious(); ) {
                seed = (Atom) li.previous();
                if (seed.getAtomicNumber() == 7) {
                    break;
                }
            }
            backbone = findPolymer(atoms, seed, null);
        }
        Character chainID = getChainID(num);
        String segID = getSegID(chainID, segIDs);
        Polymer c = new Polymer(chainID, segID, true);
        if (backbone.size() > 2 && divideBackbone(backbone, c)) {
            for (Atom a : c.getAtomList()) {
                atoms.remove(a);
            }
            logger.fine(" Sequenced chain: " + c.getName());
            molecularAssembly.addMSNode(c);
            num++;
        } else {
            moleculeNum++;
            Molecule hetero = new Molecule("" + moleculeNum + "-Hetero");
            atom = backbone.get(0);
            List<Atom> heteroAtomList = getAtomListFromPool();
            collectAtoms(atom, heteroAtomList);
            for (Atom a : heteroAtomList) {
                hetero.addMSNode(a);
            }
            for (Atom a : hetero.getAtomList()) {
                atoms.remove(a);
            }
            molecularAssembly.addMSNode(hetero);
        }
    }
}