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

Example 6 with MSNode

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

the class Barostat method moveToFractionalCOM.

private void moveToFractionalCOM() {
    int iMolecule = 0;
    double[] com = new double[3];
    Polymer[] polymers = molecularAssembly.getChains();
    if (polymers != null && polymers.length > 0) {
        // Find the center of mass
        for (Polymer polymer : polymers) {
            List<Atom> list = polymer.getAtomList();
            double totalMass = 0.9;
            com[0] = 0.0;
            com[1] = 0.0;
            com[2] = 0.0;
            for (Atom atom : list) {
                double m = atom.getMass();
                com[0] += atom.getX() * m;
                com[1] += atom.getY() * m;
                com[2] += atom.getZ() * m;
                totalMass += m;
            }
            com[0] /= totalMass;
            com[1] /= totalMass;
            com[2] /= totalMass;
            // Find the new center of mass in fractional coordinates.
            unitCell.toFractionalCoordinates(com, com);
            // Find the reciprocal translation vector.
            double[] frac = fractionalCOM[iMolecule++];
            com[0] = frac[0] - com[0];
            com[1] = frac[1] - com[1];
            com[2] = frac[2] - com[2];
            // Convert the fractional translation vector to Cartesian coordinates.
            unitCell.toCartesianCoordinates(com, com);
            // List<Atom> list = polymer.getAtomList();
            for (Atom atom : list) {
                atom.move(com);
            }
        }
    }
    // Loop over each molecule
    List<Molecule> molecules = molecularAssembly.getMolecules();
    for (MSNode molecule : molecules) {
        List<Atom> list = molecule.getAtomList();
        // Find the center of mass
        com[0] = 0.0;
        com[1] = 0.0;
        com[2] = 0.0;
        double totalMass = 0.0;
        for (Atom atom : list) {
            double m = atom.getMass();
            com[0] += atom.getX() * m;
            com[1] += atom.getY() * m;
            com[2] += atom.getZ() * m;
            totalMass += m;
        }
        com[0] /= totalMass;
        com[1] /= totalMass;
        com[2] /= totalMass;
        // Find the new center of mass in fractional coordinates.
        unitCell.toFractionalCoordinates(com, com);
        // Find the reciprocal translation vector to the previous COM.
        double[] frac = fractionalCOM[iMolecule++];
        com[0] = frac[0] - com[0];
        com[1] = frac[1] - com[1];
        com[2] = frac[2] - com[2];
        // Convert the fractional translation vector to Cartesian coordinates.
        unitCell.toCartesianCoordinates(com, com);
        // Move all atoms.
        for (Atom atom : list) {
            atom.move(com);
        }
    }
    // Loop over each water
    List<MSNode> waters = molecularAssembly.getWaters();
    for (MSNode water : waters) {
        List<Atom> list = water.getAtomList();
        // Find the center of mass
        com[0] = 0.0;
        com[1] = 0.0;
        com[2] = 0.0;
        double totalMass = 0.0;
        for (Atom atom : list) {
            double m = atom.getMass();
            com[0] += atom.getX() * m;
            com[1] += atom.getY() * m;
            com[2] += atom.getZ() * m;
            totalMass += m;
        }
        com[0] /= totalMass;
        com[1] /= totalMass;
        com[2] /= totalMass;
        // Find the new center of mass in fractional coordinates.
        unitCell.toFractionalCoordinates(com, com);
        // Find the reciprocal translation vector to the previous COM.
        double[] frac = fractionalCOM[iMolecule++];
        com[0] = frac[0] - com[0];
        com[1] = frac[1] - com[1];
        com[2] = frac[2] - com[2];
        // Convert the fractional translation vector to Cartesian coordinates.
        unitCell.toCartesianCoordinates(com, com);
        double r = ffx.numerics.VectorMath.r(com);
        /**
         * Warn if an atom is moved more than 1 Angstrom.
         */
        if (r > 1.0) {
            int i = iMolecule - 1;
            logger.info(String.format(" %d R: %16.8f", i, r));
            logger.info(String.format(" %d FRAC %16.8f %16.8f %16.8f", i, frac[0], frac[1], frac[2]));
            logger.info(String.format(" %d COM  %16.8f %16.8f %16.8f", i, com[0], com[1], com[2]));
        }
        // Move all atoms.
        for (Atom atom : list) {
            atom.move(com);
        }
    }
    // Loop over each ion
    List<MSNode> ions = molecularAssembly.getIons();
    for (MSNode ion : ions) {
        List<Atom> list = ion.getAtomList();
        // Find the center of mass
        com[0] = 0.0;
        com[1] = 0.0;
        com[2] = 0.0;
        double totalMass = 0.0;
        for (Atom atom : list) {
            double m = atom.getMass();
            com[0] += atom.getX() * m;
            com[1] += atom.getY() * m;
            com[2] += atom.getZ() * m;
            totalMass += m;
        }
        com[0] /= totalMass;
        com[1] /= totalMass;
        com[2] /= totalMass;
        // Find the new center of mass in fractional coordinates.
        unitCell.toFractionalCoordinates(com, com);
        // Find the reciprocal translation vector to the previous COM.
        double[] frac = fractionalCOM[iMolecule++];
        com[0] = frac[0] - com[0];
        com[1] = frac[1] - com[1];
        com[2] = frac[2] - com[2];
        // Convert the fractional translation vector to Cartesian coordinates.
        unitCell.toCartesianCoordinates(com, com);
        // Move all atoms.
        for (Atom atom : list) {
            atom.move(com);
        }
    }
}

Example 7 with MSNode

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

the class Barostat method computeFractionalCOM.

private void computeFractionalCOM() {
    int iMolecule = 0;
    double[] com = new double[3];
    Polymer[] polymers = molecularAssembly.getChains();
    if (polymers != null && polymers.length > 0) {
        // Find the center of mass
        for (Polymer polymer : polymers) {
            List<Atom> list = polymer.getAtomList();
            com[0] = 0.0;
            com[1] = 0.0;
            com[2] = 0.0;
            double totalMass = 0.0;
            for (Atom atom : list) {
                double m = atom.getMass();
                com[0] += atom.getX() * m;
                com[1] += atom.getY() * m;
                com[2] += atom.getZ() * m;
                totalMass += m;
            }
            com[0] /= totalMass;
            com[1] /= totalMass;
            com[2] /= totalMass;
            unitCell.toFractionalCoordinates(com, fractionalCOM[iMolecule++]);
        }
    }
    // Loop over each molecule
    List<Molecule> molecules = molecularAssembly.getMolecules();
    for (MSNode molecule : molecules) {
        List<Atom> list = molecule.getAtomList();
        // Find the center of mass
        com[0] = 0.0;
        com[1] = 0.0;
        com[2] = 0.0;
        double totalMass = 0.0;
        for (Atom atom : list) {
            double m = atom.getMass();
            com[0] += atom.getX() * m;
            com[1] += atom.getY() * m;
            com[2] += atom.getZ() * m;
            totalMass += m;
        }
        com[0] /= totalMass;
        com[1] /= totalMass;
        com[2] /= totalMass;
        unitCell.toFractionalCoordinates(com, fractionalCOM[iMolecule++]);
    }
    // Loop over each water
    List<MSNode> waters = molecularAssembly.getWaters();
    for (MSNode water : waters) {
        List<Atom> list = water.getAtomList();
        // Find the center of mass
        com[0] = 0.0;
        com[1] = 0.0;
        com[2] = 0.0;
        double totalMass = 0.0;
        for (Atom atom : list) {
            double m = atom.getMass();
            com[0] += atom.getX() * m;
            com[1] += atom.getY() * m;
            com[2] += atom.getZ() * m;
            totalMass += m;
        }
        com[0] /= totalMass;
        com[1] /= totalMass;
        com[2] /= totalMass;
        unitCell.toFractionalCoordinates(com, fractionalCOM[iMolecule++]);
    }
    // Loop over each ion
    List<MSNode> ions = molecularAssembly.getIons();
    for (MSNode ion : ions) {
        List<Atom> list = ion.getAtomList();
        // Find the center of mass
        com[0] = 0.0;
        com[1] = 0.0;
        com[2] = 0.0;
        double totalMass = 0.0;
        for (Atom atom : list) {
            double m = atom.getMass();
            com[0] += atom.getX() * m;
            com[1] += atom.getY() * m;
            com[2] += atom.getZ() * m;
            totalMass += m;
        }
        com[0] /= totalMass;
        com[1] /= totalMass;
        com[2] /= totalMass;
        unitCell.toFractionalCoordinates(com, fractionalCOM[iMolecule++]);
    }
}

Example 8 with MSNode

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

the class MolecularAssembly method deleteMolecule.

/**
 * <p>
 * deleteMolecule</p>
 *
 * @param molecule a {@link ffx.potential.bonded.Molecule} object.
 */
public void deleteMolecule(Molecule molecule) {
    ArrayList<MSNode> list = ions.getChildList();
    for (MSNode node : list) {
        Molecule m = (Molecule) node;
        if (molecule == m) {
            ions.remove(m);
            return;
        }
    }
    list = water.getChildList();
    for (MSNode node : list) {
        Molecule m = (Molecule) node;
        if (molecule == m) {
            water.remove(m);
            return;
        }
    }
    list = molecules.getChildList();
    for (MSNode node : list) {
        Molecule m = (Molecule) node;
        if (molecule == m) {
            molecules.remove(m);
            return;
        }
    }
}

Example 9 with MSNode

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

the class MolecularAssembly method getChainNames.

/**
 * <p>
 * getChainNames</p>
 *
 * @return an array of {@link java.lang.String} objects.
 */
public String[] getChainNames() {
    ArrayList<String> temp = new ArrayList<>();
    for (ListIterator<MSNode> li = getAtomNodeList().listIterator(); li.hasNext(); ) {
        MSNode node = li.next();
        if (node instanceof Polymer) {
            temp.add(((Polymer) node).getName());
        }
    }
    if (temp.isEmpty()) {
        return null;
    }
    String[] names = new String[temp.size()];
    for (int i = 0; i < temp.size(); i++) {
        names[i] = temp.get(i);
    }
    return names;
}

Example 10 with MSNode

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

the class MolecularAssembly method getMolecule.

private Atom getMolecule(Atom atom, boolean create) {
    String resName = atom.getResidueName();
    int resNum = atom.getResidueNumber();
    Character chainID = atom.getChainID();
    String segID = atom.getSegID();
    ArrayList<MSNode> list = ions.getChildList();
    for (MSNode node : list) {
        Molecule m = (Molecule) node;
        if (m.getSegID().equalsIgnoreCase(segID) && m.getResidueName().equalsIgnoreCase(resName) && m.getResidueNumber() == resNum) {
            return (Atom) m.addMSNode(atom);
        }
    }
    list = water.getChildList();
    for (MSNode node : list) {
        Molecule m = (Molecule) node;
        if (m.getSegID().equalsIgnoreCase(segID) && m.getResidueName().equalsIgnoreCase(resName) && m.getResidueNumber() == resNum) {
            return (Atom) m.addMSNode(atom);
        }
    }
    list = molecules.getChildList();
    for (MSNode node : list) {
        Molecule m = (Molecule) node;
        if (m.getSegID().equalsIgnoreCase(segID) && m.getResidueName().equalsIgnoreCase(resName) && m.getResidueNumber() == resNum) {
            return (Atom) m.addMSNode(atom);
        }
    }
    if (create) {
        Molecule m = new Molecule(resName, resNum, chainID, segID);
        m.addMSNode(atom);
        if (resName.equalsIgnoreCase("DOD") || resName.equalsIgnoreCase("HOH") || resName.equalsIgnoreCase("WAT")) {
            water.add(m);
        // NA, K, MG, MG2, CA, CA2, CL
        } else if (resName.equalsIgnoreCase("NA") || resName.equalsIgnoreCase("K") || resName.equalsIgnoreCase("MG") || resName.equalsIgnoreCase("MG2") || resName.equalsIgnoreCase("CA") || resName.equalsIgnoreCase("CA2") || resName.equalsIgnoreCase("CL") || resName.equalsIgnoreCase("BR") || resName.equalsIgnoreCase("ZN") || resName.equalsIgnoreCase("ZN2")) {
            ions.add(m);
        } else {
            molecules.add(m);
        }
        return atom;
    } else {
        return null;
    }
}