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

Example 6 with ROLS

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

the class MolecularAssembly method renderWire.

private Shape3D renderWire() {
    ArrayList<ROLS> bonds = getBondList();
    int numbonds = bonds.size();
    if (numbonds < 1) {
        return null;
    }
    Vector3d bondmidpoint = new Vector3d();
    double[] mid = { 0, 0, 0 };
    Vector3d v1 = new Vector3d();
    Vector3d v2 = new Vector3d();
    float[] a1 = { 0, 0, 0 };
    float[] a2 = { 0, 0, 0 };
    float[] col = new float[4];
    Bond bond;
    Atom atom1, atom2;
    LineArray la = new LineArray(4 * numbonds, GeometryArray.COORDINATES | GeometryArray.COLOR_4 | GeometryArray.NORMALS);
    la.setCapability(LineArray.ALLOW_COORDINATE_WRITE);
    la.setCapability(LineArray.ALLOW_COORDINATE_READ);
    la.setCapability(LineArray.ALLOW_COLOR_WRITE);
    la.setCapability(LineArray.ALLOW_COUNT_READ);
    la.setCapability(LineArray.ALLOW_INTERSECT);
    la.setCapability(LineArray.ALLOW_FORMAT_READ);
    atomLookUp = new Atom[4 * numbonds];
    int i = 0;
    col[3] = 0.9f;
    for (ListIterator<ROLS> li = bonds.listIterator(); li.hasNext(); ) {
        bond = (Bond) li.next();
        bond.setWire(la, i);
        atom1 = bond.getAtom(0);
        atom2 = bond.getAtom(1);
        atom1.getV3D(v1);
        atom2.getV3D(v2);
        a1[0] = (float) v1.x;
        a1[1] = (float) v1.y;
        a1[2] = (float) v1.z;
        a2[0] = (float) v2.x;
        a2[1] = (float) v2.y;
        a2[2] = (float) v2.z;
        // Find the bond center
        bondmidpoint.add(v1, v2);
        bondmidpoint.scale(0.5d);
        bondmidpoint.get(mid);
        // Atom #1
        Atom.AtomColor.get(atom1.getAtomicNumber()).get(col);
        atomLookUp[i] = atom1;
        la.setCoordinate(i, a1);
        la.setColor(i, col);
        la.setNormal(i, a2);
        i++;
        atomLookUp[i] = atom1;
        la.setCoordinate(i, mid);
        la.setColor(i, col);
        la.setNormal(i, a2);
        i++;
        // Atom #2
        Atom.AtomColor.get(atom2.getAtomicNumber()).get(col);
        atomLookUp[i] = atom2;
        la.setCoordinate(i, a2);
        la.setColor(i, col);
        la.setNormal(i, a1);
        i++;
        atomLookUp[i] = atom2;
        la.setCoordinate(i, mid);
        la.setColor(i, col);
        la.setNormal(i, a1);
        i++;
    }
    ColoringAttributes cola = new ColoringAttributes(new Color3f(), ColoringAttributes.SHADE_GOURAUD);
    Appearance app = new Appearance();
    lineAttributes = new LineAttributes();
    lineAttributes.setLineWidth(RendererCache.bondwidth);
    lineAttributes.setCapability(LineAttributes.ALLOW_WIDTH_WRITE);
    lineAttributes.setLineAntialiasingEnable(true);
    app.setLineAttributes(lineAttributes);
    app.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ);
    app.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE);
    RenderingAttributes ra = new RenderingAttributes();
    ra.setAlphaTestValue(0.1f);
    ra.setAlphaTestFunction(RenderingAttributes.GREATER);
    ra.setDepthBufferEnable(true);
    ra.setDepthBufferWriteEnable(true);
    app.setRenderingAttributes(ra);
    app.setColoringAttributes(cola);
    Shape3D wireframe = new Shape3D(la, app);
    // PickTool.setCapabilities(wire, PickTool.INTERSECT_COORD);
    wireframe.setUserData(this);
    wireframe.setBounds(new BoundingSphere(new Point3d(0, 0, 0), 1000.0));
    try {
        wireframe.setBoundsAutoCompute(false);
    } catch (Exception e) {
        e.printStackTrace();
    }
    wireframe.setCapability(Shape3D.ALLOW_GEOMETRY_READ);
    wireframe.setCapability(Shape3D.ALLOW_APPEARANCE_READ);
    wireframe.setCapability(Shape3D.ALLOW_LOCAL_TO_VWORLD_READ);
    return wireframe;
}

Example 7 with ROLS

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

the class PhMD method meltdown.

private void meltdown() {
    writeSnapshot(".meltdown-");
    ffe.energy(false, true);
    if (ffe.getBondEnergy() > 1000) {
        for (ROLS rols : previousTarget.getBondList()) {
            ((Bond) rols).log();
        }
    }
    if (ffe.getAngleEnergy() > 1000) {
        for (ROLS rols : previousTarget.getAngleList()) {
            ((Angle) rols).log();
        }
    }
    if (ffe.getVanDerWaalsEnergy() > 1000) {
        for (Atom a1 : previousTarget.getAtomList()) {
            for (Atom a2 : mola.getAtomArray()) {
                if (a1 == a2 || a1.getBond(a2) != null) {
                    continue;
                }
                double dist = sqrt(pow((a1.getX() - a2.getX()), 2) + pow((a1.getY() - a2.getY()), 2) + pow((a1.getZ() - a2.getZ()), 2));
                if (dist < 0.8 * (a1.getVDWR() + a2.getVDWR())) {
                    logger.warning(String.format("Close vdW contact for atoms: \n   %s\n   %s", a1, a2));
                }
            }
        }
    }
    logger.severe(String.format("Temperature above critical threshold: %f", thermostat.getCurrentTemperature()));
}

Example 8 with ROLS

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

the class RosenbluthChiAllMove method measureLysine.

public double[] measureLysine(Residue residue, boolean print) {
    if (!residue.getName().contains("LY") || (residue.getAminoAcid3() != AminoAcid3.LYS && residue.getAminoAcid3() != AminoAcid3.LYD)) {
        logger.severe("Yeah that ain't a lysine.");
    }
    double[] chi = new double[4];
    ArrayList<ROLS> torsions = residue.getTorsionList();
    Atom N = (Atom) residue.getAtomNode("N");
    Atom CA = (Atom) residue.getAtomNode("CA");
    Atom CB = (Atom) residue.getAtomNode("CB");
    Atom CD = (Atom) residue.getAtomNode("CD");
    Atom CE = (Atom) residue.getAtomNode("CE");
    Atom CG = (Atom) residue.getAtomNode("CG");
    Atom NZ = (Atom) residue.getAtomNode("NZ");
    logger.info(String.format(" Here's the atoms I found: \n%s\n%s\n%s\n%s\n%s\n%s\n%s", N, CA, CB, CD, CE, CG, NZ));
    logger.info(String.format(" Num torsions: %d", torsions.size()));
    int count = 0;
    for (ROLS rols : torsions) {
        Torsion torsion = (Torsion) rols;
        torsion.energy(false);
        logger.info(String.format(" Torsion numba %d: %s", count++, torsion));
        if (torsion.compare(N, CA, CB, CG)) {
            chi[0] = torsion.getValue();
            if (print) {
                logger.info(torsion.toString());
            }
        }
        if (torsion.compare(CA, CB, CG, CD)) {
            chi[1] = torsion.getValue();
            if (print) {
                logger.info(torsion.toString());
            }
        }
        if (torsion.compare(CB, CG, CD, CE)) {
            chi[2] = torsion.getValue();
            if (print) {
                logger.info(torsion.toString());
            }
        }
        if (torsion.compare(CG, CD, CE, NZ)) {
            chi[3] = torsion.getValue();
            if (print) {
                logger.info(torsion.toString());
            }
        }
    }
    return chi;
}

Example 9 with ROLS

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

the class RosenbluthOBMC method mcStep.

/**
 * Does all the work for a move. Moveset is a continuous 360 degree spin of
 * the chi[0] torsion. U_or in Frenkel's notation (uDep here) is the
 * associated torsion energy. Evaluation criterion: P_accept = Min( 1,
 * (Wn/Wo)*exp(-beta(U[n]-U[o]) )
 */
private boolean mcStep() {
    numMovesProposed++;
    boolean accepted;
    // Select a target residue.
    int which = ThreadLocalRandom.current().nextInt(targets.size());
    Residue target = targets.get(which);
    ResidueState origState = target.storeState();
    List<ROLS> chiList = target.getTorsionList();
    Torsion chi0 = getChiZeroTorsion(target);
    writeSnapshot("orig");
    /* Create old and new trial sets, calculate Wn and Wo, and choose a move bn.
            When doing strictly chi[0] moves, Frenkel/Smit's 'old' and 'new' configurations
            are the same state. The distinction is made here only to aid in future generalization.
         */
    List<MCMove> oldTrialSet = createTrialSet(target, origState, trialSetSize - 1);
    List<MCMove> newTrialSet = createTrialSet(target, origState, trialSetSize);
    report = new StringBuilder();
    report.append(String.format(" Rosenbluth Rotamer MC Move: %4d\n", numMovesProposed));
    report.append(String.format("    residue:   %s\n", target.toString()));
    report.append(String.format("    chi0:      %s\n", chi0.toString()));
    MCMove proposal = calculateRosenbluthFactors(target, chi0, origState, oldTrialSet, origState, newTrialSet);
    /* Calculate the independent portion of the total old-conf energy.
            Then apply the move and calculate the independent total new-conf energy.
         */
    setState(target, origState);
    writeSnapshot("uIndO");
    double uIndO = getTotalEnergy() - getTorsionEnergy(chi0);
    proposal.move();
    writeSnapshot("uIndN");
    double uIndN = getTotalEnergy() - getTorsionEnergy(chi0);
    // Apply acceptance criterion.
    double temperature = thermostat.getCurrentTemperature();
    double beta = 1.0 / (BOLTZMANN * temperature);
    double dInd = uIndN - uIndO;
    double dIndE = FastMath.exp(-beta * dInd);
    double criterion = (Wn / Wo) * FastMath.exp(-beta * (uIndN - uIndO));
    double metropolis = Math.min(1, criterion);
    double rng = ThreadLocalRandom.current().nextDouble();
    report.append(String.format("    theta:     %3.2f\n", ((RosenbluthChi0Move) proposal).theta));
    report.append(String.format("    criterion: %1.4f\n", criterion));
    report.append(String.format("       Wn/Wo:     %.2f\n", Wn / Wo));
    report.append(String.format("       uIndN,O:  %7.2f\t%7.2f\n", uIndN, uIndO));
    report.append(String.format("       dInd(E):  %7.2f\t%7.2f\n", dInd, dIndE));
    report.append(String.format("    rng:       %1.4f\n", rng));
    if (rng < metropolis) {
        numMovesAccepted++;
        report.append(String.format(" Accepted.\n"));
        accepted = true;
    } else {
        proposal.revertMove();
        report.append(String.format(" Denied.\n"));
        accepted = false;
    }
    logger.info(report.toString());
    // Cleanup.
    Wn = 0.0;
    Wo = 0.0;
    return accepted;
}