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

Example 56 with Rotamer

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

the class RosenbluthChiAllMove method boltzmannTorsionSet.

private TrialSet boltzmannTorsionSet(Torsion tors, int chiIndex, int setSize, String snapSuffix) {
    report.append(String.format("    TrialSet for Chi%d\t\t(Theta uDep uExt)\n", chiIndex));
    TrialSet trialSet = new TrialSet(setSize);
    double[] origChi = RotamerLibrary.measureRotamer(target, false);
    int i = 0;
    while (i < setSize) {
        double theta = rand.nextDouble(360.0) - 180;
        double[] newChi = new double[origChi.length];
        System.arraycopy(origChi, 0, newChi, 0, origChi.length);
        newChi[chiIndex] = theta;
        Rotamer newState = createRotamer(target, newChi);
        RotamerLibrary.applyRotamer(target, newState);
        double uBond = tors.energy(false);
        double criterion = FastMath.exp(-beta * uBond);
        double rng = rand.nextDouble();
        if (rng < criterion) {
            trialSet.theta[i] = theta;
            trialSet.rotamer[i] = newState;
            trialSet.uDep[i] = uBond;
            trialSet.uExt[i] = totalEnergy() - uBond;
            i++;
            writeSnapshot(snapSuffix, true);
            report.append(String.format("       %3s %d:      %5.2f\t%5.2f\t%5.2f\n", snapSuffix, i, theta, trialSet.uDep[i - 1], trialSet.uExt[i - 1]));
        }
    }
    target.revertState(origState);
    updateAll();
    return trialSet;
}