Examples with NeighborList ffx.potential.nonbonded.NeighborList used on opensource projects

Example 1 with NeighborList

use of ffx.potential.nonbonded.NeighborList in project ffx by mjschnie.

the class RotamerOptimization method distanceMatrix.

/**
 * Calculates a residue-residue distance matrix.
 * <p>
 * Residue-residue distance is defined as the shortest atom-atom distance in
 * any possible rotamer-rotamer pair if the residues are neighbors (central
 * atom-central atom distances are within a cutoff). Otherewise, distances
 * are set to a default of Double.MAX_VALUE.
 * </p>
 * <p>
 * The intent of using a neighbor list is to avoid tediously searching
 * rotamer- rotamer pairs when two residues are so far apart we will never
 * need the exact distance. We use the distance matrix for adding residues
 * to the sliding window and determining whether to set 3-body energy to
 * 0.0.
 * </p>
 * <p>
 * If the central atoms are too distant from each other, we can safely
 * assume no atoms will ever be close enough for addition to sliding window
 * or to cause explicit calculation of 3-body energy.
 * </p>
 */
private void distanceMatrix() {
    distanceMatrix = new double[numResidues - 1][][][];
    long numDistances = 0L;
    for (int i = 0; i < (numResidues - 1); i++) {
        Residue residuei = allResiduesArray[i];
        int lengthRi;
        try {
            if (checkIfForced(residuei)) {
                lengthRi = 1;
            } else {
                lengthRi = residuei.getRotamers(library).length;
            }
        } catch (IndexOutOfBoundsException ex) {
            if (useForcedResidues) {
                logger.warning(ex.toString());
            } else {
                logIfMaster(format(" Non-forced Residue i %s has null rotamers.", residuei.toFormattedString(false, true)), Level.WARNING);
            }
            continue;
        }
        distanceMatrix[i] = new double[lengthRi][][];
        for (int ri = 0; ri < lengthRi; ri++) {
            distanceMatrix[i][ri] = new double[numResidues][];
            for (int j = (i + 1); j < numResidues; j++) {
                Residue residuej = allResiduesArray[j];
                int lengthRj;
                try {
                    if (checkIfForced(residuej)) {
                        lengthRj = 1;
                    } else {
                        lengthRj = residuej.getRotamers(library).length;
                    }
                } catch (IndexOutOfBoundsException ex) {
                    if (useForcedResidues) {
                        logger.warning(ex.toString());
                    } else {
                        logIfMaster(format(" Residue j %s has null rotamers.", residuej.toFormattedString(false, true)));
                    }
                    continue;
                }
                distanceMatrix[i][ri][j] = new double[lengthRj];
                numDistances += lengthRj;
                if (!lazyMatrix) {
                    fill(distanceMatrix[i][ri][j], Double.MAX_VALUE);
                } else {
                    fill(distanceMatrix[i][ri][j], -1.0);
                }
            }
        }
    }
    logger.info(format(" Number of pairwise distances: %d", numDistances));
    if (!lazyMatrix) {
        ResidueState[] orig = ResidueState.storeAllCoordinates(allResiduesList);
        int nMultiRes = 0;
        /**
         * Build a list that contains one atom from each Residues: CA from
         * amino acids, C1 from nucleic acids, or the first atom otherwise.
         */
        Atom[] atoms = new Atom[numResidues];
        for (int i = 0; i < numResidues; i++) {
            Residue residuei = allResiduesArray[i];
            atoms[i] = residuei.getReferenceAtom();
            if (residuei instanceof MultiResidue) {
                ++nMultiRes;
            }
        }
        /**
         * Use of the pre-existing ParallelTeam causes a conflict when
         * MultiResidues must re-init the force field. Temporary solution
         * for sequence optimization: if > 1 residue optimized, run on only
         * one thread.
         */
        int nThreads = 1;
        if (molecularAssembly.getPotentialEnergy().getParallelTeam() != null) {
            nThreads = (nMultiRes > 1) ? 1 : molecularAssembly.getPotentialEnergy().getParallelTeam().getThreadCount();
        } else {
            // Suggested: nThreads = (nMultiRes > 1) ? 1 : ParallelTeam.getDefaultThreadCount();
            nThreads = 16;
        }
        ParallelTeam parallelTeam = new ParallelTeam(nThreads);
        Crystal crystal = molecularAssembly.getCrystal();
        int nSymm = crystal.spaceGroup.getNumberOfSymOps();
        logger.info("\n Computing Residue Distance Matrix");
        double nlistCutoff = Math.max(Math.max(distance, twoBodyCutoffDist), threeBodyCutoffDist);
        /**
         * I think this originated from the fact that side-chain
         * (and later nucleic acid) atoms could be fairly distant
         * from the reference atom.
         */
        double magicNumberBufferOfUnknownOrigin = 25.0;
        nlistCutoff += magicNumberBufferOfUnknownOrigin;
        NeighborList neighborList = new NeighborList(null, crystal, atoms, nlistCutoff, 0.0, parallelTeam);
        // Expand coordinates
        double[][] xyz = new double[nSymm][3 * numResidues];
        double[] in = new double[3];
        double[] out = new double[3];
        for (int iSymOp = 0; iSymOp < nSymm; iSymOp++) {
            SymOp symOp = crystal.spaceGroup.getSymOp(iSymOp);
            for (int i = 0; i < numResidues; i++) {
                int i3 = i * 3;
                int iX = i3 + 0;
                int iY = i3 + 1;
                int iZ = i3 + 2;
                Atom atom = atoms[i];
                in[0] = atom.getX();
                in[1] = atom.getY();
                in[2] = atom.getZ();
                crystal.applySymOp(in, out, symOp);
                xyz[iSymOp][iX] = out[0];
                xyz[iSymOp][iY] = out[1];
                xyz[iSymOp][iZ] = out[2];
            }
        }
        // Build the residue neighbor-list.
        int[][][] lists = new int[nSymm][numResidues][];
        boolean[] use = new boolean[numResidues];
        fill(use, true);
        boolean forceRebuild = true;
        boolean printLists = false;
        long neighborTime = -System.nanoTime();
        neighborList.buildList(xyz, lists, use, forceRebuild, printLists);
        neighborTime += System.nanoTime();
        logger.info(format(" Built residue neighbor list:           %8.3f sec", neighborTime * 1.0e-9));
        DistanceRegion distanceRegion = new DistanceRegion(parallelTeam.getThreadCount(), numResidues, crystal, lists, neighborList.getPairwiseSchedule());
        long parallelTime = -System.nanoTime();
        try {
            parallelTeam.execute(distanceRegion);
        } catch (Exception e) {
            String message = " Exception compting residue distance matrix.";
            logger.log(Level.SEVERE, message, e);
        }
        parallelTime += System.nanoTime();
        logger.info(format(" Pairwise distance matrix:              %8.3f sec\n", parallelTime * 1.0e-9));
        ResidueState.revertAllCoordinates(allResiduesList, orig);
        try {
            parallelTeam.shutdown();
        } catch (Exception ex) {
            logger.warning(format(" Exception shutting down parallel team for the distance matrix: %s", ex.toString()));
        }
    }
}