Examples with DoubleIndexPair ffx.utilities.DoubleIndexPair used on opensource projects

Example 1 with DoubleIndexPair

use of ffx.utilities.DoubleIndexPair in project ffx by mjschnie.

the class Rescore method rescore.

public File[] rescore(File[] modelFiles) {
    int numFiles = modelFiles.length;
    DoubleIndexPair[] energies = new DoubleIndexPair[numFiles];
    File[] rescoredFiles = new File[numFiles];
    for (int i = 0; i < numFiles; i++) {
        rescoredFiles[i] = rescoreSingle(modelFiles[i], rscType, energies, i);
    }
    Arrays.sort(energies);
    ArrayList<Integer> acceptedFileIndices = new ArrayList<>();
    int numAccepted = 1;
    acceptedFileIndices.add(energies[0].getIndex());
    double minEnergy = energies[0].getDoubleValue();
    if (acceptThreshold > 0.0) {
        for (int i = 1; i < numFiles; i++) {
            DoubleIndexPair currentPair = energies[i];
            double e = currentPair.getDoubleValue();
            if (e - minEnergy <= acceptThreshold) {
                acceptedFileIndices.add(currentPair.getIndex());
                ++numAccepted;
            } else {
                break;
            }
        }
    } else {
        numAccepted = numToAccept < numFiles ? numToAccept : numFiles;
        for (int i = 1; i < numAccepted; i++) {
            acceptedFileIndices.add(energies[i].getIndex());
        }
    }
    for (int i = 0; i < numAccepted; i++) {
        File filei = rescoredFiles[energies[i].getIndex()];
        Path pathi;
        pathi = generatePath(filei);
        String relPath = pwdPath.relativize(pathi).toString();
        logger.info(String.format(" Accepted: %s at %10.6f kcal/mol", relPath, energies[i].getDoubleValue()));
    }
    for (int i = numAccepted; i < numFiles; i++) {
        File filei = rescoredFiles[energies[i].getIndex()];
        Path pathi;
        pathi = generatePath(filei);
        String relPath = pwdPath.relativize(pathi).toString();
        logger.info(String.format(" Rejected: %s at %10.6f kcal/mol", relPath, energies[i].getDoubleValue()));
    }
    try (BufferedWriter bw = new BufferedWriter(new FileWriter(resultsFile, true))) {
        Path rscFilePath = generatePath(resultsFile);
        String rscFileName = pwdPath.relativize(rscFilePath).toString();
        logger.info(String.format(" Printing accepted files to rescore file %s", rscFileName));
        if (acceptThreshold > 0.0) {
            String message = String.format("Minimum potential energy: %f, threshold = %6.4f", minEnergy, acceptThreshold);
            bw.write(message);
            message = " " + message + "\n";
            logger.info(message);
        } else {
            double maxEnergy = energies[numAccepted - 1].getDoubleValue();
            String message = String.format("Minimum potential energy: %f, maximum accepted energy %f", minEnergy, maxEnergy);
            bw.write(message);
            message = " " + message + "\n";
            logger.info(message);
        }
        bw.newLine();
        bw.newLine();
        String message = String.format("Number of files accepted: %d", numAccepted);
        bw.write(message);
        bw.newLine();
        logger.info(String.format(" %s", message));
        for (int i = 0; i < numAccepted; i++) {
            int fileIndex = energies[i].getIndex();
            File pointedFile = rescoredFiles[fileIndex];
            Path pointedPath = generatePath(pointedFile);
            String relPath = pwdPath.relativize(pointedPath).toString();
            double thisEnergy = energies[i].getDoubleValue();
            logger.info(String.format(" Accepted file %d energy %9.3f < %9.3f kcal/mol", (i + 1), thisEnergy, minEnergy + acceptThreshold));
            logger.info(String.format(" %s", relPath));
            try {
                bw.write(String.format("Accepted file: %s rank %d energy %f\n", relPath, (i + 1), thisEnergy));
                if (printModels) {
                    bw.newLine();
                    try (BufferedReader br = new BufferedReader(new FileReader(pointedFile))) {
                        String line = br.readLine();
                        while (line != null) {
                            bw.write(line);
                            bw.newLine();
                            line = br.readLine();
                        }
                    }
                    bw.newLine();
                }
            } catch (IOException ex) {
                logger.warning(String.format(" File %s had exception printing to rescore file %s", relPath, ex.toString()));
            }
        }
        message = String.format("\n Number of files not accepted: %d", numFiles - numAccepted);
        logger.info(String.format(" %s", message));
        bw.newLine();
        bw.write(message);
        bw.newLine();
        if (includeRejected) {
            for (int i = numAccepted; i < numFiles; i++) {
                int fileIndex = energies[i].getIndex();
                File pointedFile = rescoredFiles[fileIndex];
                Path pointedPath = generatePath(pointedFile);
                String relPath = pwdPath.relativize(pointedPath).toString();
                double thisEnergy = energies[i].getDoubleValue();
                message = String.format("Non-accepted file: %s rank %d energy %f", relPath, (i + 1), thisEnergy);
                logger.info(String.format(" %s", message));
                try {
                    bw.write(message);
                    bw.newLine();
                } catch (IOException ex) {
                    logger.warning(String.format(" File %s had exception printing to rescore file %s", relPath, ex.toString()));
                }
            }
        }
    } catch (IOException ex) {
        logger.warning(String.format(" Exception in writing rescore file: %s", ex.toString()));
    }
    return rescoredFiles;
}

Example 2 with DoubleIndexPair

use of ffx.utilities.DoubleIndexPair in project ffx by mjschnie.

the class RotamerOptimization method eliminateNABackboneRotamers.

/**
 * Eliminates NA backbone rotamers with corrections greater than threshold.
 * The int[] parameter allows the method to know how many Rotamers for each
 * residue have previously been pruned; currently, this means any Rotamer
 * pruned by reconcileNARotamersWithPriorResidues.
 * <p>
 * A nucleic correction threshold of 0 skips the entire method; this check
 * is presently being performed inside the method in case it is called again
 * at some point.
 *
 * @param residues Residues to eliminate bad backbone rotamers over.
 * @param numEliminatedRotamers Number of previously eliminated rotamers per
 * residue.
 */
private void eliminateNABackboneRotamers(Residue[] residues, int[] numEliminatedRotamers) {
    /* Atom atoms[] = molecularAssembly.getAtomArray();
         int nAtoms = atoms.length;
         String begin[] = new String[nAtoms];
         for (int i = 0; i < nAtoms; i++) {
         begin[i] = atoms[i].toString();
         } */
    if (nucleicCorrectionThreshold != 0) {
        logIfMaster(format(" Eliminating nucleic acid rotamers with correction vectors larger than %5.3f A", nucleicCorrectionThreshold));
        logIfMaster(format(" A minimum of %d rotamers per NA residue will carry through to energy calculations.", minNumberAcceptedNARotamers));
        ArrayList<Residue> resList = new ArrayList<>();
        resList.addAll(Arrays.asList(residues));
        ResidueState[] origCoordinates = ResidueState.storeAllCoordinates(resList);
        for (int j = 0; j < residues.length; j++) {
            Residue nucleicResidue = residues[j];
            Rotamer[] rotamers = nucleicResidue.getRotamers(library);
            if (nucleicResidue.getResidueType() == NA && rotamers != null) {
                int nrotamers = rotamers.length;
                // Default to all rotamers that have not previously been
                // eliminated; subtract as rotamers are rejected.
                int numAcceptedRotamers = nrotamers - numEliminatedRotamers[j];
                if (minNumberAcceptedNARotamers >= numAcceptedRotamers) {
                    continue;
                }
                ArrayList<DoubleIndexPair> rejectedRotamers = new ArrayList<>();
                for (int i = 0; i < nrotamers; i++) {
                    if (!check(j, i)) {
                        try {
                            RotamerLibrary.applyRotamer(nucleicResidue, rotamers[i], nucleicCorrectionThreshold);
                        } catch (NACorrectionException error) {
                            double rejectedCorrection = error.getCorrection();
                            numAcceptedRotamers--;
                            DoubleIndexPair rejected = new DoubleIndexPair(i, rejectedCorrection);
                            rejectedRotamers.add(rejected);
                        }
                    }
                }
                int numAdditionalRotamersToAccept = minNumberAcceptedNARotamers - numAcceptedRotamers;
                if (numAdditionalRotamersToAccept > 0) {
                    DoubleIndexPair[] rejectedArray = new DoubleIndexPair[rejectedRotamers.size()];
                    for (int i = 0; i < rejectedArray.length; i++) {
                        rejectedArray[i] = rejectedRotamers.get(i);
                    }
                    Arrays.sort(rejectedArray);
                    rejectedRotamers = new ArrayList<>();
                    rejectedRotamers.addAll(Arrays.asList(rejectedArray));
                    for (int i = 0; i < numAdditionalRotamersToAccept; i++) {
                        rejectedRotamers.remove(0);
                    }
                }
                for (DoubleIndexPair rotToReject : rejectedRotamers) {
                    eliminateRotamer(residues, j, rotToReject.getIndex(), print);
                    logIfMaster(format(" Correction magnitude was %6.4f A > %5.3f A", rotToReject.getDoubleValue(), nucleicCorrectionThreshold));
                }
            }
            nucleicResidue.revertState(origCoordinates[j]);
        // revertSingleResidueCoordinates(nucleicResidue, originalCoordinates[j]);
        }
    }
}

Example 3 with DoubleIndexPair

use of ffx.utilities.DoubleIndexPair in project ffx by mjschnie.

the class Rescore method rescoreSingle.

private File rescoreSingle(File modelFile, RescoreStrategy rscType, DoubleIndexPair[] energies, int i) {
    Path filepath = generatePath(modelFile);
    if (filepath == null) {
        logger.warning(String.format(" Could not generate path to file %s", modelFile.toPath()));
        return null;
    }
    String filename = pwdPath.relativize(filepath).toString();
    File retFile = modelFile;
    try {
        MolecularAssembly assembly = utils.open(filename);
        switch(rscType) {
            case NO_RESCORE:
                logger.warning(" Rescore is being called with rscType = NO_RESCORE");
                break;
            case ENERGY_EVAL:
                break;
            case MINIMIZE:
                logger.info(String.format("\n Running minimize on %s", filename));
                logger.info(String.format(" RMS gradient convergence criteria: %f", eps));
                utils.energy(assembly);
                utils.minimize(assembly, eps);
                String ext = FilenameUtils.getExtension(filename);
                ext = ".".concat(ext);
                if (resultDir != null) {
                    filename = FilenameUtils.getBaseName(filename);
                    filename = FilenameUtils.concat(resultPath.toString(), filename);
                } else {
                    filename = FilenameUtils.removeExtension(filename);
                }
                filename = filename.concat(fileSuffix).concat(ext);
                retFile = new File(filename);
                if (ext.toUpperCase().contains("XYZ")) {
                    utils.saveAsXYZ(assembly, retFile);
                } else {
                    utils.saveAsPDB(assembly, retFile);
                }
                break;
            case XRAY_MIN:
                logger.info(String.format("\n Running x-ray minimize on %s", filename));
                DiffractionFile diffractionFile = null;
                if (diffractionFiles.isEmpty()) {
                    diffractionFile = new DiffractionFile(assembly, 1.0, false);
                    diffractionFiles.add(diffractionFile);
                }
                CompositeConfiguration properties = Keyword.loadProperties(modelFile);
                DiffractionData diffractionData = new DiffractionData(assembly, properties, SolventModel.POLYNOMIAL, diffractionFiles.toArray(new DiffractionFile[diffractionFiles.size()]));
                diffractionData.scaleBulkFit();
                diffractionData.printStats();
                utils.energy(assembly);
                RefinementMinimize refinementMinimize = new RefinementMinimize(diffractionData, refinementMode);
                if (eps < 0.0) {
                    eps = refinementMinimize.getEps();
                }
                logger.info(String.format("\n RMS gradient convergence criteria: %8.5f max number of iterations %d", eps, maxiter));
                refinementMinimize.minimize(eps, maxiter);
                diffractionData.scaleBulkFit();
                diffractionData.printStats();
                ext = FilenameUtils.getExtension(filename);
                ext = ".".concat(ext);
                if (resultDir != null) {
                    filename = FilenameUtils.getBaseName(filename);
                    filename = FilenameUtils.concat(resultPath.toString(), filename);
                } else {
                    filename = FilenameUtils.removeExtension(filename);
                }
                filename = filename.concat(fileSuffix);
                diffractionData.writeData(filename + ".mtz");
                filename = filename.concat(ext);
                diffractionData.writeModel(filename);
                retFile = new File(filename);
                if (diffractionFile != null) {
                    try {
                        diffractionFiles.remove(diffractionFile);
                    } catch (UnsupportedOperationException ex) {
                        // This should never occur, because diffractionFiles should be of a List type supporting remove(object).
                        diffractionFiles = new ArrayList<>();
                    }
                }
                break;
            case RS_MIN:
                logger.info(String.format("\n Running real-space minimize on %s", filename));
                RealSpaceFile realspaceFile = null;
                if (mapFiles.isEmpty()) {
                    realspaceFile = new RealSpaceFile(assembly);
                    mapFiles.add(realspaceFile);
                }
                properties = Keyword.loadProperties(modelFile);
                RealSpaceData realspaceData = new RealSpaceData(assembly, properties, new ParallelTeam(), mapFiles.toArray(new RealSpaceFile[mapFiles.size()]));
                utils.energy(assembly);
                refinementMinimize = new RefinementMinimize(realspaceData, refinementMode);
                if (eps < 0.0) {
                    eps = 1.0;
                }
                logger.info(String.format("\n RMS gradient convergence criteria: %8.5f max number of iterations %d", eps, maxiter));
                refinementMinimize.minimize(eps, maxiter);
                ext = FilenameUtils.getExtension(filename);
                ext = ".".concat(ext);
                if (resultDir != null) {
                    filename = FilenameUtils.getBaseName(filename);
                    filename = FilenameUtils.concat(resultPath.toString(), filename);
                } else {
                    filename = FilenameUtils.removeExtension(filename);
                }
                filename = filename.concat(fileSuffix).concat(ext);
                retFile = new File(filename);
                if (ext.toUpperCase().contains("XYZ")) {
                    utils.saveAsXYZ(assembly, retFile);
                } else {
                    utils.saveAsPDB(assembly, retFile);
                }
                if (realspaceFile != null) {
                    try {
                        mapFiles.remove(realspaceFile);
                    } catch (UnsupportedOperationException ex) {
                        // This should never occur, because diffractionFiles should be of a List type supporting remove(object).
                        mapFiles = new ArrayList<>();
                    }
                }
                break;
            default:
                logger.severe(" No valid rescore type: FFX will not continue.");
        }
        double e = utils.returnEnergy(assembly);
        energies[i] = new DoubleIndexPair(i, e);
        utils.close(assembly);
    } catch (Exception ex) {
        logger.warning(String.format(" Exception rescoring on file %s", filename));
        logger.info(ex.toString());
    }
    return retFile;
}