Examples with RealSpaceData ffx.realspace.RealSpaceData used on opensource projects

Example 1 with RealSpaceData

use of ffx.realspace.RealSpaceData in project ffx by mjschnie.

the class RefinementEnergy method setLambda.

/**
 * {@inheritDoc}
 */
@Override
public void setLambda(double lambda) {
    for (MolecularAssembly molecularAssembly : molecularAssemblies) {
        ForceFieldEnergy forceFieldEnergy = molecularAssembly.getPotentialEnergy();
        forceFieldEnergy.setLambda(lambda);
    }
    if (data instanceof DiffractionData) {
        XRayEnergy xRayEnergy = (XRayEnergy) dataEnergy;
        xRayEnergy.setLambda(lambda);
    } else if (data instanceof RealSpaceData) {
        RealSpaceEnergy realSpaceEnergy = (RealSpaceEnergy) dataEnergy;
        realSpaceEnergy.setLambda(lambda);
    }
}

Example 2 with RealSpaceData

use of ffx.realspace.RealSpaceData in project ffx by mjschnie.

the class RefinementEnergy method getdEdXdL.

/**
 * {@inheritDoc}
 */
@Override
public void getdEdXdL(double[] gradient) {
    double weight = data.getWeight();
    if (thermostat != null) {
        kTScale = Thermostat.convert / (thermostat.getTargetTemperature() * Thermostat.kB);
    }
    int assemblysize = molecularAssemblies.length;
    /**
     * Compute the chemical energy and gradient.
     */
    for (int i = 0; i < assemblysize; i++) {
        ForceFieldEnergy forcefieldEnergy = molecularAssemblies[i].getPotentialEnergy();
        Arrays.fill(gChemical[i], 0.0);
        forcefieldEnergy.getdEdXdL(gChemical[i]);
    }
    for (int i = 0; i < assemblysize; i++) {
        for (int j = 0; j < nXYZ; j++) {
            gradient[j] += gChemical[i][j];
        }
    }
    /**
     * Normalize gradients for multiple-counted atoms.
     */
    if (assemblysize > 1) {
        for (int i = 0; i < nXYZ; i++) {
            gradient[i] /= assemblysize;
        }
    }
    for (int i = 0; i < nXYZ; i++) {
        gradient[i] *= kTScale;
    }
    /**
     * Compute the X-ray target energy and gradient.
     */
    if (gXray == null || gXray.length != nXYZ) {
        gXray = new double[nXYZ];
    } else {
        for (int j = 0; j < nXYZ; j++) {
            gXray[j] = 0.0;
        }
    }
    if (data instanceof DiffractionData) {
        XRayEnergy xRayEnergy = (XRayEnergy) dataEnergy;
        xRayEnergy.getdEdXdL(gXray);
    } else if (data instanceof RealSpaceData) {
        RealSpaceEnergy realSpaceEnergy = (RealSpaceEnergy) dataEnergy;
        realSpaceEnergy.getdEdXdL(gXray);
    }
    // Add the chemical and X-ray gradients.
    for (int i = 0; i < nXYZ; i++) {
        gradient[i] += weight * gXray[i];
    }
}

Example 3 with RealSpaceData

use of ffx.realspace.RealSpaceData in project ffx by mjschnie.

the class RefinementEnergy method getdEdL.

/**
 * {@inheritDoc}
 */
@Override
public double getdEdL() {
    double dEdL = 0.0;
    if (thermostat != null) {
        kTScale = Thermostat.convert / (thermostat.getTargetTemperature() * Thermostat.kB);
    }
    int assemblysize = molecularAssemblies.length;
    /**
     * Compute the chemical energy and gradient.
     */
    for (int i = 0; i < assemblysize; i++) {
        ForceFieldEnergy forceFieldEnergy = molecularAssemblies[i].getPotentialEnergy();
        double curdEdL = forceFieldEnergy.getdEdL();
        dEdL += (curdEdL - dEdL) / (i + 1);
    }
    dEdL *= kTScale;
    double weight = data.getWeight();
    if (data instanceof DiffractionData) {
        XRayEnergy xRayEnergy = (XRayEnergy) dataEnergy;
        dEdL += weight * xRayEnergy.getdEdL();
    } else if (data instanceof RealSpaceData) {
        RealSpaceEnergy realSpaceEnergy = (RealSpaceEnergy) dataEnergy;
        dEdL += weight * realSpaceEnergy.getdEdL();
    }
    return dEdL;
}

Example 4 with RealSpaceData

use of ffx.realspace.RealSpaceData 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;
}