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Example 1 with CIFFilter

use of ffx.xray.parsers.CIFFilter in project ffx by mjschnie.

the class TimerTest method main.

public static void main(String[] args) {
    // Parameters collection from original Timer script
    String pdbname = System.getProperty("pdbFile", "1N7S.pdb");
    String mtzname = System.getProperty("mtzFile", null);
    String cifname = System.getProperty("cifFile", null);
    final boolean ciOnly = false;
    final String info = "SNARE complex";
    final double r = 19.412671496011;
    final double rfree = 21.555930987573;
    final double sigmaA = 0.9336853524690557;
    final double sigmaW = 0.13192537249786418;
    boolean ci = System.getProperty("ffx.ci", "false").equalsIgnoreCase("true");
    if (!ci && ciOnly) {
        crystalStats = null;
        return;
    }
    int index = pdbname.lastIndexOf(".");
    String name = pdbname.substring(0, index);
    // load the structure
    MolecularAssembly molecularAssembly;
    File structure, mtzFile, cifFile;
    structure = new File(pdbname);
    PotentialsFileOpener opener = new PotentialsFileOpener(structure);
    opener.run();
    molecularAssembly = opener.getAssembly();
    mtzFile = new File(mtzname);
    cifFile = new File(cifname);
    // load any properties associated with it
    CompositeConfiguration properties = Keyword.loadProperties(structure);
    // read in Fo/sigFo/FreeR
    MTZFilter mtzFilter = new MTZFilter();
    CIFFilter cifFilter = new CIFFilter();
    Crystal crystal = Crystal.checkProperties(properties);
    Resolution resolution = Resolution.checkProperties(properties);
    if (crystal == null || resolution == null) {
        if (mtzname != null) {
            reflectionList = mtzFilter.getReflectionList(mtzFile);
        } else {
            reflectionList = cifFilter.getReflectionList(cifFile);
        }
    } else {
        reflectionList = new ReflectionList(crystal, resolution);
    }
    refinementData = new DiffractionRefinementData(properties, reflectionList);
    if (mtzname != null) {
    // assertTrue(info + " mtz file should be read in without errors",
    // mtzFilter.readFile(mtzFile, reflectionList, refinementData,
    // properties));
    } else {
    // assertTrue(info + " cif file should be read in without errors",
    // cifFilter.readFile(cifFile, reflectionList, refinementData,
    // properties));
    }
    ForceFieldFilter forceFieldFilter = new ForceFieldFilter(properties);
    ForceField forceField = forceFieldFilter.parse();
    // associate molecular assembly with the structure, set up forcefield
    molecularAssembly.setForceField(forceField);
    PDBFilter pdbFile = new PDBFilter(structure, molecularAssembly, forceField, properties);
    pdbFile.readFile();
    pdbFile.applyAtomProperties();
    molecularAssembly.finalize(true, forceField);
    ForceFieldEnergy energy = ForceFieldEnergy.energyFactory(molecularAssembly, pdbFile.getCoordRestraints());
    List<Atom> atomList = molecularAssembly.getAtomList();
    Atom[] atomArray = atomList.toArray(new Atom[atomList.size()]);
    // set up FFT and run it
    parallelTeam = new ParallelTeam();
    CrystalReciprocalSpace crs = new CrystalReciprocalSpace(reflectionList, atomArray, parallelTeam, parallelTeam, false);
    crs.computeDensity(refinementData.fc);
    refinementData.setCrystalReciprocalSpace_fc(crs);
    crs = new CrystalReciprocalSpace(reflectionList, atomArray, parallelTeam, parallelTeam, true);
    crs.computeDensity(refinementData.fs);
    refinementData.setCrystalReciprocalSpace_fs(crs);
    ScaleBulkMinimize scaleBulkMinimize = new ScaleBulkMinimize(reflectionList, refinementData, crs, parallelTeam);
    scaleBulkMinimize.minimize(6, 1.0e-4);
    SigmaAMinimize sigmaAMinimize = new SigmaAMinimize(reflectionList, refinementData, parallelTeam);
    sigmaAMinimize.minimize(7, 2.0e-2);
    SplineMinimize splineMinimize = new SplineMinimize(reflectionList, refinementData, refinementData.spline, SplineEnergy.Type.FOFC);
    splineMinimize.minimize(7, 1e-5);
    crystalStats = new CrystalStats(reflectionList, refinementData);
    scaleBulkMinimize = new ScaleBulkMinimize(reflectionList, refinementData, refinementData.crs_fs, parallelTeam);
    ScaleBulkEnergy scaleBulkEnergy = scaleBulkMinimize.getScaleBulkEnergy();
    int n = scaleBulkMinimize.getNumberOfVariables();
    double[] x = new double[n];
    double[] g = new double[n];
    scaleBulkMinimize.getCoordinates(x);
    scaleBulkEnergy.energyAndGradient(x, g);
    double delta = 1.0e-4;
    double tolerance = 1.0e-4;
    logger.info(String.format("SCATTER TEST"));
    for (int i = 0; i < 30; i++) {
        long time = -System.nanoTime();
        scaleBulkEnergy.energyAndGradient(x, g);
        time += System.nanoTime();
        logger.info(String.format(" Time %12.8f", time * 1.0e-9));
    }
}
Also used : ParallelTeam(edu.rit.pj.ParallelTeam) ForceFieldFilter(ffx.potential.parsers.ForceFieldFilter) ForceFieldEnergy(ffx.potential.ForceFieldEnergy) ReflectionList(ffx.crystal.ReflectionList) ForceField(ffx.potential.parameters.ForceField) PDBFilter(ffx.potential.parsers.PDBFilter) CompositeConfiguration(org.apache.commons.configuration.CompositeConfiguration) Atom(ffx.potential.bonded.Atom) PotentialsFileOpener(ffx.potential.utils.PotentialsFileOpener) MolecularAssembly(ffx.potential.MolecularAssembly) CIFFilter(ffx.xray.parsers.CIFFilter) File(java.io.File) MTZFilter(ffx.xray.parsers.MTZFilter) Crystal(ffx.crystal.Crystal) Resolution(ffx.crystal.Resolution)

Aggregations

ParallelTeam (edu.rit.pj.ParallelTeam)1 Crystal (ffx.crystal.Crystal)1 ReflectionList (ffx.crystal.ReflectionList)1 Resolution (ffx.crystal.Resolution)1 ForceFieldEnergy (ffx.potential.ForceFieldEnergy)1 MolecularAssembly (ffx.potential.MolecularAssembly)1 Atom (ffx.potential.bonded.Atom)1 ForceField (ffx.potential.parameters.ForceField)1 ForceFieldFilter (ffx.potential.parsers.ForceFieldFilter)1 PDBFilter (ffx.potential.parsers.PDBFilter)1 PotentialsFileOpener (ffx.potential.utils.PotentialsFileOpener)1 CIFFilter (ffx.xray.parsers.CIFFilter)1 MTZFilter (ffx.xray.parsers.MTZFilter)1 File (java.io.File)1 CompositeConfiguration (org.apache.commons.configuration.CompositeConfiguration)1