Examples with PDBFilter ffx.potential.parsers.PDBFilter used on opensource projects

Example 31 with PDBFilter

use of ffx.potential.parsers.PDBFilter in project ffx by mjschnie.

the class CrystalReciprocalSpaceTest method test1NSFPermanent.

@Test
public void test1NSFPermanent() {
    String filename = "ffx/xray/structures/1NSF.pdb";
    int index = filename.lastIndexOf(".");
    String name = filename.substring(0, index);
    // load the structure
    ClassLoader cl = this.getClass().getClassLoader();
    File structure = new File(cl.getResource(filename).getPath());
    // load any properties associated with it
    CompositeConfiguration properties = Keyword.loadProperties(structure);
    Crystal crystal = new Crystal(115.996, 115.996, 44.13, 90.0, 90.0, 120.0, "P6");
    Resolution resolution = new Resolution(1.89631);
    ReflectionList reflectionList = new ReflectionList(crystal, resolution);
    DiffractionRefinementData refinementData = new DiffractionRefinementData(properties, reflectionList);
    ForceFieldFilter forceFieldFilter = new ForceFieldFilter(properties);
    ForceField forceField = forceFieldFilter.parse();
    // associate molecular assembly with the structure, set up forcefield
    MolecularAssembly molecularAssembly = new MolecularAssembly(name);
    molecularAssembly.setFile(structure);
    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 parallelTeam = new ParallelTeam();
    CrystalReciprocalSpace crs = new CrystalReciprocalSpace(reflectionList, atomArray, parallelTeam, parallelTeam);
    crs.computeAtomicDensity(refinementData.fc);
    // tests
    ComplexNumber b = new ComplexNumber(-496.999, 431.817);
    HKL hkl = reflectionList.getHKL(1, 9, 4);
    ComplexNumber a = refinementData.getFc(hkl.index());
    System.out.println("1 9 4: " + a.toString() + " | " + b.toString() + " | " + a.divides(b).toString());
    assertEquals("1 9 4 reflection should be correct", -493.7799429881329, a.re(), 0.0001);
    assertEquals("1 9 4 reflection should be correct", 460.7022632345927, a.im(), 0.0001);
    b.re(-129.767);
    b.im(-76.9812);
    hkl = reflectionList.getHKL(5, 26, 8);
    a = refinementData.getFc(hkl.index());
    System.out.println("5 26 8: " + a.toString() + " | " + b.toString() + " | " + a.divides(b).toString());
    assertEquals("5 26 8 reflection should be correct", -123.05535567943377, a.re(), 0.0001);
    assertEquals("5 26 8 reflection should be correct", -74.59007322382718, a.im(), 0.0001);
}

Example 32 with PDBFilter

use of ffx.potential.parsers.PDBFilter 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));
    }
}

Example 33 with PDBFilter

use of ffx.potential.parsers.PDBFilter in project ffx by mjschnie.

the class PotentialsUtils method saveAsSIFTPDB.

public void saveAsSIFTPDB(MolecularAssembly[] assemblies, File file, String[] resAndScore) {
    if (assemblies == null) {
        logger.info(" Assembly to save was null.");
    } else if (file == null) {
        logger.info(" No valid file provided to save assembly to.");
    } else if (resAndScore == null) {
        logger.info(" Res and score array was null.");
    } else {
        PDBFilter pdbFilter = new PDBFilter(file, Arrays.asList(assemblies), null, null);
        pdbFilter.writeSIFTFile(file, false, resAndScore);
        lastFilter = pdbFilter;
    }
}