Examples with DiffractionRefinementData ffx.xray.DiffractionRefinementData used on opensource projects

Example 1 with DiffractionRefinementData

use of ffx.xray.DiffractionRefinementData in project ffx by mjschnie.

the class MTZFilter method averageFcs.

/**
 * Average the computed structure factors for two systems.
 *
 * @param mtzFile1 This file will be overwritten and become the new average.
 * @param mtzFile2 Second MTZ file.
 * @param reflectionlist List of HKLs.
 * @param iter The iteration in the running average.
 * @param properties The CompositeConfiguration defines the properties of
 * each system.
 */
public void averageFcs(File mtzFile1, File mtzFile2, ReflectionList reflectionlist, int iter, CompositeConfiguration properties) {
    DiffractionRefinementData fcdata1 = new DiffractionRefinementData(properties, reflectionlist);
    DiffractionRefinementData fcdata2 = new DiffractionRefinementData(properties, reflectionlist);
    readFcs(mtzFile1, reflectionlist, fcdata1, properties);
    readFcs(mtzFile2, reflectionlist, fcdata2, properties);
    // compute running average using mtzFile1 as current average
    System.out.println("iteration for averaging: " + iter);
    for (int i = 0; i < reflectionlist.hkllist.size(); i++) {
        fcdata1.fc[i][0] += (fcdata2.fc[i][0] - fcdata1.fc[i][0]) / iter;
        fcdata1.fc[i][1] += (fcdata2.fc[i][1] - fcdata1.fc[i][1]) / iter;
        fcdata1.fs[i][0] += (fcdata2.fs[i][0] - fcdata1.fs[i][0]) / iter;
        fcdata1.fs[i][1] += (fcdata2.fs[i][1] - fcdata1.fs[i][1]) / iter;
    }
    // overwrite original MTZ
    MTZWriter mtzOut = new MTZWriter(reflectionlist, fcdata1, mtzFile1.getName(), MTZType.FCONLY);
    mtzOut.write();
}

Example 2 with DiffractionRefinementData

use of ffx.xray.DiffractionRefinementData in project ffx by mjschnie.

the class CIFFilterTest method testCIFFilter3DYC.

@Test
public void testCIFFilter3DYC() {
    String filename = "ffx/xray/structures/3DYC.ent";
    ClassLoader cl = this.getClass().getClassLoader();
    File cifFile = new File(cl.getResource(filename).getPath());
    // load any properties associated with it
    CompositeConfiguration properties = Keyword.loadProperties(cifFile);
    CIFFilter cifFilter = new CIFFilter();
    ReflectionList reflectionList = cifFilter.getReflectionList(cifFile);
    assertNotNull(" Reflection list should not be null", reflectionList);
    DiffractionRefinementData refinementData = new DiffractionRefinementData(properties, reflectionList);
    assertTrue(" CIF data not read in correctly", cifFilter.readFile(cifFile, reflectionList, refinementData, properties));
    HKL hkl = reflectionList.getHKL(58, 0, 13);
    assertEquals("58 0 13 F", 99.7, refinementData.getF(hkl.index()), 0.01);
    assertEquals("58 0 13 sigF", 69.7, refinementData.getSigF(hkl.index()), 0.01);
    assertEquals("58 0 13 freeR value", 1, refinementData.freer[hkl.index()]);
    hkl = reflectionList.getHKL(28, 20, 5);
    assertEquals("28 20 5 F", 428.1, refinementData.getF(hkl.index()), 0.01);
    assertEquals("28 20 5 sigF", 10.1, refinementData.getSigF(hkl.index()), 0.01);
    assertEquals("28 20 5 freeR value", 0, refinementData.freer[hkl.index()]);
}

Example 3 with DiffractionRefinementData

use of ffx.xray.DiffractionRefinementData in project ffx by mjschnie.

the class CIFFilterTest method testCIFFilter2DRM.

@Test
public void testCIFFilter2DRM() {
    String filename = "ffx/xray/structures/2DRM.cif";
    ClassLoader cl = this.getClass().getClassLoader();
    File cifFile = new File(cl.getResource(filename).getPath());
    // load any properties associated with it
    CompositeConfiguration properties = Keyword.loadProperties(cifFile);
    CIFFilter cifFilter = new CIFFilter();
    ReflectionList reflectionList = cifFilter.getReflectionList(cifFile);
    assertNull(" Reflection list should be null", reflectionList);
    Crystal crystal = new Crystal(29.969, 37.861, 44.506, 90.28, 90.11, 90.64, "P1");
    Resolution resolution = new Resolution(1.30);
    reflectionList = new ReflectionList(crystal, resolution);
    DiffractionRefinementData refinementData = new DiffractionRefinementData(properties, reflectionList);
    assertTrue(" CIF data not read correctly", cifFilter.readFile(cifFile, reflectionList, refinementData, properties));
    HKL hkl = reflectionList.getHKL(-21, -6, 7);
    assertEquals("-21 -6 7 F", 18.6, refinementData.getF(hkl.index()), 0.01);
    assertEquals("-21 -6 7 sigF", 3.6, refinementData.getSigF(hkl.index()), 0.01);
    assertEquals("-21 -6 7 freeR value", 0, refinementData.freer[hkl.index()]);
    hkl = reflectionList.getHKL(-21, -6, 8);
    assertEquals("-21 -6 7 F", 20.2, refinementData.getF(hkl.index()), 0.01);
    assertEquals("-21 -6 7 sigF", 5.0, refinementData.getSigF(hkl.index()), 0.01);
    assertEquals("-21 -6 7 freeR value", 1, refinementData.freer[hkl.index()]);
}