Examples with ForceFieldEnergy ffx.potential.ForceFieldEnergy used on opensource projects

Example 1 with ForceFieldEnergy

use of ffx.potential.ForceFieldEnergy in project ffx by mjschnie.

the class RefinementEnergy method getd2EdL2.

/**
 * {@inheritDoc}
 */
@Override
public double getd2EdL2() {
    double d2EdL2 = 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 curE = forceFieldEnergy.getd2EdL2();
        d2EdL2 += (curE - d2EdL2) / (i + 1);
    }
    d2EdL2 *= kTScale;
    /**
     * No 2nd derivative for scattering term.
     */
    return d2EdL2;
}

Example 2 with ForceFieldEnergy

use of ffx.potential.ForceFieldEnergy 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 3 with ForceFieldEnergy

use of ffx.potential.ForceFieldEnergy in project ffx by mjschnie.

the class PotentialsFileOpener method run.

/**
 * At present, parses the PDB, XYZ, INT, or ARC file from the constructor
 * and creates MolecularAssembly and properties objects.
 */
@Override
public void run() {
    int numFiles = allFiles.length;
    for (int i = 0; i < numFiles; i++) {
        File fileI = allFiles[i];
        Path pathI = allPaths[i];
        MolecularAssembly assembly = new MolecularAssembly(pathI.toString());
        assembly.setFile(fileI);
        CompositeConfiguration properties = Keyword.loadProperties(fileI);
        ForceFieldFilter forceFieldFilter = new ForceFieldFilter(properties);
        ForceField forceField = forceFieldFilter.parse();
        String[] patches = properties.getStringArray("patch");
        for (String patch : patches) {
            logger.info(" Attempting to read force field patch from " + patch + ".");
            CompositeConfiguration patchConfiguration = new CompositeConfiguration();
            try {
                patchConfiguration.addProperty("propertyFile", fileI.getCanonicalPath());
            } catch (IOException e) {
                logger.log(Level.INFO, " Error loading {0}.", patch);
            }
            patchConfiguration.addProperty("parameters", patch);
            forceFieldFilter = new ForceFieldFilter(patchConfiguration);
            ForceField patchForceField = forceFieldFilter.parse();
            forceField.append(patchForceField);
            if (RotamerLibrary.addRotPatch(patch)) {
                logger.info(String.format(" Loaded rotamer definitions from patch %s.", patch));
            }
        }
        assembly.setForceField(forceField);
        if (new PDBFileFilter().acceptDeep(fileI)) {
            filter = new PDBFilter(fileI, assembly, forceField, properties);
        } else if (new XYZFileFilter().acceptDeep(fileI)) {
            filter = new XYZFilter(fileI, assembly, forceField, properties);
        } else if (new INTFileFilter().acceptDeep(fileI) || new ARCFileFilter().accept(fileI)) {
            filter = new INTFilter(fileI, assembly, forceField, properties);
        } else {
            throw new IllegalArgumentException(String.format(" File %s could not be recognized as a valid PDB, XYZ, INT, or ARC file.", pathI.toString()));
        }
        /* If on-open mutations requested, add them to filter. */
        if (mutationsToApply != null && !mutationsToApply.isEmpty()) {
            if (!(filter instanceof PDBFilter)) {
                throw new UnsupportedOperationException("Applying mutations during open only supported by PDB filter atm.");
            }
            ((PDBFilter) filter).mutate(mutationsToApply);
        }
        if (filter.readFile()) {
            if (!(filter instanceof PDBFilter)) {
                Utilities.biochemistry(assembly, filter.getAtomList());
            }
            filter.applyAtomProperties();
            assembly.finalize(true, forceField);
            // ForceFieldEnergy energy = ForceFieldEnergy.energyFactory(assembly, filter.getCoordRestraints());
            ForceFieldEnergy energy;
            if (nThreads > 0) {
                energy = ForceFieldEnergy.energyFactory(assembly, filter.getCoordRestraints(), nThreads);
            } else {
                energy = ForceFieldEnergy.energyFactory(assembly, filter.getCoordRestraints());
            }
            assembly.setPotential(energy);
            assemblies.add(assembly);
            propertyList.add(properties);
            if (filter instanceof PDBFilter) {
                PDBFilter pdbFilter = (PDBFilter) filter;
                List<Character> altLocs = pdbFilter.getAltLocs();
                if (altLocs.size() > 1 || altLocs.get(0) != ' ') {
                    StringBuilder altLocString = new StringBuilder("\n Alternate locations found [ ");
                    for (Character c : altLocs) {
                        // Do not report the root conformer.
                        if (c == ' ') {
                            continue;
                        }
                        altLocString.append(format("(%s) ", c));
                    }
                    altLocString.append("]\n");
                    logger.info(altLocString.toString());
                }
                /**
                 * Alternate conformers may have different chemistry, so
                 * they each need to be their own MolecularAssembly.
                 */
                for (Character c : altLocs) {
                    if (c.equals(' ') || c.equals('A')) {
                        continue;
                    }
                    MolecularAssembly newAssembly = new MolecularAssembly(pathI.toString());
                    newAssembly.setForceField(assembly.getForceField());
                    pdbFilter.setAltID(newAssembly, c);
                    pdbFilter.clearSegIDs();
                    if (pdbFilter.readFile()) {
                        String fileName = assembly.getFile().getAbsolutePath();
                        newAssembly.setName(FilenameUtils.getBaseName(fileName) + " " + c);
                        filter.applyAtomProperties();
                        newAssembly.finalize(true, assembly.getForceField());
                        // energy = ForceFieldEnergy.energyFactory(newAssembly, filter.getCoordRestraints());
                        if (nThreads > 0) {
                            energy = ForceFieldEnergy.energyFactory(assembly, filter.getCoordRestraints(), nThreads);
                        } else {
                            energy = ForceFieldEnergy.energyFactory(assembly, filter.getCoordRestraints());
                        }
                        newAssembly.setPotential(energy);
                        assemblies.add(newAssembly);
                    }
                }
            }
        } else {
            logger.warning(String.format(" Failed to read file %s", fileI.toString()));
        }
    }
    activeAssembly = assemblies.get(0);
    activeProperties = propertyList.get(0);
}

Example 4 with ForceFieldEnergy

use of ffx.potential.ForceFieldEnergy in project ffx by mjschnie.

the class UIUtils method energy.

@Override
public ForceFieldEnergy energy(MolecularAssembly assembly) {
    Optional<FFXSystem> origSys = switchTo(assembly);
    ForceFieldEnergy ffe = modelingShell.energy();
    switchBack(origSys);
    return ffe;
}

Example 5 with ForceFieldEnergy

use of ffx.potential.ForceFieldEnergy in project ffx by mjschnie.

the class CrystalReciprocalSpaceTest method test1N7SPermanent.

/**
 * Test of permanent method, of class CrystalReciprocalSpace.
 */
@Test
public void test1N7SPermanent() {
    String filename = "ffx/xray/structures/1N7S.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());
    PotentialsUtils potutil = new PotentialsUtils();
    MolecularAssembly mola = potutil.open(structure);
    CompositeConfiguration properties = mola.getProperties();
    Crystal crystal = new Crystal(39.767, 51.750, 132.938, 90.00, 90.00, 90.00, "P212121");
    Resolution resolution = new Resolution(1.45);
    ReflectionList reflectionList = new ReflectionList(crystal, resolution);
    DiffractionRefinementData refinementData = new DiffractionRefinementData(properties, reflectionList);
    mola.finalize(true, mola.getForceField());
    ForceFieldEnergy energy = mola.getPotentialEnergy();
    List<Atom> atomList = mola.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(-828.584, -922.704);
    HKL hkl = reflectionList.getHKL(1, 1, 4);
    ComplexNumber a = refinementData.getFc(hkl.index());
    System.out.println("1 1 4: " + a.toString() + " | " + b.toString() + " | " + a.divides(b).toString());
    assertEquals("1 1 4 reflection should be correct", -753.4722104328416, a.re(), 0.0001);
    assertEquals("1 1 4 reflection should be correct", -1012.1341308707799, a.im(), 0.0001);
    b.re(-70.4582);
    b.im(-486.142);
    hkl = reflectionList.getHKL(2, 1, 10);
    a = refinementData.getFc(hkl.index());
    System.out.println("2 1 10: " + a.toString() + " | " + b.toString() + " | " + a.divides(b).toString());
    assertEquals("2 1 10 reflection should be correct", -69.39660884054359, a.re(), 0.0001);
    assertEquals("2 1 10 reflection should be correct", -412.0147625765328, a.im(), 0.0001);
}