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

Example 1 with XYZFilter

use of ffx.potential.parsers.XYZFilter 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 2 with XYZFilter

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

the class MolecularDynamics method assemblyInfo.

protected void assemblyInfo() {
    assemblies.stream().parallel().forEach((ainfo) -> {
        MolecularAssembly mola = ainfo.getAssembly();
        CompositeConfiguration aprops = ainfo.props;
        File file = mola.getFile();
        String filename = FilenameUtils.removeExtension(file.getAbsolutePath());
        File archFile = ainfo.archiveFile;
        if (archFile == null) {
            archFile = new File(filename + ".arc");
            ainfo.archiveFile = XYZFilter.version(archFile);
        }
        if (ainfo.pdbFile == null) {
            String extName = FilenameUtils.getExtension(file.getName());
            if (extName.toLowerCase().startsWith("pdb")) {
                ainfo.pdbFile = file;
            } else {
                ainfo.pdbFile = new File(filename + ".pdb");
            }
        }
        if (ainfo.xyzFilter == null) {
            ainfo.xyzFilter = new XYZFilter(file, mola, mola.getForceField(), aprops);
        }
        if (ainfo.pdbFilter == null) {
            ainfo.pdbFilter = new PDBFilter(ainfo.pdbFile, mola, mola.getForceField(), aprops);
        }
    });
}

Example 3 with XYZFilter

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

the class MainPanel method saveAsXYZ.

/**
 * Save the currently selected FFXSystem to disk.
 *
 * @param file File to save the system to.
 * @since 1.0
 */
public void saveAsXYZ(File file) {
    FFXSystem system = hierarchy.getActive();
    if (system != null && !system.isClosing()) {
        File saveFile = file;
        if (saveFile == null) {
            resetFileChooser();
            fileChooser.setCurrentDirectory(pwd);
            fileChooser.setFileFilter(xyzFileFilter);
            fileChooser.setAcceptAllFileFilterUsed(false);
            int result = fileChooser.showSaveDialog(this);
            if (result == JFileChooser.APPROVE_OPTION) {
                saveFile = fileChooser.getSelectedFile();
                pwd = saveFile.getParentFile();
            }
        }
        if (saveFile != null) {
            SystemFilter filter = new XYZFilter(saveFile, system, null, null);
            if (filter.writeFile(saveFile, false)) {
                // Refresh Panels with the new System name
                hierarchy.setActive(system);
                activeFilter = filter;
            }
        }
    }
}

Example 4 with XYZFilter

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

the class AbstractOSRW method setOptimization.

public void setOptimization(boolean osrwOptimization, MolecularAssembly molAss) {
    this.osrwOptimization = osrwOptimization;
    this.molecularAssembly = molAss;
    File file = molecularAssembly.getFile();
    String fileName = FilenameUtils.removeExtension(file.getAbsolutePath());
    String ext = FilenameUtils.getExtension(file.getAbsolutePath());
    if (systemFilter == null) {
        if (ext.toUpperCase().contains("XYZ")) {
            optFile = new File(fileName + "_opt.xyz");
            systemFilter = new XYZFilter(optFile, molecularAssembly, null, null);
        } else {
            optFile = new File(fileName + "_opt.pdb");
            systemFilter = new PDBFilter(optFile, molecularAssembly, null, null);
        }
    }
}

Example 5 with XYZFilter

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

the class MainPanel method saveAsP1.

/**
 * Save the currently selected FFXSystem to disk.
 *
 * @param file File to save the system to.
 * @since 1.0
 */
public void saveAsP1(File file) {
    FFXSystem system = hierarchy.getActive();
    if (system != null && !system.isClosing()) {
        File saveFile = file;
        if (saveFile == null) {
            resetFileChooser();
            fileChooser.setCurrentDirectory(pwd);
            fileChooser.setFileFilter(xyzFileFilter);
            fileChooser.setAcceptAllFileFilterUsed(false);
            int result = fileChooser.showSaveDialog(this);
            if (result == JFileChooser.APPROVE_OPTION) {
                saveFile = fileChooser.getSelectedFile();
                pwd = saveFile.getParentFile();
            }
        }
        if (saveFile != null) {
            XYZFilter filter = new XYZFilter(saveFile, system, null, null);
            ForceField forceField = system.getForceField();
            final double a = forceField.getDouble(ForceFieldDouble.A_AXIS, 10.0);
            final double b = forceField.getDouble(ForceFieldDouble.B_AXIS, a);
            final double c = forceField.getDouble(ForceFieldDouble.C_AXIS, a);
            final double alpha = forceField.getDouble(ForceFieldDouble.ALPHA, 90.0);
            final double beta = forceField.getDouble(ForceFieldDouble.BETA, 90.0);
            final double gamma = forceField.getDouble(ForceFieldDouble.GAMMA, 90.0);
            final String spacegroup = forceField.getString(ForceFieldString.SPACEGROUP, "P1");
            Crystal crystal = new Crystal(a, b, c, alpha, beta, gamma, spacegroup);
            if (filter.writeFileAsP1(saveFile, false, crystal)) {
                // Refresh Panels with the new System name
                hierarchy.setActive(system);
            }
            activeFilter = filter;
        }
    }
}