Examples with ForceField ffx.potential.parameters.ForceField used on opensource projects

Example 6 with ForceField

use of ffx.potential.parameters.ForceField in project ffx by mjschnie.

the class TitrationUtils method titratingMultiresidueFactory.

/**
 * Create a MultiResidue from the given Residue by adding its alternated
 * protonation state(s) as alternate possibilities.
 */
public static MultiResidue titratingMultiresidueFactory(MolecularAssembly mola, Residue res) {
    ForceField ff = mola.getForceField();
    Potential potential = mola.getPotentialEnergy();
    if (!(potential instanceof ForceFieldEnergy)) {
        logger.warning(String.format("TitrationFactory only supported by ForceFieldEnergy potentials."));
        throw new IllegalStateException();
    }
    ForceFieldEnergy ffe = (ForceFieldEnergy) potential;
    /* Create new titration state. */
    Titration titration = Titration.lookup(res);
    String targetName = (titration.protForm != res.getAminoAcid3()) ? titration.protForm.toString() : titration.deprotForm.toString();
    int resNumber = res.getResidueNumber();
    Residue.ResidueType resType = res.getResidueType();
    Residue newRes = new Residue(targetName, resNumber, resType);
    /* Wrap both states in a MultiResidue. */
    MultiResidue multiRes = new MultiResidue(res, ff, ffe);
    Polymer polymer = findResiduePolymer(res, mola);
    polymer.addMultiResidue(multiRes);
    multiRes.addResidue(newRes);
    /* Begin in protonated state by default. */
    multiRes.setActiveResidue(titration.protForm);
    propagateInactiveResidues(multiRes, false);
    ffe.reInit();
    return multiRes;
}

Example 7 with ForceField

use of ffx.potential.parameters.ForceField 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;
        }
    }
}

Example 8 with ForceField

use of ffx.potential.parameters.ForceField in project ffx by mjschnie.

the class MainPanel method openInit.

/**
 * Attempts to load the supplied file
 *
 * @param files Files to open
 * @param commandDescription Description of the command that created this
 * file.
 * @return a {@link java.lang.Thread} object.
 */
private UIFileOpener openInit(List<File> files, String commandDescription) {
    if (files == null) {
        return null;
    }
    File file = new File(FilenameUtils.normalize(files.get(0).getAbsolutePath()));
    // Set the Current Working Directory based on this file.
    setCWD(file.getParentFile());
    // Get "filename" from "filename.extension".
    String name = file.getName();
    String extension = FilenameUtils.getExtension(name);
    // Create the CompositeConfiguration properties.
    CompositeConfiguration properties = Keyword.loadProperties(file);
    forceFieldFilter = new ForceFieldFilter(properties);
    ForceField forceField = forceFieldFilter.parse();
    // Create an FFXSystem for this file.
    FFXSystem newSystem = new FFXSystem(file, commandDescription, properties);
    String[] patches = properties.getStringArray("patch");
    for (String patch : patches) {
        logger.info(" Attempting to read force field patch from " + patch + ".");
        CompositeConfiguration patchConfiguration = new CompositeConfiguration();
        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));
        }
    }
    newSystem.setForceField(forceField);
    // Decide what parser to use.
    SystemFilter systemFilter = null;
    if (xyzFileFilter.acceptDeep(file)) {
        // Use the TINKER Cartesian Coordinate File Parser.
        systemFilter = new XYZFilter(files, newSystem, forceField, properties);
    } else if (intFileFilter.acceptDeep(file)) {
        // Use the TINKER Internal Coordinate File Parser.
        systemFilter = new INTFilter(files, newSystem, forceField, properties);
    } else {
        // Use the PDB File Parser.
        systemFilter = new PDBFilter(files, newSystem, forceField, properties);
    }
    setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
    activeFilter = systemFilter;
    // return new UIFileOpener(systemFilter, this);
    UIFileOpener fileOpener = new UIFileOpener(systemFilter, this);
    if (fileOpenerThreads > 0) {
        fileOpener.setNThreads(fileOpenerThreads);
    }
    return fileOpener;
}

Example 9 with ForceField

use of ffx.potential.parameters.ForceField in project ffx by mjschnie.

the class MainPanel method openFromPDB.

/**
 * Opens a file from the PDB
 */
public void openFromPDB() {
    if (openThread != null && openThread.isAlive()) {
        return;
    }
    String code = JOptionPane.showInputDialog("Enter the PDB Identifier (4 characters)", "");
    if (code == null) {
        return;
    }
    code = code.toLowerCase().trim();
    if (code == null || code.length() != 4) {
        return;
    }
    String fileName = code + ".pdb";
    String path = getPWD().getAbsolutePath();
    File pdbFile = new File(path + File.separatorChar + fileName);
    CompositeConfiguration properties = Keyword.loadProperties(pdbFile);
    forceFieldFilter = new ForceFieldFilter(properties);
    ForceField forceField = forceFieldFilter.parse();
    FFXSystem newSystem = new FFXSystem(pdbFile, "PDB", properties);
    newSystem.setForceField(forceField);
    if (!pdbFile.exists()) {
        String fromURL = pdbForID(code);
        pdbFile = downloadURL(fromURL);
        if (pdbFile == null || !pdbFile.exists()) {
            return;
        }
    } else {
        String message = String.format(" Reading the local copy of the PDB file %s.", pdbFile);
        logger.info(message);
    }
    PDBFilter pdbFilter = new PDBFilter(pdbFile, newSystem, forceField, properties);
    setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
    UIFileOpener openFile = new UIFileOpener(pdbFilter, this);
    if (fileOpenerThreads > 0) {
        openFile.setNThreads(fileOpenerThreads);
    }
    openThread = new Thread(openFile);
    openThread.start();
    setPanel(GRAPHICS);
}

Example 10 with ForceField

use of ffx.potential.parameters.ForceField in project ffx by mjschnie.

the class MainPanel method openInit.

/**
 * Attempts to load the supplied file
 *
 * @param file File to open
 * @param commandDescription Description of the command that created this
 * file.
 * @return a {@link java.lang.Thread} object.
 */
private UIFileOpener openInit(File file, String commandDescription) {
    if (file == null || !file.isFile() || !file.canRead()) {
        return null;
    }
    file = new File(FilenameUtils.normalize(file.getAbsolutePath()));
    // Set the Current Working Directory based on this file.
    setCWD(file.getParentFile());
    // Get "filename" from "filename.extension".
    String name = file.getName();
    String extension = FilenameUtils.getExtension(name);
    /**
     * Run a Force Field X script.
     */
    if (extension.equalsIgnoreCase("ffx") || extension.equalsIgnoreCase("groovy")) {
        ModelingShell shell = getModelingShell();
        shell.runFFXScript(file);
        boolean shutDown = Boolean.parseBoolean(System.getProperty("ffx.shutDown", "true"));
        if (java.awt.GraphicsEnvironment.isHeadless() && shutDown) {
            exit();
        } else {
            return null;
        }
    }
    // Create the CompositeConfiguration properties.
    CompositeConfiguration properties = Keyword.loadProperties(file);
    // Create an FFXSystem for this file.
    FFXSystem newSystem = new FFXSystem(file, commandDescription, properties);
    // Create a Force Field.
    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();
        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));
        }
    }
    newSystem.setForceField(forceField);
    SystemFilter systemFilter = null;
    // Decide what parser to use.
    if (xyzFileFilter.acceptDeep(file)) {
        // Use the TINKER Cartesian Coordinate File Parser.
        systemFilter = new XYZFilter(file, newSystem, forceField, properties);
    } else if (intFileFilter.acceptDeep(file)) {
        // Use the TINKER Internal Coordinate File Parser.
        systemFilter = new INTFilter(file, newSystem, forceField, properties);
    } else {
        // Use the PDB File Parser.
        systemFilter = new PDBFilter(file, newSystem, forceField, properties);
    }
    setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
    activeFilter = systemFilter;
    UIFileOpener fileOpener = new UIFileOpener(systemFilter, this);
    if (fileOpenerThreads > 0) {
        fileOpener.setNThreads(fileOpenerThreads);
    }
    return fileOpener;
// return new UIFileOpener(systemFilter, this);
}