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

Example 1 with ConversionFilter

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

the class MainPanel method convertInit.

/**
 * Attempts to load from the supplied data structure
 *
 * @param data Data structure to load from
 * @param file Source file
 * @param commandDescription Description of the command that created this
 * file.
 * @return A thread-based UIDataConverter
 */
private UIDataConverter convertInit(Object data, File file, String commandDescription) {
    if (data == null) {
        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);
    ConversionFilter convFilter = null;
    // Decide what parser to use.
    if (biojavaDataFilter.accept(data)) {
        convFilter = new BiojavaFilter((Structure) data, newSystem, forceField, properties);
    } else {
        throw new IllegalArgumentException("Not a recognized data structure.");
    }
    setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
    activeConvFilter = convFilter;
    return new UIDataConverter(data, file, convFilter, this);
}