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

Example 1 with MergeFilter

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

the class MainPanel method merge.

/**
 * Merge two or more selected FSystem Nodes into one FSystem node. There are
 * a few gotchas that need to be fixed
 *
 * @param nodesToMerge a {@link java.util.ArrayList} object.
 */
public void merge(ArrayList<MSNode> nodesToMerge) {
    ArrayList<MSNode> activeNodes = new ArrayList<MSNode>();
    for (MSNode node : nodesToMerge) {
        if (node != null && !(node instanceof MSRoot)) {
            activeNodes.add(node);
        }
    }
    if (activeNodes.size() <= 1) {
        return;
    }
    // Set up a structure to hold the new system
    FFXSystem active = hierarchy.getActive();
    File file = SystemFilter.version(hierarchy.getActive().getFile());
    FFXSystem system = new FFXSystem(file, "Merge Result", active.getProperties());
    system.setKeyFile(active.getKeyFile());
    system.setKeywords(KeyFilter.open(active.getKeyFile()));
    // Fill arrays with the atoms and bonds from the systems to be combined
    ArrayList<Atom> mergedAtoms = new ArrayList<Atom>();
    ArrayList<Bond> mergedBonds = new ArrayList<Bond>();
    ArrayList<FFXSystem> systems = new ArrayList<FFXSystem>();
    TransformGroup parentTransformGroup = null;
    FFXSystem parentSystem;
    Transform3D parentTransform3D = new Transform3D();
    Vector3d parentPosition = new Vector3d();
    Vector3d atomPosition = new Vector3d();
    // TINKER Atom Numbers start at 1
    int atomNum = 1;
    Vector3d zero = new Vector3d(0.0, 0.0, 0.0);
    for (MSNode m : activeNodes) {
        parentSystem = (FFXSystem) m.getMSNode(FFXSystem.class);
        if (parentSystem == null) {
            return;
        }
        if (!systems.contains(parentSystem)) {
            graphicsCanvas.updateSceneWait(parentSystem, false, true, RendererCache.ViewModel.WIREFRAME, false, null);
            systems.add(parentSystem);
        }
        // Move each atom into the global frame by applying the System
        // Transform to
        // relative atomic position
        parentTransformGroup = parentSystem.getOriginToRot();
        parentTransformGroup.getTransform(parentTransform3D);
        parentTransform3D.get(parentPosition);
        parentTransform3D.setTranslation(zero);
        // parentTransform3D.setScale(1.0d);
        ArrayList<Atom> atoms = m.getAtomList();
        ArrayList<ROLS> bonds = m.getBondList();
        for (Atom atom : atoms) {
            atom.removeFromParent();
            atom.setXyzIndex(atomNum++);
            mergedAtoms.add(atom);
            atom.getV3D(atomPosition);
            parentTransform3D.transform(atomPosition);
            atomPosition.add(parentPosition);
            atom.moveTo(atomPosition);
        }
        for (ROLS msm : bonds) {
            Bond bond = (Bond) msm;
            bond.removeFromParent();
            mergedBonds.add((Bond) msm);
        }
    }
    for (FFXSystem sys : systems) {
        close(sys);
    }
    MergeFilter mergeFilter = new MergeFilter(system, mergedAtoms, mergedBonds);
    UIFileOpener fileOpener = new UIFileOpener(mergeFilter, this);
    if (fileOpenerThreads > 0) {
        fileOpener.setNThreads(fileOpenerThreads);
    }
    Thread thread = new Thread(fileOpener);
    thread.start();
}