package jalview.gui; import java.util.List; import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel; import ext.edu.ucsf.rbvi.strucviz2.StructureManager; import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.ext.rbvi.chimera.ChimeraXCommands; import jalview.gui.StructureViewer.ViewerType; import jalview.io.DataSourceType; import jalview.structure.AtomSpec; import jalview.structure.StructureCommand; import jalview.structure.StructureSelectionManager; public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel { public static final String CHIMERAX_SESSION_EXTENSION = ".cxs"; public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame, StructureSelectionManager ssm, PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol) { super(chimeraViewFrame, ssm, pdbentry, sequenceIs, protocol); setStructureCommands(new ChimeraXCommands()); } @Override protected List getChimeraPaths() { return StructureManager.getChimeraPaths(true); } @Override protected void addChimeraModel(PDBEntry pe, List modelsToMap) { /* * ChimeraX hack: force chimera model name to pdbId here */ int modelNumber = chimeraMaps.size() + 1; String command = "setattr #" + modelNumber + " models name " + pe.getId(); executeCommand(new StructureCommand(command), false); modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL, modelNumber, 0)); } /** * {@inheritDoc} * * @return */ @Override protected String getCommandFileExtension() { return ".cxc"; } /** * Returns the file extension to use for a saved viewer session file (.cxs) * * @return * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#sesformat */ @Override public String getSessionFileExtension() { return CHIMERAX_SESSION_EXTENSION; } @Override public String getHelpURL() { return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html"; } @Override protected ViewerType getViewerType() { return ViewerType.CHIMERAX; } @Override protected String getModelId(int pdbfnum, String file) { return String.valueOf(pdbfnum + 1); } /** * Returns a model of the structure positions described by the ChimeraX format atomspec * @param atomSpec * @return */ @Override protected AtomSpec parseAtomSpec(String atomSpec) { return AtomSpec.fromChimeraXAtomspec(atomSpec); } }