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<String> getChimeraPaths()
+ {
+ return StructureManager.getChimeraPaths(true);
+ }
+
+ @Override
+ protected void addChimeraModel(PDBEntry pe,
+ List<ChimeraModel> 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);
}
}