5 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
6 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
7 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
8 import jalview.datamodel.PDBEntry;
9 import jalview.datamodel.SequenceI;
10 import jalview.ext.rbvi.chimera.ChimeraXCommands;
11 import jalview.gui.StructureViewer.ViewerType;
12 import jalview.io.DataSourceType;
13 import jalview.structure.AtomSpec;
14 import jalview.structure.StructureCommand;
15 import jalview.structure.StructureSelectionManager;
17 public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
19 public static final String CHIMERAX_SESSION_EXTENSION = ".cxs";
21 public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,
22 StructureSelectionManager ssm, PDBEntry[] pdbentry,
23 SequenceI[][] sequenceIs, DataSourceType protocol)
25 super(chimeraViewFrame, ssm, pdbentry, sequenceIs, protocol);
26 setStructureCommands(new ChimeraXCommands());
30 protected List<String> getChimeraPaths()
32 return StructureManager.getChimeraPaths(true);
36 protected void addChimeraModel(PDBEntry pe,
37 List<ChimeraModel> modelsToMap)
40 * ChimeraX hack: force chimera model name to pdbId here
42 int modelNumber = chimeraMaps.size() + 1;
43 String command = "setattr #" + modelNumber + " models name "
45 executeCommand(new StructureCommand(command), false);
46 modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
56 protected String getCommandFileExtension()
62 * Returns the file extension to use for a saved viewer session file (.cxs)
65 * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#sesformat
68 public String getSessionFileExtension()
70 return CHIMERAX_SESSION_EXTENSION;
74 public String getHelpURL()
76 return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
80 protected ViewerType getViewerType()
82 return ViewerType.CHIMERAX;
86 protected String getModelId(int pdbfnum, String file)
88 return String.valueOf(pdbfnum + 1);
92 * Returns a model of the structure positions described by the ChimeraX format atomspec
97 protected AtomSpec parseAtomSpec(String atomSpec)
99 return AtomSpec.fromChimeraXAtomspec(atomSpec);