3 import jalview.datamodel.PDBEntry;
4 import jalview.datamodel.SequenceI;
5 import jalview.io.DataSourceType;
6 import jalview.structure.StructureSelectionManager;
10 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
11 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
12 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
14 public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
17 public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,
18 StructureSelectionManager ssm, PDBEntry[] pdbentry,
19 SequenceI[][] sequenceIs, DataSourceType protocol)
21 super(chimeraViewFrame, ssm, pdbentry, sequenceIs, protocol);
25 protected List<String> getChimeraPaths()
27 return StructureManager.getChimeraPaths(true);
31 protected void addChimeraModel(PDBEntry pe,
32 List<ChimeraModel> modelsToMap)
35 * ChimeraX hack: force chimera model name to pdbId here
37 int modelNumber = chimeraMaps.size() + 1;
38 String command = "setattr #" + modelNumber + " models name "
40 executeCommand(command, false);
41 modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
51 protected String getCommandFileExtension()
62 protected String getOpenCommandFileCommand(String path)
64 return "open " + path;
71 protected String getSaveSessionCommand(String filepath)
73 return "save session " + filepath;
77 * Returns the file extension to use for a saved viewer session file
82 public String getSessionFileExtension()
88 public String getHelpURL()
90 return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";