3 import jalview.datamodel.PDBEntry;
4 import jalview.datamodel.SequenceI;
5 import jalview.ext.rbvi.chimera.ChimeraXCommands;
6 import jalview.gui.StructureViewer.ViewerType;
7 import jalview.io.DataSourceType;
8 import jalview.structure.StructureCommand;
9 import jalview.structure.StructureSelectionManager;
11 import java.util.List;
13 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
14 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
15 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
17 public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
20 public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,
21 StructureSelectionManager ssm, PDBEntry[] pdbentry,
22 SequenceI[][] sequenceIs, DataSourceType protocol)
24 super(chimeraViewFrame, ssm, pdbentry, sequenceIs, protocol);
25 setStructureCommands(new ChimeraXCommands());
29 protected List<String> getChimeraPaths()
31 return StructureManager.getChimeraPaths(true);
35 protected void addChimeraModel(PDBEntry pe,
36 List<ChimeraModel> modelsToMap)
39 * ChimeraX hack: force chimera model name to pdbId here
41 int modelNumber = chimeraMaps.size() + 1;
42 String command = "setattr #" + modelNumber + " models name "
44 executeCommand(new StructureCommand(command), false);
45 modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
55 protected String getCommandFileExtension()
61 * Returns the file extension to use for a saved viewer session file
66 public String getSessionFileExtension()
72 public String getHelpURL()
74 return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
78 protected ViewerType getViewerType()
80 return ViewerType.CHIMERAX;
84 protected String getModelId(int pdbfnum, String file)
86 return String.valueOf(pdbfnum + 1);