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;
-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;
-
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
{
+ public static final String CHIMERAX_SESSION_EXTENSION = ".cxs";
public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
int modelNumber = chimeraMaps.size() + 1;
String command = "setattr #" + modelNumber + " models name "
+ pe.getId();
- executeCommand(command, false);
+ executeCommand(new StructureCommand(command), false);
modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
modelNumber, 0));
}
}
/**
- * Returns the file extension to use for a saved viewer session file
+ * 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 ".cxs";
+ return CHIMERAX_SESSION_EXTENSION;
}
@Override
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);
+ }
+
}