*/
public class ChimeraCommands extends StructureCommandsBase
{
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus");
+
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr");
+
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really");
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection");
private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models");
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue");
private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
"color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rainbow.html
private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
"rainbow chain");
@Override
public StructureCommandI focusView()
{
- // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
- return new StructureCommand("focus");
+ return FOCUS_VIEW;
}
@Override
@Override
public StructureCommandI closeViewer()
{
- // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
return CLOSE_CHIMERA;
}
@Override
public List<StructureCommandI> stopNotifications()
{
- // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
List<StructureCommandI> cmds = new ArrayList<>();
cmds.add(STOP_NOTIFY_MODELS);
cmds.add(STOP_NOTIFY_SELECTION);
return GET_SELECTION;
}
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return LIST_RESIDUE_ATTRIBUTES;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ // this alternative command
+ // list residues spec ':*/attName' attr attName
+ // doesn't report 'None' values (which is good), but
+ // fails for 'average.bfactor' (which is bad):
+ return new StructureCommand("list residues attr '" + attName + "'");
+ }
+
}