public class ChimeraXCommands extends ChimeraCommands
{
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#resattr
- private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("info resattr");
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
+ "info resattr");
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
- private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand("exit");
+ private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand(
+ "exit");
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
- private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("info notify stop selection jalview");
+ private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
+ "info notify stop selection jalview");
- private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("info notify stop models jalview");
+ private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
+ "info notify stop models jalview");
// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#selection
private static final StructureCommand GET_SELECTION = new StructureCommand(
}
/**
- * Returns a viewer command to set the given residue attribute value on
- * residues specified by the AtomSpecModel, for example
+ * Returns a viewer command to set the given residue attribute value on residues
+ * specified by the AtomSpecModel, for example
*
* <pre>
* setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
* Returns the range(s) formatted as a ChimeraX atomspec, for example
* <p>
* #1/A:2-20,30-40/B:10-20|#2/A:12-30
+ * <p>
+ * Note there is no need to explicitly exclude ALTLOC atoms when
+ * {@code alphaOnly == true}, as this is the default behaviour of ChimeraX (a
+ * change from Chimera)
*
* @return
*/
// TODO @P if RNA - add nucleotide flag to AtomSpecModel?
sb.append("@CA");
}
- // todo: is there ChimeraX syntax to exclude altlocs?
}
return sb.toString();
}
public List<StructureCommandI> startNotifications(String uri)
{
List<StructureCommandI> cmds = new ArrayList<>();
- cmds.add(new StructureCommand("info notify start models jalview prefix ModelChanged url " + uri));
- cmds.add(new StructureCommand("info notify start selection jalview prefix SelectionChanged url " + uri));
+ cmds.add(new StructureCommand(
+ "info notify start models jalview prefix ModelChanged url "
+ + uri));
+ cmds.add(new StructureCommand(
+ "info notify start selection jalview prefix SelectionChanged url "
+ + uri));
return cmds;
}