Atom.structure_category throwing exception is awkward

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.0.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-12-03)
Description
Atoms.structure_categories raises an exception if any atom does not have a category assigned.  I think it should just give the string "unassigned" for those.  Current exception makes it hard to use correctly for exampl to find all ligands would have to iterate through and check each atom instead of atoms[atoms.structure_categories == 'ligand'].

Got this error trying zone mouse mode on markers (file attached).  Previously reported in ticekt #2644.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-12-03)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/chimerax/src/bundles/surface/test.cmm format
markers

Opened 1 marker sets containing 3 markers  

> ui mousemode rightMode zone

Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 463, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_down")  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/mouse_modes/mousemodes.py", line 392, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 216, in mouse_down  
self._show_zone(res)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 52, in _show_zone  
nres = self._show_near_residues(residue, show_ligands=ribbon)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/zone/zone.py", line 126, in _show_near_residues  
cats = all_atoms.structure_categories  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
IndexError: Unknown structure category  
  
IndexError: Unknown structure category  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/molc.py", line 195, in get_prop  
cget(self._c_pointers, n, pointer(values))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.2.24
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: test.cmm

test.cmm​

[goddard@…]

Added by email2trac

[Eric Pettersen]

Non-atomic atoms are now in category "other".