Opened 10 years ago

Closed 10 years ago

#238 closed defect (fixed)

cannot intersect built-in selector with atom names

Reported by: Elaine Meng Owned by: Tom Goddard
Priority: blocker Milestone:
Component: Command Line Version:
Keywords: Cc: Conrad Huang
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

commands like "show helix & @n,ca,c,o" or "show @n,ca,c,o & protein" give a traceback:

Traceback (most recent call last):
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/cmd_line/gui.py", line 119, in on_enter
cmd = Command(session, cmd_text, final=True)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 1759, in init
self.parse_text(text, final=final, _used_aliases=_used_aliases)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2168, in parse_text
prev_annos = self._process_positional_arguments()
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 2034, in _process_positional_arguments
value, text = self._parse_arg(anno, text, session, False)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 1884, in _parse_arg
value, replacement, rest = annotation.parse(text, session)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 1039, in parse
return anno.parse(text, session)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/cli.py", line 901, in parse
objects = aspec.evaluate(session)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/atomspec.py", line 639, in evaluate
results = Objects.intersect(left_results, right_results)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/objects.py", line 99, in intersect
atoms = (right.atoms() & left.atoms()))
TypeError: 'Atoms' object is not callable

Change History (2)

comment:1 by Eric Pettersen, 10 years ago

Owner: changed from Eric Pettersen to Tom Goddard
Status: newassigned

comment:2 by Tom Goddard, 10 years ago

Resolution: fixed
Status: assignedclosed

Fixed.

Oops! Broke this at the end of last week when I was optimizing extremely slow selections with 400 molecules open.

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