Opened 9 years ago

Closed 9 years ago

#435 closed defect (fixed)

strand command-line selector broken

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

Description

trying to use atomspec "strand" gives error (e.g. "sel strand")

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 146, in execute
cmd.run(cmd_text)
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 2172, in run
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 2027, 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 1874, 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 1124, 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 983, 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 647, in evaluate
results = self._left_spec.evaluate(session, models)
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 584, in evaluate
self._specifier.find_matches(session, models, results)
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 537, in find_matches
f(session, models, results)
File "/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/commands/selectors.py", line 95, in _strands_selector
strands = m.residues.filter(m.residues.is_sheet)
AttributeError: 'Residues' object has no attribute 'is_sheet'

Change History (2)

comment:1 by pett, 9 years ago

Component: UnassignedCommand Line
Status: newaccepted

comment:2 by pett, 9 years ago

Resolution: fixed
Status: acceptedclosed

Fixed. Conrad missed the 'strand' and 'coil' selectors when he changed Chimera's internal nomenclature from 'sheet' to 'strand'.

--Eric

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