Opened 9 years ago
Closed 9 years ago
#435 closed defect (fixed)
strand command-line selector broken
Reported by: | Elaine Meng | Owned by: | pett |
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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 , 9 years ago
Component: | Unassigned → Command Line |
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Status: | new → accepted |
comment:2 by , 9 years ago
Resolution: | → fixed |
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Status: | accepted → closed |
Fixed. Conrad missed the 'strand' and 'coil' selectors when he changed Chimera's internal nomenclature from 'sheet' to 'strand'.
--Eric