Boolean attribute tests now failing

[Elaine Meng]

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-11-03)
Description
For boolean attributes, previously working examples now give traceback.  I'm pretty sure they used to work because they are examples in the atomspec manpage, and I'd tested all the examples.

sel @@display
sel ~@@display

Log:
UCSF ChimeraX version: 0.8 (2018-11-03)  
How to cite UCSF ChimeraX  

open /Users/meng/Desktop/chidata/super8.msf

open /Users/meng/Desktop/chidata/super8.msf

Summary of feedback from opening /Users/meng/Desktop/chidata/super8.msf  
---  
note | Alignment identifier is super8.msf  
  
Opened 8 sequences from super8.msf  

open 2gbp format mmCIF fromDatabase pdb

open 2gbp format mmCIF fromDatabase pdb

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
  

color :start-55 green

color :start-55 green

color :100-end purple

color :100-end purple

close

close

open 2gbp

open 2gbp

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
  

color :start-55 green

color :start-55 green

color :56-end purple

color :56-end purple

close

close

open 2gbp

open 2gbp

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
  

color :150-end purple

color :150-end purple

rainbow chains

rainbow chains

select :150

select :150

7 atoms, 7 bonds selected  

rainbow

rainbow

color :150-end purple

color :150-end purple

close

close

open 2gbp

open 2gbp

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
  

label :150

label :150

label :1

label :1

color :150-end purple

color :150-end purple

color :start-149 green

color :start-149 green

close

close

open 1gcn

open 1gcn

1gcn title:  
X-ray analysis of glucagon and its relationship to receptor binding
[more info...]  
  
Chain information for 1gcn #1  
---  
Chain | Description  
A | glucagon  
  
  

color :5-end yellow

color :5-end yellow

color :15-end purple

color :15-end purple

close

close

open 2gbp

open 2gbp

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #1  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
  

open 2gbp

open 2gbp

2gbp title:  
Sugar and signal-transducer binding sites of the escherichia coli galactose
chemoreceptor protein [more info...]  
  
Chain information for 2gbp #2  
---  
Chain | Description  
A | D-galactose/D-glucose binding protein  
  
  

label :150

label :150

color :150-end purple

color :150-end purple

close

close

open 4hhb

open 4hhb

4hhb title:  
The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution
[more info...]  
  
Chain information for 4hhb #1  
---  
Chain | Description  
A C | hemoglobin (deoxy) (α chain)  
B D | hemoglobin (deoxy) (β chain)  
  
  

color red :start-55

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

color :start-55 red

color :start-55 red

color :56-end purple

color :56-end purple

color red :start-55

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

color :start-55 red

color :start-55 red

rainbow

rainbow

label :55

label :55

label delete

label delete

label :30

label :30

color :start-30 magenta

color :start-30 magenta

color :31-end sky blue

color :31-end sky blue

rainbow

rainbow

color :150-end pink

color :150-end pink

select :150

select :150

4 atoms selected  

hide

hide

label delete

label delete

show sel

show sel

label sel

label sel

color ::color=pink magenta

color ::color=pink magenta

label delete

label delete

close

close

open 4hhb

open 4hhb

4hhb title:  
The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution
[more info...]  
  
Chain information for 4hhb #1  
---  
Chain | Description  
A C | hemoglobin (deoxy) (α chain)  
B D | hemoglobin (deoxy) (β chain)  
  
  

color :arg blue target a

color :arg blue target a

display :arg

display :arg

color @@color=blue magenta

color @@color=blue magenta

color tan target r

color tan target r

color @@color=magenta blue

color @@color=magenta blue

QLineEdit::setSelection: Invalid start position (-1)  

QLineEdit::setSelection: Invalid start position (-1)  

color @@color=blue dodger blue

color @@color=blue dodger blue

color @@color=dodger blue salmon

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

color @@color='dodger blue' salmon

color @@color='dodger blue' salmon

color @@color="98,50,45" red

color @@color="98,50,45" red

color @@color='98,50,45' red

color @@color='98,50,45' red

color @@color=#FA8072 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

color @@color='#FA8072' red

color @@color='#FA8072' red

color @@color=red crimson

color @@color=red crimson

color @@color='#DC143C' pale green

color @@color='#DC143C' pale green

color @@color=pale green brown

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons',
'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

color @@color="pale green" brown

color @@color="pale green" brown

color @@color=brown red

color @@color=brown red

color @@/color=100,0,0 lime

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

color @@/color='100,0,0' lime

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

color @@/color=rgb(100,0,0) lime

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

color @@/color='rgb(100,0,0)' lime

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

QLineEdit::setSelection: Invalid start position (-1)  

QLineEdit::setSelection: Invalid start position (-1)  

select @@/color=red

Expected an objects specifier or a keyword  

select @@ color=red

select @@ color=red

134 atoms, 122 bonds selected  

~select

~select

Nothing selected  

select @@ color='#FF0000'

select @@ color='#FF0000'

134 atoms, 122 bonds selected  

select @@ color='100,0,0,100'

select @@ color='100,0,0,100'

134 atoms, 122 bonds selected  

select @@ color='100,0,0'

select @@ color='100,0,0'

134 atoms, 122 bonds selected  

color sel chartreuse

color sel chartreuse

select @@ color='50,100,0'

select @@ color='50,100,0'

Nothing selected  

select @@ color='#7FFF00'

select @@ color='#7FFF00'

134 atoms, 122 bonds selected  

color sel red

color sel red

~select

~select

Nothing selected  

select @@color='rgb(255,0,0)'

select @@color='rgb(255,0,0)'

134 atoms, 122 bonds selected  

color sel dark red

color sel dark red

~select

~select

Nothing selected  

select @@color='rgb(54,0,0)'

select @@color='rgb(54,0,0)'

Nothing selected  

select @@color='#8B0000'

select @@color='#8B0000'

134 atoms, 122 bonds selected  

color sel red

color sel red

select @@color='100,0,0'

select @@color='100,0,0'

134 atoms, 122 bonds selected  

color sel dark red

color sel dark red

select @@color='54,0,0'

select @@color='54,0,0'

Nothing selected  

color @@color=darkred medium orchid

color @@color=darkred medium orchid

select @@color='medium orchid'

select @@color='medium orchid'

134 atoms, 122 bonds selected  

select @@color='#BA55D3'

select @@color='#BA55D3'

134 atoms, 122 bonds selected  

~select

~select

Nothing selected  

select @@color='#BA55D3'

select @@color='#BA55D3'

134 atoms, 122 bonds selected  

color sel magenta

color sel magenta

select @@color='100,0,100'

select @@color='100,0,100'

134 atoms, 122 bonds selected  

select @@color=

Expected an objects specifier or a keyword  

select @@color='rgb(255,0,255)'

select @@color='rgb(255,0,255)'

134 atoms, 122 bonds selected  

select @@color='rgba(255,0,255,0)'

select @@color='rgba(255,0,255,0)'

Nothing selected  

select @@color='rgba(255,0,255,255)'

select @@color='rgba(255,0,255,255)'

134 atoms, 122 bonds selected  

select @@color='#ff00ff'

select @@color='#ff00ff'

134 atoms, 122 bonds selected  

select @@color='#ff00ff'

select @@color='#ff00ff'

134 atoms, 122 bonds selected  

~cartoon

~cartoon

show :hem only

show :hem only

Traceback (most recent call last):  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 219, in execute  
    cmd.run(cmd_text)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2542, in run  
    prev_annos = self._process_positional_arguments()  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2328, 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/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2191, in _parse_arg  
    value, replacement, rest = annotation.parse(text, session)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 1065, in parse  
    objects = aspec.evaluate(session)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 972, in evaluate  
    results = self._left_spec.evaluate(session, models, top=False)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 898, in evaluate  
    return self.find_matches(session, models, results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 901, in find_matches  
    self._specifier.find_matches(session, models, results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 396, in find_matches  
    model_spec.find_matches(session, model_list, results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 557, in find_matches  
    _add_model_parts(session, model, self.sub_parts, results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 577, in _add_model_parts  
    chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 513, in find_selected_parts  
    subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 513, in find_selected_parts  
    subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 502, in find_selected_parts  
    atoms = self._filter_parts(model, atoms, num_atoms)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 521, in _filter_parts  
    None, self.my_attrs)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1744, in atomspec_filter  
    return self._atomspec_filter_atom(atoms, num_atoms, parts, attrs)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1823, in _atomspec_filter_atom  
    selected = self._atomspec_attr_filter(atoms, selected, attrs)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1780, in _atomspec_attr_filter  
    s = numpy.vectorize(choose)(objects)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/numpy/lib/function_base.py", line 1972, in __call__  
    return self._vectorize_call(func=func, args=vargs)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/numpy/lib/function_base.py", line 2042, in _vectorize_call  
    ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/numpy/lib/function_base.py", line 2002, in _get_ufunc_and_otypes  
    outputs = func(*inputs)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 823, in matcher  
    return op(v, attr_value)  
TypeError: truth() takes exactly one argument (2 given)  
  
TypeError: truth() takes exactly one argument (2 given)  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 823, in matcher  
return op(v, attr_value)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 219, in execute  
    cmd.run(cmd_text)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2542, in run  
    prev_annos = self._process_positional_arguments()  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2328, 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/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2191, in _parse_arg  
    value, replacement, rest = annotation.parse(text, session)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 1065, in parse  
    objects = aspec.evaluate(session)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 972, in evaluate  
    results = self._left_spec.evaluate(session, models, top=False)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 916, in evaluate  
    results = self._atomspec.evaluate(session, models, top=False)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 898, in evaluate  
    return self.find_matches(session, models, results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 901, in find_matches  
    self._specifier.find_matches(session, models, results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 396, in find_matches  
    model_spec.find_matches(session, model_list, results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 557, in find_matches  
    _add_model_parts(session, model, self.sub_parts, results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 577, in _add_model_parts  
    chain_spec.find_selected_parts(model, atoms, num_atoms, my_results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 513, in find_selected_parts  
    subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 513, in find_selected_parts  
    subpart.find_selected_parts(model, atoms, num_atoms, sub_results)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 502, in find_selected_parts  
    atoms = self._filter_parts(model, atoms, num_atoms)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 521, in _filter_parts  
    None, self.my_attrs)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1744, in atomspec_filter  
    return self._atomspec_filter_atom(atoms, num_atoms, parts, attrs)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1823, in _atomspec_filter_atom  
    selected = self._atomspec_attr_filter(atoms, selected, attrs)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1780, in _atomspec_attr_filter  
    s = numpy.vectorize(choose)(objects)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/numpy/lib/function_base.py", line 1972, in __call__  
    return self._vectorize_call(func=func, args=vargs)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/numpy/lib/function_base.py", line 2042, in _vectorize_call  
    ufunc, otypes = self._get_ufunc_and_otypes(func=func, args=args)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/numpy/lib/function_base.py", line 2002, in _get_ufunc_and_otypes  
    outputs = func(*inputs)  
  File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 823, in matcher  
    return op(v, attr_value)  
TypeError: truth() takes exactly one argument (2 given)  
  
TypeError: truth() takes exactly one argument (2 given)  
  
File
"/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/atomspec.py", line 823, in matcher  
return op(v, attr_value)  
  
See log for complete Python traceback.  
  

QLineEdit::setSelection: Invalid start position (-1)  

show @@bfactor>40

show @@bfactor>40




OpenGL version: 4.1 NVIDIA-10.32.0 355.11.10.10.40.102
OpenGL renderer: NVIDIA GeForce GTX 675MX OpenGL Engine
OpenGL vendor: NVIDIA Corporation

[Conrad Huang]

Fixed in 8eaeff88d.

A whole section code of dealing with presence/absence of attribute got lost when wildcard code was added. It's back now.