Opened 15 months ago

Closed 15 months ago

#15780 closed defect (can't reproduce)

MatchMaker: circular import of _sw

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "E:/sui lab/pink/final-pdb/pk-51-90-final.pdb"

Chain information for pk-51-90-final.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
  

> open "E:/sui lab/pink/202405new
> map/pk-90-fkbp51/cryosparc_P6_J3235_002_volume_map_sharp.mrc"

Opened cryosparc_P6_J3235_002_volume_map_sharp.mrc as #2, grid size
280,280,280, pixel 0.87, shown at level 0.141, step 2, values float32  

> set bgColor white

> lighting soft

> volume #2 step 1

> hide #!2 models

> color #1 cyan transparency 0

> graphics silhouettes true

> select /B

5196 atoms, 5280 bonds, 1 pseudobond, 637 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel dodger blue

> select /C

2639 atoms, 2694 bonds, 2 pseudobonds, 343 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel gold

> select /D

3229 atoms, 3287 bonds, 409 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel hot pink

> color sel magenta

> color sel violet

> select clear

> hide atoms

> select ::name="ADP"

54 atoms, 58 bonds, 2 residues, 1 model selected  

> show sel atoms

> color sel red

> color sel byhetero

> select clear

> select ::name="MG"

2 atoms, 2 residues, 1 model selected  

> show sel atoms

> color sel lime

> select clear

> show #!2 models

> color #2 #dfdfdf models transparency 0

> transparency 50

> volume #2 level 0.1627

> ui tool show "Hide Dust"

> surface dust #2 size 5.22

> volume #2 level 0.09858

> volume #2 level 0.1199

> volume #2 level 0.1093

> surface dust #2 size 6.75

> volume #2 level 0.1413

> open "E:/sui lab/pink/final-pdb/pk-90A-37-final-coot-1.pdb"

Chain information for pk-90A-37-final-coot-1.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
E | No description available  
  

> hide #!2 models

> hide #!1 models

> select #3/C:441

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

78 atoms, 80 bonds, 11 residues, 1 model selected  

> select up

1822 atoms, 1859 bonds, 234 residues, 1 model selected  

> select ~sel

28733 atoms, 29217 bonds, 7 pseudobonds, 3548 residues, 6 models selected  

> hide sel & #!3 cartoons

> hide sel & #!3 atoms

> select clear

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> select #3

14295 atoms, 14535 bonds, 4 pseudobonds, 1756 residues, 2 models selected  

> show sel cartoons

> select clear

> select #3/B:171

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

49 atoms, 49 bonds, 6 residues, 1 model selected  

> select up

5178 atoms, 5262 bonds, 635 residues, 1 model selected  

> select clear

> ui tool show Matchmaker

Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 484, in get_module  
m = importlib.import_module(self.package_name)  
File "D:\ChimeraX 1.3\bin\lib\importlib\\__init__.py", line 127, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\match_maker\\__init__.py", line 15, in <module>  
from .match import CP_SPECIFIC_SPECIFIC, CP_SPECIFIC_BEST, CP_BEST_BEST  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\match_maker\match.py",
line 18, in <module>  
from chimerax.alignment_algs import NEEDLEMAN_WUNSCH as AA_NEEDLEMAN_WUNSCH, \  
File "D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_algs\\__init__.py", line 14, in <module>  
from . import _sw as SmithWaterman  
ImportError: cannot import name '_sw' from partially initialized module
'chimerax.alignment_algs' (most likely due to a circular import) (D:\ChimeraX
1.3\bin\lib\site-packages\chimerax\alignment_algs\\__init__.py)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 553, in start_tool  
api = self._get_api(session.logger)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 503, in _get_api  
m = self.get_module()  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 486, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
MatchMaker's module: cannot import name '_sw' from partially initialized
module 'chimerax.alignment_algs' (most likely due to a circular import)
(D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\alignment_algs\\__init__.py)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1659, in
<lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\cmd.py", line 219, in
ui_tool_show  
bi.start_tool(session, name)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker
in bundle ChimeraX-MatchMaker:  
Error importing bundle ChimeraX-MatchMaker's module: cannot import name '_sw'
from partially initialized module 'chimerax.alignment_algs' (most likely due
to a circular import) (D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_algs\\__init__.py)  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker
in bundle ChimeraX-MatchMaker:  
Error importing bundle ChimeraX-MatchMaker's module: cannot import name '_sw'
from partially initialized module 'chimerax.alignment_algs' (most likely due
to a circular import) (D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_algs\\__init__.py)  
  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show Matchmaker

Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 484, in get_module  
m = importlib.import_module(self.package_name)  
File "D:\ChimeraX 1.3\bin\lib\importlib\\__init__.py", line 127, in
import_module  
return _bootstrap._gcd_import(name[level:], package, level)  
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import  
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load  
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked  
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked  
File "<frozen importlib._bootstrap_external>", line 850, in exec_module  
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed  
File "D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\match_maker\\__init__.py", line 15, in <module>  
from .match import CP_SPECIFIC_SPECIFIC, CP_SPECIFIC_BEST, CP_BEST_BEST  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\match_maker\match.py",
line 18, in <module>  
from chimerax.alignment_algs import NEEDLEMAN_WUNSCH as AA_NEEDLEMAN_WUNSCH, \  
File "D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_algs\\__init__.py", line 14, in <module>  
from . import _sw as SmithWaterman  
ImportError: cannot import name '_sw' from partially initialized module
'chimerax.alignment_algs' (most likely due to a circular import) (D:\ChimeraX
1.3\bin\lib\site-packages\chimerax\alignment_algs\\__init__.py)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 553, in start_tool  
api = self._get_api(session.logger)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 503, in _get_api  
m = self.get_module()  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 486, in get_module  
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-
MatchMaker's module: cannot import name '_sw' from partially initialized
module 'chimerax.alignment_algs' (most likely due to a circular import)
(D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\alignment_algs\\__init__.py)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 1659, in
<lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\run.py",
line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2856, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\cmd.py", line 219, in
ui_tool_show  
bi.start_tool(session, name)  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker
in bundle ChimeraX-MatchMaker:  
Error importing bundle ChimeraX-MatchMaker's module: cannot import name '_sw'
from partially initialized module 'chimerax.alignment_algs' (most likely due
to a circular import) (D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_algs\\__init__.py)  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Matchmaker
in bundle ChimeraX-MatchMaker:  
Error importing bundle ChimeraX-MatchMaker's module: cannot import name '_sw'
from partially initialized module 'chimerax.alignment_algs' (most likely due
to a circular import) (D:\ChimeraX 1.3\bin\lib\site-
packages\chimerax\alignment_algs\\__init__.py)  
  
File "D:\ChimeraX 1.3\bin\lib\site-packages\chimerax\core\toolshed\info.py",
line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 517.00
OpenGL renderer: NVIDIA GeForce RTX 2060/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: LENOVO
Model: 82AX
OS: Microsoft Windows 10 家庭中文版 (Build 19045)
Memory: 17,040,195,584
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 15 months ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → MatchMaker: circular import of _sw

comment:2 by Eric Pettersen, 15 months ago

Resolution: → can't reproduce
Status: accepted → closed
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