FileReader: __init__() got an unexpected keyword argument 'all_geom'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.19.8-200.fc36.x86_64-x86_64-with-glibc2.35
ChimeraX Version: 1.5.dev202209130706 (2022-09-13 07:06:45 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Bundle 'ChimeraX-ISOLDE' custom initialization failed  
warning | Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 365, in initialize  
api._api_caller.initialize(api, session, self)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1278, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "/home/nauton/.local/share/ChimeraX/1.5/site-
packages/chimerax/isolde/__init__.py", line 70, in initialize  
from . import settings  
File "/home/nauton/.local/share/ChimeraX/1.5/site-
packages/chimerax/isolde/settings.py", line 4, in <module>  
from .restraints.constants import restraint_color_defaults  
File "/home/nauton/.local/share/ChimeraX/1.5/site-
packages/chimerax/isolde/restraints/__init__.py", line 11, in <module>  
from ..molobject import RestraintChangeTracker  
File "/home/nauton/.local/share/ChimeraX/1.5/site-
packages/chimerax/isolde/molobject.py", line 41, in <module>  
_c_functions = CFunctions(os.path.splitext(libfile)[0])  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 25, in __init__  
self._c_lib = ctypes_open(library_path)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 262, in ctypes_open  
lib = ctypes.PyDLL(lib_path)  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/ctypes/__init__.py", line
374, in __init__  
self._handle = _dlopen(self._name, mode)  
OSError: /home/nauton/.local/share/ChimeraX/1.5/site-
packages/chimerax/isolde/libmolc.so: undefined symbol:
_ZNK10atomstruct7Residue9find_atomERKSs  
  
UCSF ChimeraX version: 1.5.dev202209130706 (2022-09-13)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Job Queue"

> open /WORK/ALDOLASE-2022/OPT-QMMM/ALDOLASE-F6R-ONIOM.log format log

Opened ALDOLASE-F6R-ONIOM.log as a Gaussian output file  

> view sel

> select /a:1@@serial_number=3367

1 atom, 1 residue, 1 model selected  

> label sel attribute name

> select clear

[Repeated 1 time(s)]

> select /a:1@@serial_number=3367

1 atom, 1 residue, 1 model selected  

> ~label sel atoms

> select clear

[Repeated 1 time(s)]

> select /a:1@@serial_number=3367

1 atom, 1 residue, 1 model selected  

> select clear

> close session

> ui tool show "Build Structure"

> build start atom "custom built"

> build modify /het:1@He C 4 geometry tetrahedral name C1

> select /het:1@H11

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H11 C 4 geometry tetrahedral name C2

> select /het:1@H23

1 atom, 1 residue, 1 model selected  

> select add /het:1@H21

2 atoms, 1 residue, 1 model selected  

> select add /het:1@H22

3 atoms, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /het:1@C2

1 atom, 1 residue, 1 model selected  

> build modify /het:1@C2 C 3 geometry tetrahedral

> select /het:1@H21

1 atom, 1 residue, 1 model selected  

> select add /het:1@H22

2 atoms, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /het:1@C2

1 atom, 1 residue, 1 model selected  

> build modify /het:1@C2 C 3 geometry trigonal

> select /het:1@H22

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H22 C 3 geometry tetrahedral name C3

> select /het:1@H21

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H21 O 1 name O1

> select clear

> select /het:1@C3

1 atom, 1 residue, 1 model selected  

> build modify /het:1@C3 C 4 geometry tetrahedral

> select /het:1@H31

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H31 C 4 geometry tetrahedral name C4

> select clear

> select /het:1@H41

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H41 C 4 geometry tetrahedral name C5

> select /het:1@H51

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H51 C 4 geometry tetrahedral name C6

> select /het:1@H32

1 atom, 1 residue, 1 model selected  

> select /het:1@H33

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H33 O 2 geometry tetrahedral name O2

> select /het:1@H43

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H43 O 2 geometry tetrahedral name O3

> select /het:1@H53

1 atom, 1 residue, 1 model selected  

> select /het:1@H52

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H52 O 2 geometry tetrahedral name O4

> select /het:1@H61

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H61 O 2 geometry tetrahedral name O5

> select /het:1@H5

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H5 P 4 geometry tetrahedral name P1

> select /het:1@H5

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H5 O 1 name O6

> select /het:1@H1

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H1 O 1 name O7

> select /het:1@H11

1 atom, 1 residue, 1 model selected  

> build modify /het:1@H11 O 1 name O8

> ui tool show "Build QM Input"

settings migrated from version 2  

job started: local Gaussian job "test"  
job finished: local Gaussian job "test"  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX-daily/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/home/nauton/.local/share/ChimeraX/1.5/site-
packages/SEQCROW/managers/job_manager.py", line 310, in job_finished  
job.update_structure(job.theory.geometry.chix_atomicstructure)  
File "/home/nauton/.local/share/ChimeraX/1.5/site-packages/SEQCROW/jobs.py",
line 186, in update_structure  
fr = FileReader(self.output_name, just_geom=False, all_geom=True)  
TypeError: __init__() got an unexpected keyword argument 'all_geom'  
  
Error processing trigger "job finished":  
TypeError: __init__() got an unexpected keyword argument 'all_geom'  
  
File "/home/nauton/.local/share/ChimeraX/1.5/site-packages/SEQCROW/jobs.py",
line 186, in update_structure  
fr = FileReader(self.output_name, just_geom=False, all_geom=True)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 515.65.01
OpenGL renderer: NVIDIA RTX A2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: fr_FR.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: Fedora Linux 36 
Architecture: 64bit ELF
Virtual Machine: none
CPU: 40 Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz
Cache Size: 14080 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       3.6Gi        54Gi        75Mi       4.0Gi        58Gi
	Swap:           39Gi          0B        39Gi

Graphics:
	0000:73:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA106 [RTX A2000] [10de:2531] (rev a1)	
	Subsystem: Dell Device [1028:151d]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.6.15.1
    cftime: 1.6.1
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.2
    ChimeraX-AtomicLibrary: 7.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0
    ChimeraX-CheckWaters: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0.2
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5.dev202209130706
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.0.0
    filelock: 3.7.1
    fonttools: 4.37.1
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    ipykernel: 6.15.1
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.1
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.1
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.1
    python-dateutil: 2.8.2
    pytz: 2022.2.1
    pyzmq: 23.2.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    Send2Trash: 1.8.0
    SEQCROW: 1.5.3
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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
    stack-data: 0.5.0
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.8.1

[Tony Schaefer]

should be fixed in SEQCROW 1.5.4
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Wednesday, September 14, 2022 12:06 PM
Cc: chimerax-bug-report@cgl.ucsf.edu <chimerax-bug-report@cgl.ucsf.edu>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #7593: FileReader: __init__() got an unexpected keyword argument 'all_geom' (was: ChimeraX bug report submission)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#7593: FileReader: __init__() got an unexpected keyword argument 'all_geom'
--------------------------------------------+---------------------------
          Reporter:  chimerax-bug-report@…  |      Owner:  Tony Schaefer
              Type:  defect                 |     Status:  assigned
          Priority:  normal                 |  Milestone:
         Component:  Third Party            |    Version:
        Resolution:                         |   Keywords:
        Blocked By:                         |   Blocking:
Notify when closed:                         |   Platform:  all
           Project:  ChimeraX               |
--------------------------------------------+---------------------------
Changes (by pett):

 * status:  new => assigned
 * component:  Unassigned => Third Party
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Tony Schaefer


--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7593#comment:1>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
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