XMAS: 'Tabular' object has no attribute 'peptide_pairs'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\pganguly\\\OneDrive - St. Jude Children's Research
> Hospital\\\ERdj6\\\Erdj6_BiP
> Alphafold\\\ERdj6_35-504\\\test_1bc31_relaxed_rank_1_model_3.pdb"

Chain information for test_1bc31_relaxed_rank_1_model_3.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> toolshed show

Downloading bundle ChimeraX_XMAS-1.1.3-py3-none-any.whl  

Errors may have occurred when running pip:  

pip standard error:  
\---  
  
[notice] A new release of pip is available: 23.0 -> 24.0  
[notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip
install --upgrade pip  
\---  

pip standard output:  
\---  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing c:\users\pganguly\downloads\chimerax_xmas-1.1.3-py3-none-any.whl  
Collecting seaborn  
Downloading seaborn-0.13.2-py3-none-any.whl (294 kB)  
\-------------------------------------- 294.9/294.9 kB 8.9 MB/s eta 0:00:00  
Requirement already satisfied: ChimeraX-Core>=1.6 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-XMAS==1.1.3) (1.6.1)  
Requirement already satisfied: ChimeraX-UI>=1.6 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-XMAS==1.1.3) (1.28.4)  
Collecting openpyxl  
Downloading openpyxl-3.1.2-py2.py3-none-any.whl (249 kB)  
\------------------------------------- 250.0/250.0 kB 15.0 MB/s eta 0:00:00  
Collecting qtrangeslider  
Downloading QtRangeSlider-0.1.5-py3-none-any.whl (33 kB)  
Collecting pandas  
Downloading pandas-2.2.1-cp39-cp39-win_amd64.whl (11.6 MB)  
\--------------------------------------- 11.6/11.6 MB 59.5 MB/s eta 0:00:00  
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI>=1.6->ChimeraX-
XMAS==1.1.3) (1.0)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI>=1.6->ChimeraX-
XMAS==1.1.3) (1.1.1)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-UI>=1.6->ChimeraX-
XMAS==1.1.3) (1.2)  
Collecting et-xmlfile  
Downloading et_xmlfile-1.1.0-py3-none-any.whl (4.7 kB)  
Requirement already satisfied: tzdata>=2022.7 in c:\program
files\chimerax\bin\lib\site-packages (from pandas->ChimeraX-XMAS==1.1.3)
(2023.3)  
Requirement already satisfied: python-dateutil>=2.8.2 in c:\program
files\chimerax\bin\lib\site-packages (from pandas->ChimeraX-XMAS==1.1.3)
(2.8.2)  
Requirement already satisfied: numpy<2,>=1.22.4 in c:\program
files\chimerax\bin\lib\site-packages (from pandas->ChimeraX-XMAS==1.1.3)
(1.23.5)  
Requirement already satisfied: pytz>=2020.1 in c:\program
files\chimerax\bin\lib\site-packages (from pandas->ChimeraX-XMAS==1.1.3)
(2023.3)  
Requirement already satisfied: matplotlib!=3.6.1,>=3.4 in c:\program
files\chimerax\bin\lib\site-packages (from seaborn->ChimeraX-XMAS==1.1.3)
(3.6.3)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-
UI>=1.6->ChimeraX-XMAS==1.1.3) (1.3)  
Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-
UI>=1.6->ChimeraX-XMAS==1.1.3) (1.1)  
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in c:\program
files\chimerax\bin\lib\site-packages (from ChimeraX-
SelInspector~=1.0->ChimeraX-UI>=1.6->ChimeraX-XMAS==1.1.3) (1.0.1)  
Requirement already satisfied: pillow>=6.2.0 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.4->seaborn->ChimeraX-XMAS==1.1.3) (9.3.0)  
Requirement already satisfied: packaging>=20.0 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.4->seaborn->ChimeraX-XMAS==1.1.3) (23.1)  
Requirement already satisfied: fonttools>=4.22.0 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.4->seaborn->ChimeraX-XMAS==1.1.3) (4.39.3)  
Requirement already satisfied: cycler>=0.10 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.4->seaborn->ChimeraX-XMAS==1.1.3) (0.11.0)  
Requirement already satisfied: kiwisolver>=1.0.1 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.4->seaborn->ChimeraX-XMAS==1.1.3) (1.4.4)  
Requirement already satisfied: pyparsing>=2.2.1 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.4->seaborn->ChimeraX-XMAS==1.1.3) (3.0.9)  
Requirement already satisfied: contourpy>=1.0.1 in c:\program
files\chimerax\bin\lib\site-packages (from
matplotlib!=3.6.1,>=3.4->seaborn->ChimeraX-XMAS==1.1.3) (1.0.7)  
Requirement already satisfied: six>=1.5 in c:\program
files\chimerax\bin\lib\site-packages (from python-
dateutil>=2.8.2->pandas->ChimeraX-XMAS==1.1.3) (1.16.0)  
Installing collected packages: qtrangeslider, et-xmlfile, pandas, openpyxl,
seaborn, ChimeraX-XMAS  
Successfully installed ChimeraX-XMAS-1.1.3 et-xmlfile-1.1.0 openpyxl-3.1.2
pandas-2.2.1 qtrangeslider-0.1.5 seaborn-0.13.2  
\---  

Successfully installed ChimeraX-XMAS-1.1.3 et-xmlfile-1.1.0 openpyxl-3.1.2
pandas-2.2.1 qtrangeslider-0.1.5 seaborn-0.13.2  
Installed ChimeraX-XMAS (1.1.3)  

> ui tool show XMAS

Unsupported evidence file format  
Traceback (most recent call last):  
File "C:\Users\pganguly\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
File "C:\Users\pganguly\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\pganguly\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\XMAS\tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\pganguly\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
File "C:\Users\pganguly\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
  
See log for complete Python traceback.  
  
Please select pseudobonds  
Please select pseudobonds  
Please select pseudobonds  
Please select pseudobonds  
Unsupported evidence file format  
Traceback (most recent call last):  
File "C:\Users\pganguly\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\XMAS\tool.py", line 290, in <lambda>  
function = lambda _, s=selector, t=key: self.map_button_clicked(s, t)  
File "C:\Users\pganguly\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\XMAS\tool.py", line 447, in map_button_clicked  
self.map_crosslinks(self.checked_models, checked_files)  
File "C:\Users\pganguly\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\XMAS\tool.py", line 460, in map_crosslinks  
evidence = Evidence(evidence_file)  
File "C:\Users\pganguly\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
AttributeError: 'Tabular' object has no attribute 'peptide_pairs'  
  
File "C:\Users\pganguly\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\XMAS\read_evidence.py", line 38, in __init__  
self.peptide_pairs = evidence.peptide_pairs  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.100.9955
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7090
OS: Microsoft Windows 11 Enterprise (Build 22631)
Memory: 8,308,985,856
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i5-10500T CPU @ 2.30GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    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-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    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-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    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: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    et-xmlfile: 1.1.0
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openpyxl: 3.1.2
    openvr: 1.23.701
    packaging: 23.1
    pandas: 2.2.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    seaborn: 0.13.2
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0