Opened 3 years ago
Closed 2 years ago
#8885 closed defect (fixed)
add_restraint: __init__() takes 3 positional arguments but 4 were given
Reported by: | Owned by: | Tristan Croll | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Third Party | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5.dev202209210054 (2022-09-21 00:54:47 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.5.dev202209210054 (2022-09-21) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show ISOLDE > set selectionWidth 4 Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 134, in invoke return self._func(self._name, data) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/tool.py", line 42, in _launch_main_gui tw = self.tool_window = IsoldeMainWin(self) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/main_win.py", line 56, in __init__ self.restraints_tab = RestraintsTab(self.session, self.isolde, self, tabw) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/ui_base.py", line 226, in __init__ self.populate() File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/__init__.py", line 20, in populate self.addWidget(ReferenceModelPanel(session, isolde, parent, gui)) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 16, in __init__ cd = self.content = ReferenceModelDialog(session, isolde, gui, self) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 85, in __init__ opt = self.options = ReferenceModelOptions(self.session, gui, options_frame) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 464, in __init__ drfi = self.distance_fuzziness_indicator = DistanceRestraintFuzzinessIndicator(session, dsl, dfl) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 636, in __init__ self._create_dummy_model() File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py", line 704, in _create_dummy_model dr = self._dummy_restraint = drm.add_restraint(a1, a2) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py", line 2883, in add_restraint r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py", line 2864, in _get_restraints return self._plural_restraint_getter(ret[:num]) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py", line 97, in _adaptive_distance_restraints return AdaptiveDistanceRestraints(p) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py", line 556, in __init__ super().__init__(c_pointers, AdaptiveDistanceRestraint, TypeError: __init__() takes 3 positional arguments but 4 were given Error processing trigger "new frame": TypeError: __init__() takes 3 positional arguments but 4 were given File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py", line 556, in __init__ super().__init__(c_pointers, AdaptiveDistanceRestraint, See log for complete Python traceback. Forcefield cache not found or out of date. Regenerating from ffXML files. This is normal if running ISOLDE for the first time, or after upgrading OpenMM. Done loading forcefield Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py", line 134, in invoke return self._func(self._name, data) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py", line 1790, in _get_and_process_changes return self._process_changes(changes) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py", line 1775, in _process_changes changed_obj = class_funcs[1](changed_ptrs) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molobject.py", line 97, in _adaptive_distance_restraints return AdaptiveDistanceRestraints(p) File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py", line 556, in __init__ super().__init__(c_pointers, AdaptiveDistanceRestraint, TypeError: __init__() takes 3 positional arguments but 4 were given Error processing trigger "new frame": TypeError: __init__() takes 3 positional arguments but 4 were given File "/Users/saisundarrajan/Library/Application Support/ChimeraX/1.5/site- packages/chimerax/isolde/molarray.py", line 556, in __init__ super().__init__(c_pointers, AdaptiveDistanceRestraint, See log for complete Python traceback. OpenGL version: 4.1 ATI-4.10.12 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0) OS Loader Version: 577~129 Software: System Software Overview: System Version: macOS 13.3.1 (22E261) Kernel Version: Darwin 22.4.0 Time since boot: 1 day, 23 hours, 6 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP U28 4K HDR: Resolution: 6016 x 3384 UI Looks like: 3008 x 1692 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 1CR24100KL Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.0.8 Babel: 2.10.3 backcall: 0.2.0 biopython: 1.81 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 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: 1.41.3 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.dev202209210054 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-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: 2.0.7 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-StarMap: 1.1.75 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-StrudelScore: 0.2 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: 1.24.1 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 docutils: 0.19 entrypoints: 0.4 executing: 1.0.0 filelock: 3.7.1 fonttools: 4.37.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 4.12.0 ipykernel: 6.15.3 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 mrcfile: 1.4.3 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 pandas: 2.0.0 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: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 pyqtgraph: 0.13.3 python-dateutil: 2.8.2 pytz: 2022.2.1 pyzmq: 24.0.0 qtconsole: 5.3.1 QtPy: 2.2.0 RandomWords: 0.4.0 recordtype: 1.4 requests: 2.28.1 scipy: 1.9.0 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 threed-strudel: 0.9.18 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 tzdata: 2023.3 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.8.1
Change History (2)
comment:1 by , 3 years ago
Component: | Unassigned → Third Party |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → add_restraint: __init__() takes 3 positional arguments but 4 were given |
comment:2 by , 2 years ago
Resolution: | → fixed |
---|---|
Status: | assigned → closed |
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This was fixed in the ISOLDE 1.5 release (to get it just install the official ChimeraX 1.5 release and install ISOLDE into that - or you could wait a couple of weeks for 1.6). Was caused by a minor change in the ChimeraX API going from 1.4 to 1.5.