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forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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RDKit v2024 breaks meeko #96

Closed Tonylac77 closed 6 months ago

Tonylac77 commented 6 months ago

After updating to rdkit v2024.03.1 there is a failed import (rdkit.six)

Traceback (most recent call last): File "/home/dockm8/miniconda3/envs/dockm8/lib/python3.10/site-packages/streamlit/runtime/scriptrunner/script_runner.py", line 535, in _run_script exec(code, module.dict) File "/home/dockm8/DockM8/gui.py", line 14, in from scripts.docking_functions import DOCKING_PROGRAMS File "/home/dockm8/DockM8/scripts/docking_functions.py", line 12, in from meeko import PDBQTMolecule, RDKitMolCreate File "/home/dockm8/miniconda3/envs/dockm8/lib/python3.10/site-packages/meeko/init.py", line 32, in from .rdkit_mol_create import RDKitMolCreate File "/home/dockm8/miniconda3/envs/dockm8/lib/python3.10/site-packages/meeko/rdkit_mol_create.py", line 11, in from rdkit.six import StringIO ModuleNotFoundError: No module named 'rdkit.six'

diogomart commented 6 months ago

Thank you for reporting. It is fixed in ed395cc8c4c690d25a295c1ba81ee0f38c620dd4 which can be used when installing from source (not in a release yet) https://github.com/forlilab/Meeko?tab=readme-ov-file#installation-from-source