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forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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Unable to import meeko #122

Closed deb-m closed 1 month ago

deb-m commented 1 month ago

I have installed meeko v0.50 using conda as well as pip, but facing the following error with RDkit v2024.03.2

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
Cell In[14], line 1
----> 1 import meeko

File /usr/local/Caskroom/miniconda/base/envs/meeko/lib/python3.10/site-packages/meeko/__init__.py:32
     30 from .receptor_pdbqt import PDBQTReceptor
     31 from .molecule_pdbqt import PDBQTMolecule
---> 32 from .rdkit_mol_create import RDKitMolCreate
     33 from .reactive import reactive_typer
     34 from .reactive import get_reactive_config

File /usr/local/Caskroom/miniconda/base/envs/meeko/lib/python3.10/site-packages/meeko/rdkit_mol_create.py:11
      9 from rdkit.Geometry import Point3D
     10 from rdkit.Chem import AllChem
---> 11 from rdkit.six import StringIO
     12 import json
     13 import os

ModuleNotFoundError: No module named 'rdkit.six'

Upon further digging I found this post https://github.com/rdkit/rdkit/pull/2315 rdkit do not have six.py anymore, and the most recent rdkit is breaking meeko. I think if I install an 2022 version of rdkit, it will work, but it may be a good idea to remove rdkit.six dependency from the code. Thanks

diogomart commented 1 month ago

Hello, duplicates #96 and fixed in ed395cc8c4c690d25a295c1ba81ee0f38c620dd4 but not released yet.