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czodrowskilab / VSFlow

MIT License
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Newest RDKit version does not appear compatible (2024.03.1) #10

Open Jdemolvanotterloo opened 6 months ago

Jdemolvanotterloo commented 6 months ago

Hi!

When setting up VSFlow in a new environment using both the environment.yml and later again with the manual set-up, I ran into this issue:

ImportError: cannot import name 'Standardizer' from 'rdkit.Chem.MolStandardize'

The latest version from RDKit 2024.03.1 does not seem have Standardizer anymore. The previous version does, but the environment.yml file automatically installs the 2024 version for me. I am not sure if I am the only one who encountered it, but manually installing the previous version solves the problem.

Maybe something to look into, in case more people encounter this :)

GianlucaNovello commented 6 months ago

HI! How did you resolve the issue related to MolVS? I encountered problems when manually installing RDKit 2019.09.3, and it seems there are compatibility issues with MolVS.

HaotianZhangAI4Science commented 2 months ago

I solved this by using the following command to create the environment.

conda create -n vsflow python=3.8 rdkit=2021.09.5 xlrd xlsxwriter pdfrw fpdf pymol-open-source molvs matplotlib -c conda-forge