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korakot / kora

Convenient tools for Colab
MIT License
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RDKit #13

Closed YavarYeganeh closed 3 years ago

YavarYeganeh commented 3 years ago

Recently, RDKit cannot be imported on Colab.

EBjerrum commented 3 years ago

I can confirm this issue. Google colab now uses python 3.7, but the kora rdkit installs for python 3.6

Check python version in Colab: import sys sys.version OUT: 3.7.10 (default, Feb 20 2021, 21:17:23) \n[GCC 7.5.0]

Installation of RDKit is in python 3.6 !ls -d /usr/local/lib/python3.6// OUT: /usr/local/lib/python3.6/dist-packages/rdkit

A workaround until the gzipped rdkit install is fixed is to add the path with sys: import sys sys.path.append('/usr/local/lib/python3.6/dist-packages/')

but I'm not sure it will be entirely errorfree to mix python versions

YavarYeganeh commented 3 years ago

Thanks, it's working after adding the directory.

korakot commented 3 years ago

I have updated kora to use Python 3.7, and also use RDKit 2020.09.1

Please check if it works well with your case.

YavarYeganeh commented 3 years ago

I have updated kora to use Python 3.7, and also use RDKit 2020.09.1

Please check if it works well with your case.

Thanks a lot. It now works very well again.

EBjerrum commented 3 years ago

Thanks for the update, kora makes life with Colab and RDKit so much easier :-)