RyanZR/labodock

mk_prepare_ligand.py causes ModuleNotFoundError: No module named 'pandas'

Closed this issue · 3 comments

italobale commented

In the 'virtual_screening.ipynb' in the step 'Parameterise ligands with Gasteiger charges'
the following command
!mk_prepare_ligand.py -i {LIG_sdf_lFile} -o {LIG_pdbqt_dFFile}

causes this error:

Traceback (most recent call last):
  File "/usr/local/bin/mk_prepare_ligand.py", line 14, in <module>
    from meeko import MoleculePreparation
  File "/usr/local/lib/python3.10/site-packages/meeko/__init__.py", line 36, in <module>
    from . import analysis
  File "/usr/local/lib/python3.10/site-packages/meeko/analysis/__init__.py", line 7, in <module>
    from .fingerprint_interactions import FingerprintInteractions
  File "/usr/local/lib/python3.10/site-packages/meeko/analysis/fingerprint_interactions.py", line 10, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
RyanZR commented

Hi @italobale, I couldn't reproduce this error in Google Colab. Can you please specify the platform used to run the notebooks?

Meanwhile, you can attempt to resolve the issue by installing additional packages with the following code. It seems the issue might be related to running the notebook on platforms other than Google Colab, which currently is not supported.

!mamba install -c anaconda -c conda-forge pandas=1.5.3 matplotlib=3.7.1 seaborn=0.12.2
italobale commented

@RyanZR
Thanks for checking this.

When I had the issue I was running the notebook on Google Colab.

However, I tried again running the notebook on Colab, and this seems to work now.
There might have been an issue in my Colab Runtime session, which corrupted somehow the installation.

RyanZR commented

@italobale
Thanks for the update. It's great to hear that the issue resolved itself.
If you encounter this issue again, feel free to reopen the issue again.