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forlilab / waterkit

Tool to predict water molecules placement and energy in ligand binding sites
GNU General Public License v3.0
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python 3.12 breaks waterkit #12

Closed blakemertz closed 5 months ago

blakemertz commented 5 months ago

Just an FYI to waterkit users -- I just installed waterkit using the installation instructions, but my conda environment pulled python 3.12.1. 3.12 dropped support for the imp module and so until that issue is resolved within your codebase, you need to restrict the python version to be <= 3.11: https://stackoverflow.com/questions/77274572/multiqc-modulenotfounderror-no-module-named-imp

I was getting the following error when trying to run wk_prepare_receptor.py:

python /media/bak11/binaries/git/waterkit/scripts/wk_prepare_receptor.py -i MDH-258_molrep7_refmac3-coot-0.pdb -o MDH-258-xtal_prepared --pdb --amber_pdbqt
Traceback (most recent call last):
  File "/media/bak11/binaries/git/waterkit/scripts/wk_prepare_receptor.py", line 20, in <module>
    from waterkit import utils
  File "/media/bak11/binaries/git/waterkit/waterkit/__init__.py", line 8, in <module>
    from .autogrid import AutoGrid
  File "/media/bak11/binaries/git/waterkit/waterkit/autogrid.py", line 16, in <module>
    from .molecule import Molecule
  File "/media/bak11/binaries/git/waterkit/waterkit/molecule.py", line 9, in <module>
    import imp
ModuleNotFoundError: No module named 'imp'

Specifying python=3.11 when creating the environment fixed the issue.

jeeberhardt commented 5 months ago

Thanks! Will fix that as soon as possible!