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I encountered this when trying to run one of your case studies:
$ python ./DiffLinker/generate_with_protein.py \
--fragments 3hz1_modified_fragments_obabel.sdf \
--protein 3hz1_protein.pdb \
--output samples \
--model models/pockets_difflinker_full_given_anchors.ckpt \
--linker_size models/zinc_size_gnn.ckpt \
--anchors 12,22 \
--n_samples 1000 \
--max_batch_size 16 \
--random_seed 1
Traceback (most recent call last):
File "[...]/DiffLinker/generate_with_protein.py", line 14, in <module>
from src.lightning import DDPM
File "[...]/DiffLinker/src/lightning.py", line 7, in <module>
from src import metrics, utils, delinker
File "[...]/DiffLinker/src/delinker.py", line 7, in <module>
from src.delinker_utils import sascorer, calc_SC_RDKit
File "[...]/DiffLinker/src/delinker_utils/sascorer.py", line 22, in <module>
from rdkit.six.moves import cPickle
ModuleNotFoundError: No module named 'rdkit.six'
The text was updated successfully, but these errors were encountered:
rsherhod
changed the title
sascorer.py calls missing RDkit module - ModuleNotFoundError: No module named 'rdkit.six'
sascorer.py calls removed RDkit module - ModuleNotFoundError: No module named 'rdkit.six'
Apr 19, 2024
in sascorer.py
you can change from rdkit.six.moves import cPickle to import pickle,
then in line 39, change _fscores = cPickle.load(gzip.open('%s.pkl.gz' % name)) to _fscores = pickle.load(gzip.open('%s.pkl.gz' % name))
delinker_utils/sascorer.py is calling a module of RDKit that was removed in Release_2024.03.1
See change log: https://github.com/rdkit/rdkit/blob/master/ReleaseNotes.md#code-removed-in-this-release-1
I encountered this when trying to run one of your case studies:
The text was updated successfully, but these errors were encountered: