RdkitGridFeaturizer fails to featurize the datapoint since last two week
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- Python
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Description
Hi, I currently encounter an issue about RdkitGridFeaturizer in deepchem. This featurizer cannot featurize the datapoint since last monday. Two weeks ago, I used this RdkitGridFeaturizer to featurize the datapoint and this featurizer worked well. However, last Monday I used the same code to featurize the datapoint and the RdkitGridFeaturizer failed to featurize the datapoint. I set up the environment based on the deepchem tuturioal e-book and use Colab. I attach my code here and screenshot here.
featurizer = dc.feat.RdkitGridFeaturizer(voxel_width=2.0
, feature_types=['ecfp', 'splif', 'salt_bridge', 'hbond']
, flatten=True
, sanitize=True)
tasks, datasets, transformers = dc.molnet.load_pdbbind(featurizer=featurizer, set_name="refined", reload=True,
data_dir='/content/drive/MyDrive/Conda',
save_dir='/content/drive/MyDrive/Conda')


Contributor guide
Research direction
Start by reproducing the provided RdkitGridFeaturizer and load_pdbbind code in Colab, capturing the exception that is missing from the report. Compare the failing datapoint and environment with the previously working setup; done means the datapoint featurizes successfully or the incompatibility is identified and documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- machine-learning
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100