Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We鈥檒l occasionally send you account related emails.

Already on GitHub? Sign in to your account

ComplexFeaturizer failed to featurize complexes #2347

Open
Mirrty opened this issue Jan 7, 2021 · 2 comments
Open

ComplexFeaturizer failed to featurize complexes #2347

Mirrty opened this issue Jan 7, 2021 · 2 comments

Comments

@Mirrty
Copy link

Mirrty commented Jan 7, 2021

馃悰 Bug

I am having difficulties trying to generate features for protein-ligand complexes with ComplexFeaturizer:

featurizer= dc.feat.NeighborListComplexAtomicCoordinates()
featurizer.featurize([('2r58_ligand.sdf', '2r58_protein.pdb')])

Failed to featurize datapoint 0. Appending empty array

Expected behavior

Environment

  • OS: Linux Centos 8
  • Python version: 3.7
  • DeepChem version: 2.4.0-rc1.dev
  • RDKit version (optional): 2020.09.3
  • TensorFlow version (optional): 2.3.0
  • PyTorch version (optional):
  • Any other relevant information:

Additional context

2r58.zip

@ncfrey
Copy link
Contributor

ncfrey commented Jan 8, 2021

Hi @Mirrty, thanks for raising this issue! I'm working on debugging the complex featurizers and I'll let you know after I have a chance to take a look at this. My first guess is that RDKit and PDBFixer might be having trouble sanitizing and preparing your PDB file.

@Mirrty
Copy link
Author

Mirrty commented Jan 8, 2021

Thank you for your answer, @ncfrey. I am working with pdbbind dataset, so these are the examples of the files that have been downloaded with dc.molnet.load_pdbbind.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants