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’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Snap featurizer #3266

Merged
merged 10 commits into from
Mar 23, 2023
Merged

Snap featurizer #3266

merged 10 commits into from
Mar 23, 2023

Conversation

tonydavis629
Copy link
Collaborator

Pull Request Template

Description

This PR implements the featurizer described in Hu, W. et al. Strategies for Pre-training Graph Neural Networks. Preprint at https://doi.org/10.48550/arXiv.1905.12265 (2020). This is a simple featurizer for molecules with its features defined by rdkit.chem objects.

Type of change

Please check the option that is related to your PR.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
    • In this case, we recommend to discuss your modification on GitHub issues before creating the PR
  • Documentations (modification for documents)

Checklist

  • My code follows the style guidelines of this project
    • Run yapf -i <modified file> and check no errors (yapf version must be 0.32.0)
    • Run mypy -p deepchem and check no errors
    • Run flake8 <modified file> --count and check no errors
    • Run python -m doctest <modified file> and check no errors
  • I have performed a self-review of my own code
  • I have commented my code, particularly in hard-to-understand areas
  • I have made corresponding changes to the documentation
  • I have added tests that prove my fix is effective or that my feature works
  • New unit tests pass locally with my changes
  • I have checked my code and corrected any misspellings

Copy link
Member

@rbharath rbharath left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

One minor comment but otherwise good to merge in once the CI is green. Let me know once CI looks good and I'll give final thumbs up and merge


"""
# atoms
# num_atom_features = 2 # atom type, chirality tag
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Is this meant to be here? Looks like it could be commented out code or a terse comment. If it's a comment, can you elaborate a bit more so it's clearer?

Copy link
Member

@rbharath rbharath left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

One minor question about a potential docs issue

docs/source/api_reference/featurizers.rst Show resolved Hide resolved
This reverts commit a45d327.
Copy link
Member

@rbharath rbharath left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM, feel free to merge in once CI clear

@tonydavis629 tonydavis629 merged commit 536ac3a into deepchem:master Mar 23, 2023
@tonydavis629 tonydavis629 deleted the snap_featurizer branch March 30, 2023 14:21
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

Successfully merging this pull request may close these issues.

None yet

2 participants