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Atom and bond features #453

Merged
merged 37 commits into from
Nov 28, 2024
Merged

Atom and bond features #453

merged 37 commits into from
Nov 28, 2024

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sveccham
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@sveccham sveccham commented Nov 19, 2024 •
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Implements classes for featurizing atoms and bonds.

  • Implemented atom and bond featurization classes
  • Implemented classes can be used for featurizing atoms and bonds in a molecular graph in order to form inputs for graph neural networks
  • Usage example 1: from bionemo.geometric.atom_featurizers import AromaticityFeaturizer, AtomicNumFeaturizer
  • Usage example 2: from bionemo.geometric.bond_featurizers import RingFeaturizer

Usage

How does a user interact with the changed code?

from bionemo.geometric.atom_featurizers import DegreeFeaturizer
df = DegreeFeaturizer()
mol = Chem.MolFromSmiles("CCCC")
feats = df.get_features(mol.GetAtomWithIdx(0))

Testing

Tests for these changes can be run via:

pytest -v tests/bionemo/geometric/test_atom_featurizers.py
pytest -v tests/bionemo/geometric/test_bond_featurizers.py

@sveccham sveccham self-assigned this Nov 19, 2024
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@sveccham sveccham added the enhancement New feature or request label Nov 19, 2024
@sveccham sveccham marked this pull request as ready for review November 20, 2024 06:37
@sveccham sveccham marked this pull request as draft November 20, 2024 19:53
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@sveccham sveccham marked this pull request as ready for review November 20, 2024 23:28
@sveccham sveccham requested a review from scal444 November 20, 2024 23:31
scal444
scal444 reviewed Nov 21, 2024
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guoqing-zhou
guoqing-zhou reviewed Nov 26, 2024
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@sveccham sveccham enabled auto-merge (squash) November 27, 2024 23:23
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@sveccham sveccham closed this Nov 27, 2024
auto-merge was automatically disabled November 27, 2024 23:24

Pull request was closed

@sveccham sveccham reopened this Nov 27, 2024
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@sveccham sveccham enabled auto-merge (squash) November 27, 2024 23:40
DejunL
DejunL approved these changes Nov 28, 2024
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LGTM. Just a general question, I'm wondering if there is an easy way to support batch featurization where potentially different molecules can be included in the batch

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@sveccham sveccham merged commit 92369d7 into main Nov 28, 2024
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@sveccham sveccham deleted the sveccham/impl_atom_bond_feats branch November 28, 2024 03:45
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@DejunL DejunL DejunL approved these changes

@scal444 scal444 scal444 approved these changes

@guoqing-zhou guoqing-zhou guoqing-zhou approved these changes

@pstjohn pstjohn pstjohn approved these changes

@jstjohn jstjohn Awaiting requested review from jstjohn jstjohn is a code owner

@malcolmgreaves malcolmgreaves Awaiting requested review from malcolmgreaves malcolmgreaves is a code owner

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