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Implement elementary bond featurizers #463

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Implement elementary bond featurizers #463

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Implemented elementary bond featurizers like bond type, bond conjugation, and bond stereochemistry.

  • Implemented elementary bond featurizers: BondTypeFeaturizer, BondConjugationFeaturizer, BondStereochemistryFeaturizer
  • These featurizers can be used to featurize bonds in a molecule for usage in graph neural networks
  • from bionemo.geometric.bond_featurizers import BondTypeFeaturizer

Usage

from bionemo.geometric.bond_featurizers import BondTypeFeaturizer
btf = BondTypeFeaturizer()
m = Chem.MolFromSmiles("C=C")
print(btf.get_features(m.GetBondWithIdx(1)))

Testing

How do you prove that your code behaves the way you claim?

Tests for these changes can be run via:

pytest tests/bionemo/geometric/test_bond_featurizers.py

sveccham and others added 20 commits November 13, 2024 15:02
@sveccham
add rdkit dependency to bionemo-geometric
b7ce5f2
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pin rdkit version
9c1d88a
@sveccham
Merge branch 'main' into sveccham/atom_bond_feats
fb860cb
@sveccham
Merge branch 'main' into sveccham/atom_bond_feats
80bc2d8
@sveccham
added ABC base featurizer
0856999
@sveccham
atom featurizers ext
3bf42ec
@sveccham
extended bond featurizers
03aef73
@sveccham
add basic atom featurizers
6664d5f
@sveccham
linted
9d244ac
@sveccham
added missing asserts
6b48186
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lint fixes
2e555b7
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riff check for src files
e9d9166
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riff check for src files
4481912
@sveccham
ruff check for pytests
7c9a1f4
@sveccham
Merge branch 'main' into sveccham/impl_atom_bond_feats
33535f0
@sveccham
copy .csv files to subpackage
2a8c55e
@sveccham
implemented elementary bond featurizers: bond type, bond conjugation,…
e18b795 
… stereochemistry
@sveccham
ruff lint
9d30c6e
@sveccham
ruff lint
d15497f
@sveccham
Merge branch 'sveccham/impl_atom_bond_feats' into sveccham/elem_bond_…
c8e7c11 
…feats
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/build-ci

@sveccham sveccham marked this pull request as ready for review November 21, 2024 19:55
@sveccham sveccham requested a review from scal444 November 21, 2024 20:07
@sveccham sveccham self-assigned this Nov 21, 2024
scal444
scal444 reviewed Nov 22, 2024
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The additions here from the other PR are good - other comments from that PR apply here if we figure out a good solution

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@scal444 scal444 scal444 left review comments

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

@guoqing-zhou guoqing-zhou Awaiting requested review from guoqing-zhou guoqing-zhou is a code owner

@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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