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add rdkit dependency to bionemo-geometric #432

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merged 5 commits into from
Nov 15, 2024
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(NOTE: delete these instructional lines as you fill-out this PR template)

(NOTE: _template is designed to be filled-in and used as the squashed commit message for the entire PR. Italicized text is intended to be deleted as you fill in this template. Use the text between the ---)


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Most of the changes to files with extensions *.py, *.yaml, *.yml, Dockerfile* or requirements.txt DO REQUIRE both pytest- and jet- CI stages.

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@malcolmgreaves malcolmgreaves left a comment

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LGTM w/ change: provide version constraints for rdkit.

sub-packages/bionemo-geometric/pyproject.toml Outdated Show resolved Hide resolved
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@DejunL DejunL left a comment

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@sveccham Just FYI rdkit's conformer generation code can be sensitive to its dependency numpy version. I had to pin both numpy and rdkit versions to:

  "numpy==1.26.4",
  "rdkit==2023.9.5",

in order to reproduce some diffdock results

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/build-ci

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/build-ci

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/build-ci

@sveccham sveccham enabled auto-merge (squash) November 15, 2024 19:00
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/build-ci

@sveccham sveccham merged commit 5147cb8 into main Nov 15, 2024
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@sveccham sveccham deleted the sveccham/atom_bond_feats branch November 15, 2024 19:55
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3 participants