graphein

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hotfix greater than/less than operations in pdb_manager

1

#### Reference Issues/PRs #### What does this implement/fix? Explain your changes Greater than / less than comparisons in oligomer selection in `PDBManager` are switched to greater than or less than....

a-r-j

[pre-commit.ci] pre-commit autoupdate

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updates: - [github.com/psf/black: 24.4.2 → 24.8.0](https://github.com/psf/black/compare/24.4.2...24.8.0)

pre-commit-ci[bot]

Hi, I had a nasty bug, such that the DSSP features are silently omitted. This happens due to biopython returning an empty dictionary for newer DSSP versions, for which the...

edikedik

[pre-commit.ci] pre-commit autoupdate

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updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.6.0...v5.0.0) - [github.com/psf/black: 24.8.0 → 24.10.0](https://github.com/psf/black/compare/24.8.0...24.10.0)

pre-commit-ci[bot]

Fix #427

4

#### Reference Issues/PRs Fixes #427 #### Pull Request Checklist - [ ] Added a note about the modification or contribution to the `./CHANGELOG.md` file (if applicable) - [x] Added appropriate...

chris-clem

Add num_heavy_atoms as node features

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**Is your feature request related to a problem? Please describe.** There are already a lot of nice molecule node features, but I was missing the number of heavy atoms as...

chris-clem

It would be great to have add_bond_type_one_hot as an edge features for molecules. Something similar to ```python def add_bond_type_one_hot( u: str, v: str, d: Dict[str, Any], return_array: bool = True,...

chris-clem

H coords are not included when constructing molecule graph from SDF file

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**Describe the bug** H atoms are not included in `coords` when constructing molecule graph with `add_hs=True` and `path`. **To Reproduce** Colab reproducing the bug: https://colab.research.google.com/drive/122CTepC6O_-R-jbLArcbdqSQOiQseB-H?usp=sharing **Expected behavior** If `config.add_hs` is...

chris-clem

Fix incorrect node lookup in distance-based edge generation Fixes #418

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Previously, the node indices from the distance matrix were used to access rows in the full PDB DataFrame (`G.graph["pdb_df"]`), assuming their indices aligned. This caused incorrect residue pairings when the...

elementare

Using graphein 1.7.7 in colab

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**Describe the bug** Using graphein in colab: When graphin is installed in colab environment , numpy gets downgraded when using `pip install graphein` in colab. Then `from graphein.protein.config import ProteinGraphConfig`...

mahdi-shafiei