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Releases: a-r-j/graphein

v1.7.7

18 Sep 04:22
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Full Changelog: v1.7.6...v1.7.7

v1.7.6

08 Feb 00:17
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Full Changelog: v1.7.5...v1.7.6

v1.7.5

27 Oct 20:20
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  • Improve graphein.protein.tensor.io.to_pdb & prep for 1.7.5 release by @a-r-j in #352

Full Changelog: v1.7.4...v1.7.5

v.1.7.4

26 Oct 13:53
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Full Changelog: v1.7.3...v1.7.4

v1.7.3

30 Aug 12:07
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  • Change how foldcomp datasets are downloaded to specific location by @a-r-j in #339

Full Changelog: v1.7.2...v1.7.3

v1.7.2

28 Aug 15:42
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Adds support for newer biopandas releases

v1.7.1

24 Aug 13:44
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What's Changed

  • remove rogue print statement by @a-r-j in #302
  • Consistent conversion to undirected graphs by @anton-bushuiev in #301
  • Tensor fixes by @a-r-j in #307
  • Minor fixes by @a-r-j in #310
  • Fix jaxtyping syntax error by @a-r-j in #312
  • PDBManager - Bug fixes, adding necessary changes to export only first PDB model, and merging-in latest updates from master by @a-r-j in #311
  • Improve data loading performance for FoldComp Datasets by 10x by @a-r-j in #313
  • Minor fix to ensure virtual angles are returned in correct shape by @a-r-j in #315
  • Accounts for selenocysteine in sidechain torsion angle computation by @a-r-j in #316
  • Fix Protein initialisation #317 by @a-r-j in #318
  • Store temp x attr in FoldComp examples to ensure correct batching. by @a-r-j in #319
  • Fixes padding in pNerF computations by @a-r-j in #320
  • Bugfixes to angle computation and pNeRF by @a-r-j in #321
  • Add new helper functions to PDBManager by @amorehead in #322
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #325
  • Fix incorrect link to collab notebook in readme by @AH-Merii in #327
  • Update pyyaml version breaking installation by @AH-Merii in #328
  • Fix and enhance geometric node features by @anton-bushuiev in #305
  • Fix .requirements reference for extras in setup.py by @AH-Merii in #330
  • Fix handing id when loading from path by @chaitjo in #332
  • Fix nx -> pyg conversion with no edges by @anton-bushuiev in #334
  • Release v1.7.1 by @AH-Merii in #329

New Contributors

Full Changelog: v1.7.0...v1.7.1

v1.7.0

10 Apr 15:54
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Full Changelog: v1.6.0...v1.7.0

v1.6.0

18 Mar 20:08
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Full Changelog: v1.5.2...v1.6.0

1.5.2

19 Sep 16:38
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1.5.2 - 19/9/2022

Protein

  • [Bugfix] - #206 Fixes KeyError when using graphein.protein.edges.distance.node_coords
  • [Bugfix] - Includes missing data files in MANIFEST.in #205

GRN

  • [Bugfix] - #208 - Resolves SSL issues with RegNetwork.

ML

  • [Feature] - #208 support for loading local pdb files by ProteinGraphDataset and InMemoryProteinGraphDataset.

by adding a params:pdb_paths and set the self.raw_dir to the root path(self.pdb_path) of pdb_paths list (the root path should be only one, pdb files should be under the same folder).

it allows loading pdb files from the self.pdb_path instead of loading from self.raw.
If you wish to download from af2 or pdb, just set pdb_paths to None and it goes back to the former version.

CI

  • [Bugfix] - #208 explicitly installs jupyter_contrib_nbextensions in Docker.