Graphein Versions Save

What's Changed

• Handle edge case of computing chi angles for PYL #356 by @a-r-j in https://github.com/a-r-j/graphein/pull/357
• Remove Hydrogen isotopes in deprotonating by @Ruibin-Liu in https://github.com/a-r-j/graphein/pull/337
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/a-r-j/graphein/pull/358
• eliminate FutureWarning about Pandas by @StevenAZy in https://github.com/a-r-j/graphein/pull/359
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/a-r-j/graphein/pull/360
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/a-r-j/graphein/pull/361
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/a-r-j/graphein/pull/362
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/a-r-j/graphein/pull/363
• update PDB urls to avoid deprecated ftp by @a-r-j in https://github.com/a-r-j/graphein/pull/364
• Bump version strings for 1.7.6 release by @a-r-j in https://github.com/a-r-j/graphein/pull/365

New Contributors

• @Ruibin-Liu made their first contribution in https://github.com/a-r-j/graphein/pull/337
• @StevenAZy made their first contribution in https://github.com/a-r-j/graphein/pull/359

Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.5...v1.7.6

What's Changed

• Improve graphein.protein.tensor.io.to_pdb & prep for 1.7.5 release by @a-r-j in https://github.com/a-r-j/graphein/pull/352

Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.4...v1.7.5

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/a-r-j/graphein/pull/341
• Fix url for PDB sequence metadata download in PDBManager by @a-r-j in https://github.com/a-r-j/graphein/pull/346
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/a-r-j/graphein/pull/347
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/a-r-j/graphein/pull/349
• Add support for PyG 2.4+ by @a-r-j in https://github.com/a-r-j/graphein/pull/350
• Fix add_sequence_neighbour_vector by @anton-bushuiev in https://github.com/a-r-j/graphein/pull/336
• Bump versionstrings for 1.7.4 release by @a-r-j in https://github.com/a-r-j/graphein/pull/351

Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.3...v1.7.4

What's Changed

• Change how foldcomp datasets are downloaded to specific location by @a-r-j in https://github.com/a-r-j/graphein/pull/339

Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.2...v1.7.3

Adds support for newer biopandas releases

What's Changed

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

New Contributors

• @AH-Merii made their first contribution in https://github.com/a-r-j/graphein/pull/327
• @chaitjo made their first contribution in https://github.com/a-r-j/graphein/pull/332

Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.0...v1.7.1

What's Changed

• FoldComp ML Datasets by @a-r-j in https://github.com/a-r-j/graphein/pull/284
• update citation by @a-r-j in https://github.com/a-r-j/graphein/pull/287
• Development of PDBManager Class (WIP) by @amorehead in https://github.com/a-r-j/graphein/pull/272
• Support MMTF & rename pdb_path to path throughout by @a-r-j in https://github.com/a-r-j/graphein/pull/293
• Prep for 1.7.0 release by @a-r-j in https://github.com/a-r-j/graphein/pull/292
• Add autopublish workflow by @a-r-j in https://github.com/a-r-j/graphein/pull/298

Full Changelog: https://github.com/a-r-j/graphein/compare/v1.6.0...v1.7.0

What's Changed

• Correct the coordinates computation for small residue graohs, and when granularity: centroids by @manonreau in https://github.com/a-r-j/graphein/pull/220
• Logging by @a-r-j in https://github.com/a-r-j/graphein/pull/221
• Fix bug in add_k_nn_edges and add minor extension by @anton-bushuiev in https://github.com/a-r-j/graphein/pull/229
• Catch AF2 download error #225 by @a-r-j in https://github.com/a-r-j/graphein/pull/226
• Add minimal install workflow by @a-r-j in https://github.com/a-r-j/graphein/pull/230
• Modify graphs.py to handle insertions when {'insertions': True} by @manonreau in https://github.com/a-r-j/graphein/pull/223
• control protein graph construction verbosity by @davidfstein in https://github.com/a-r-j/graphein/pull/242
• fix peptide bonds for all atom graphs by @a-r-j in https://github.com/a-r-j/graphein/pull/254
• Add tensor parsing util by @a-r-j in https://github.com/a-r-j/graphein/pull/244
• Fix typo in problematic_pdbs.rst by @eltociear in https://github.com/a-r-j/graphein/pull/258
• Fix and improve the utilities for PyG by @anton-bushuiev in https://github.com/a-r-j/graphein/pull/234
• add graph construction from a dataframe by @a-r-j in https://github.com/a-r-j/graphein/pull/264
• Fix graph sequence (atomistic graphs in initialise_graph_with_metadata had duplicated residues) by @kamurani in https://github.com/a-r-j/graphein/pull/268
• Add improved error message for non standard node funcs #274 by @a-r-j in https://github.com/a-r-j/graphein/pull/275
• clean up unused files and move docs from root by @a-r-j in https://github.com/a-r-j/graphein/pull/276
• prelim path support #269 by @a-r-j in https://github.com/a-r-j/graphein/pull/277
• Switch to miniconda for build by @a-r-j in https://github.com/a-r-j/graphein/pull/278
• Improve altloc handling by @anton-bushuiev in https://github.com/a-r-j/graphein/pull/263
• Df processing #216 by @a-r-j in https://github.com/a-r-j/graphein/pull/222
• Minor patch convert_nx_to_pyg #280 by @rg314 in https://github.com/a-r-j/graphein/pull/281
• changes for 1.6.0 by @a-r-j in https://github.com/a-r-j/graphein/pull/279

New Contributors

• @manonreau made their first contribution in https://github.com/a-r-j/graphein/pull/220
• @anton-bushuiev made their first contribution in https://github.com/a-r-j/graphein/pull/229
• @pre-commit-ci made their first contribution in https://github.com/a-r-j/graphein/pull/233
• @davidfstein made their first contribution in https://github.com/a-r-j/graphein/pull/242
• @eltociear made their first contribution in https://github.com/a-r-j/graphein/pull/258

Full Changelog: https://github.com/a-r-j/graphein/compare/v1.5.2...v1.6.0

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.

1.5.1

Bugfixes

• [Patch] - #201 Adds missing MSE to graphein.protein.resi_atoms.RESI_NAMES, graphein.protein.resi_atoms.RESI_THREE_TO_1. #200
• [Patch] - #201 Fixes bug where check for same-chain always evaluates as False. #199
• [Patch] - #201 Fixes bug where deprotonation would only remove hydrogens based on atom_name rather than element_symbol. #198
• [Patch] - #201 Fixes bug in ProteinGraphDataset input validation.