v1.7.7

What's Changed

• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #367
• change mmseqs pdb data path by @kierandidi in #377
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #376
• Wire up deprotonate arg in construct_graph #374 by @a-r-j in #375
• remove typing_extension dependency by @kierandidi in #378
• Add PyG install to tutorial notebook #338 by @a-r-j in #380
• pin notebook version <7 #371 by @a-r-j in #372
• Add support for DSSP version and add rsa node features to residues with insertion codes by @biochunan in #355
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #383
• [fix] foldcomp datasets by @kierandidi in #382
• exposed fill_value to protein_to_pyg function by @kierandidi in #385
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #386
• [feat] expose bfactors in protein_to_pyg function by @kierandidi in #388
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #393
• [cleanup] change logging levels to debug to declutter output by @kierandidi in #391
• Fix cluster file loading bug in pdb_data.py by @amorehead in #396
• [fix] change progressbar for pdb download by @kierandidi in #394
• [feat] add uniprot ecnumber and cath label options to pdb manager by @kierandidi in #398
• Feat/logging cif support by @kierandidi in #402
• Add AYA to constants #387 by @a-r-j in #390
• Add cpdb support to speed up parsing by @a-r-j in #323
• add additional hetatm info to pyg parser by @a-r-j in #397
• V.1.7.7 by @a-r-j in #405
• fix: improve support for newer dssp versions #403 by @a-r-j in #404
• hotfix greater than/less than operations in pdb_manager by @a-r-j in #408

New Contributors

• @kierandidi made their first contribution in #377
• @biochunan made their first contribution in #355

Full Changelog: v1.7.6...v1.7.7

v1.7.6

What's Changed

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

New Contributors

• @Ruibin-Liu made their first contribution in #337
• @StevenAZy made their first contribution in #359

Full Changelog: v1.7.5...v1.7.6

v1.7.5

What's Changed

• 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

What's Changed

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

Full Changelog: v1.7.3...v1.7.4

v1.7.3

What's Changed

• 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

Adds support for newer biopandas releases

v1.7.1

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

• @AH-Merii made their first contribution in #327
• @chaitjo made their first contribution in #332

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

v1.7.0

What's Changed

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

Full Changelog: v1.6.0...v1.7.0

v1.6.0

What's Changed

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

New Contributors

• @manonreau made their first contribution in #220
• @anton-bushuiev made their first contribution in #229
• @pre-commit-ci made their first contribution in #233
• @davidfstein made their first contribution in #242
• @eltociear made their first contribution in #258

Full Changelog: v1.5.2...v1.6.0

1.5.2

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.