graphein

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.

Protein

• [Feature] - #186 adds support for scaling node sizes in plots by a computed feature. Contribution by @cimranm
• [Feature] - #189 adds support for parallelised download from the PDB.
• [Feature] - #189 adds support for: van der waals interactions, vdw clashes, pi-stacking interactions, t_stacking interactions, backbone carbonyl-carbonyl interactions, salt bridges
• [Feature] - #189 adds a residue_id column to PDB dfs to enable easier accounting in atom graphs.
• [Feature] - #189 refactors torch geometric datasets to use parallelised download for faster dataset preparation.
• [Feature] - #165 adds support for direct AF2 graph construction.
• [Feature] - #165 adds support for selecting model indices from PDB files.
• [Feature] - #165 adds support for extracting interface subgraphs from complexes.
• [Feature] - #165 adds support for computing the radius of gyration of a structure.
• [Feature] - #165 adds support for adding distances to protein edges.
• [Feature] - #165 adds support for fully connected edges in protein graphs.
• [Feature] - #165 adds support for distance window-based edges for protein graphs.
• [Feature] - #165 adds support for transformer-like positional encoding of protein sequences.
• [Feature] - #165 adds support for plddt-like colouring of AF2 graphs
• [Feature] - #165 adds support for plotting PyG Data object (e.g. for logging to WandB).
• [Feature] - #170 Adds support for viewing edges in graphein.protein.visualisation.asteroid_plot. Contribution by @avivko.
• [Patch] - #178 Fixes #171 and optimizes graphein.protein.features.nodes.dssp. Contribution by @avivko.
• [Patch] - #174 prevents insertions always being removed. Resolves #173. Contribution by @OliverT1.
• [Patch] - #165 Refactors HETATM selections.

Molecules

• [Feature] - #165 adds additional graph-level molecule features.
• [Feature] - #165 adds support for generating conformers (and 3D graphs) from SMILES inputs
• [Feature] - #163 Adds support for molecule graph generation from an RDKit.Chem.Mol input.
• [Feature] - #163 Adds support for multiprocess molecule graph construction.

RNA

• [Feature] - #165 adds support for 3D RNA graph construction.
• [Feature] - #165 adds support for generating RNA SS from sequence using the Nussinov Algorithm.

Changes

• [Patch] - #187 updates sequence retrieval due to UniProt API changes.
• [Patch] - #189 fixes bug where chains and PDB identifiers were not properly aligned in ml.ProteinGraphDataset.
• [Patch] - #163 uses tqdm.contrib.process_map insteap of multiprocessing.Pool.map to provide progress bars in multiprocessing.
• [Fix] - #165 makes returned subgraphs editable objects rather than views
• [Fix] - #165 fixes global logging set to "debug".
• [Fix] - #165 uses rich progress for protein graph construction.
• [Fix] - #165 sets saner default for node size in 3d plotly plots
• [Dependency] - #165 Changes CLI to use rich-click instead of click for prettier formatting.
• [Package] - #165 Adds support for logging with loguru and rich
• [Package] - Pin BioPandas version to 0.4.1 to support additional parsing features.

Breaking Changes

• #165 adds RNA SS edges into graphein.protein.edges.base_pairing
• #163 changes separate filetype input paths to graphein.molecule.graphs.construct_graph. Interface is simplified to simply path="some/path.extension" instead of separate inputs like mol2_path=... and sdf_path=....
• #189 refactors PDB download util. Now returns path to download file, does not accept a config object but instead receives the output directory path directly.

1.5.0rc1

Protein

• [Feature] - #165 adds support for direct AF2 graph construction.
• [Feature] - #165 adds support for selecting model indices from PDB files.
• [Feature] - #165 adds support for extracting interface subgraphs from complexes.
• [Feature] - #165 adds support for computing the radius of gyration of a structure.
• [Feature] - #165 adds support for adding distances to protein edges.
• [Feature] - #165 adds support for fully connected edges in protein graphs.
• [Feature] - #165 adds support for distance window-based edges for protein graphs.
• [Feature] - #165 adds support for transformer-like positional encoding of protein sequences.
• [Feature] - #165 adds support for plddt-like colouring of AF2 graphs
• [Feature] - #165 adds support for plotting PyG Data object (e.g. for logging to WandB).
• [Feature] - #170 Adds support for viewing edges in graphein.protein.visualisation.asteroid_plot. Contribution by @avivko.
• [Patch] - #178 Fixes #171 and optimizes graphein.protein.features.nodes.dssp. Contribution by @avivko.
• [Patch] - #174 prevents insertions always being removed. Resolves #173. Contribution by @OliverT1.
• [Patch] - #165 Refactors HETATM selections.

Molecules

• [Feature] - #165 adds additional graph-level molecule features.
• [Feature] - #165 adds support for generating conformers (and 3D graphs) from SMILES inputs
• [Feature] - #163 Adds support for molecule graph generation from an RDKit.Chem.Mol input.
• [Feature] - #163 Adds support for multiprocess molecule graph construction.

RNA

• [Feature] - #165 adds support for 3D RNA graph construction.
• [Feature] - #165 adds support for generating RNA SS from sequence using the Nussinov Algorithm.

Changes

• [Patch] - #163 uses tqdm.contrib.process_map insteap of multiprocessing.Pool.map to provide progress bars in multiprocessing.
• [Fix] - #165 makes returned subgraphs editable objects rather than views
• [Fix] - #165 fixes global logging set to "debug".
• [Fix] - #165 uses rich progress for protein graph construction.
• [Fix] - #165 sets saner default for node size in 3d plotly plots
• [Dependency] - #165 Changes CLI to use rich-click instead of click for prettier formatting.
• [Package] - #165 Adds support for logging with loguru and rich
• [Package] - Pin BioPandas version to 0.4.1 to support additional parsing features.

Breaking Changes

• #165 adds RNA SS edges into graphein.protein.edges.base_pairing
• #163 changes separate filetype input paths to graphein.molecule.graphs.construct_graph. Interface is simplified to simply path="some/path.extension" instead of separate inputs like mol2_path=... and sdf_path=....

What's Changed

• Patch 1 by @amorehead in https://github.com/a-r-j/graphein/pull/154
• update eigenvector computation method #156 by @a-r-j in https://github.com/a-r-j/graphein/pull/158
• Add support for molecular graphs by @yuanqidu in https://github.com/a-r-j/graphein/pull/157
• 1.4.0 by @a-r-j in https://github.com/a-r-j/graphein/pull/159
• 1.4.0 by @a-r-j in https://github.com/a-r-j/graphein/pull/160

New Contributors

• @amorehead made their first contribution in https://github.com/a-r-j/graphein/pull/154
• @yuanqidu made their first contribution in https://github.com/a-r-j/graphein/pull/157

Full Changelog: https://github.com/a-r-j/graphein/compare/v.1.3.0...v1.4.0

What's Changed

• add sequence distance edges #115 by @a-r-j in https://github.com/a-r-j/graphein/pull/141
• add graph equality funtions #142 by @a-r-j in https://github.com/a-r-j/graphein/pull/143
• Coarsening #128 by @a-r-j in https://github.com/a-r-j/graphein/pull/144
• bugfix to distance edge func #146 by @a-r-j in https://github.com/a-r-j/graphein/pull/147
• Vector bugfix #148 by @a-r-j in https://github.com/a-r-j/graphein/pull/149
• Hydrogen bond acceptor/donor features by @a-r-j in https://github.com/a-r-j/graphein/pull/150
• [WIP] Add dataloader classes by @a-r-j in https://github.com/a-r-j/graphein/pull/71
• Update doc dependency by @a-r-j in https://github.com/a-r-j/graphein/pull/151
• Update to v1.3.0 by @a-r-j in https://github.com/a-r-j/graphein/pull/152

Full Changelog: https://github.com/a-r-j/graphein/compare/v1.2.1...v.1.3.0

What's Changed

• [WIP][Protein] add vector node features. by @a-r-j in https://github.com/a-r-j/graphein/pull/124

• [WIP] add PDB and PyMol utilities [utils] by @a-r-j in https://github.com/a-r-j/graphein/pull/121

• fix edges functions adding nodes to graphs with chain selections #134 by @a-r-j in https://github.com/a-r-j/graphein/pull/136

• [Feature] - #124 adds support for vector features associated protein protein geometry. #120 #122

• [Feature] - #124 adds visualisation of vector features in 3D graph plots.

• [Feature] - #121 adds functions for saving graph data to PDB files.

• [Bugfix] - #136 changes generator comprehension when updating coordinates in subgraphs to list comprehension to allow pickling

• [Bugfix] - #136 fixes bug in edge construction functions using chain selections where nodes from unselected chains would be added to the graph.

Breaking Changes

• #124 refactors graphein.protein.graphs.compute_rgroup_dataframe and moves it to graphein.protein.utils. All internal references have been moved accordingly.

Full Changelog: https://github.com/a-r-j/graphein/compare/v1.2.0...v1.2.1

[Feature] - #104 adds support for asteroid plots and distance matrix visualisation.
[Feature] - #104 adds support for protein graph analytics (graphein.protein.analysis)
[Feature] - #110 adds support for secondary structure & surface-based subgraphs
[Feature] - #113 adds CLI support(!)
[Feature] - #116 adds support for onehot-encoded amino acid features as node attributes.
[Feature] - #119 Adds plotly-based visualisation for PPI Graphs
[Bugfix] - #110 fixes minor bug in asa where it would fail if added as a first/only dssp feature.
[Bugfix] - #110 Adds install for DSSP in Dockerfile
[Bugfix] - #110 Adds conda install & DSSP to tests
[Bugfix] - #119 Delaunay Triangulation computed over all atoms by default. Adds an option to restrict it to certain atom types.
[Bugfix] - #119 Minor fixes to stability of RNA Graph Plotting
[Bugfix] - #119 add tolerance parameter to add_atomic_edges
[Documentation] - #104 Adds notebooks for visualisation, RNA SS Graphs, protein graph analytics
[Documentation] - #119 Overhaul of docs & tutorial notebooks. Adds interactive plots to docs, improves docstrings, doc formatting, doc requirements.

Breaking Changes

#119 - Refactor RNA Graph constants from graphein.rna.graphs to graphein.rna.constants. Only problematic if constants were accessed directly. All internal references have been moved accordingly.

• Fixes to dockerfile
• Bugfixes on handling of insertions/altlocs in protein dataframes

Adds subgraphing support, bugfixes as per changelog.