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Recent Releases of graphein

graphein - v1.7.7

What's Changed

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

New Contributors

  • @kierandidi made their first contribution in https://github.com/a-r-j/graphein/pull/377
  • @biochunan made their first contribution in https://github.com/a-r-j/graphein/pull/355

Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.6...v1.7.7

- Jupyter Notebook
Published by a-r-j over 1 year ago

graphein - v1.7.6

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

- Jupyter Notebook
Published by a-r-j about 2 years ago

graphein - v1.7.5

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

- Jupyter Notebook
Published by a-r-j over 2 years ago

graphein - v.1.7.4

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

- Jupyter Notebook
Published by a-r-j over 2 years ago

graphein - v1.7.3

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

- Jupyter Notebook
Published by a-r-j over 2 years ago

graphein - v1.7.2

Adds support for newer biopandas releases

- Jupyter Notebook
Published by a-r-j over 2 years ago

graphein - v1.7.1

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

- Jupyter Notebook
Published by a-r-j over 2 years ago

graphein - v1.7.0

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

- Jupyter Notebook
Published by a-r-j almost 3 years ago

graphein - v1.6.0

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

- Jupyter Notebook
Published by a-r-j almost 3 years ago

graphein - 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.

- Jupyter Notebook
Published by a-r-j over 3 years ago

graphein - 1.5.1

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.

- Jupyter Notebook
Published by a-r-j over 3 years ago

graphein - v1.5.0

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.

- Jupyter Notebook
Published by a-r-j over 3 years ago

graphein - v1.5.0rc1

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=....

- Jupyter Notebook
Published by a-r-j over 3 years ago

graphein - v1.4.0

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

- Jupyter Notebook
Published by a-r-j almost 4 years ago

graphein - v1.3.0

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

- Jupyter Notebook
Published by a-r-j almost 4 years ago

graphein - v1.2.1

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

- Jupyter Notebook
Published by a-r-j almost 4 years ago

graphein - v1.2.0

[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 addatomicedges [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.

- Jupyter Notebook
Published by a-r-j almost 4 years ago

graphein - v1.1.1

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

- Jupyter Notebook
Published by a-r-j about 4 years ago

graphein - v1.1.0

Adds subgraphing support, bugfixes as per changelog.

- Jupyter Notebook
Published by a-r-j about 4 years ago