Graphein Versions Save

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.