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.