Graphein

New Features

- [PDBManager] - [272](https://github.com/a-r-j/graphein/pull/272) Adds a utility for creating custom dataset splits from the PDB.
- [FoldComp Dataset] - [284](https://github.com/a-r-j/graphein/pull/284) - Create ML datasets from FoldComp databases.
- [ESM] - [284](https://github.com/a-r-j/graphein/pull/284) - Wrapper for ESMFold batch folding & embedding.
- [Downloads] MMTF downloading now supported in download utilities. [272](https://github.com/a-r-j/graphein/pull/272)

API Changes

- The `pdb_path` argument to many functions (e.g. `graphein.protein.graphs.construct_graph`) has been renamed to `path` as this can now accept MMTF files in addition to PDB files.
- `Protein` tensors have coordinates renamed from `Protein.x` to `Protein.coords`. [272](https://github.com/a-r-j/graphein/pull/272)

Other changes

- Tensor types are now defined using [`jaxtyping`](https://github.com/google/jaxtyping), removing the `torchtyping` dependency [#272](https://github.com/a-r-j/graphein/pull/272)
- Drops explicit Python 3.7 support. Colab now runs on 3.8+. [272](https://github.com/a-r-j/graphein/pull/272)
- Dockerfile now builds from `pytorch/pytorch:1.13.0-cuda11.6-cudnn8-runtime` (replaces `pytorch/pytorch:1.9.1-cuda11.1-cudnn8-runtime`) [272](https://github.com/a-r-j/graphein/pull/272)
- Missing `os` import fixed in [297(https://github.com/a-r-j/graphein/pull/297). Fixes [#296](https://github.com/a-r-j/graphein/issues/296)

New Features

- [Metrics] - [245](https://github.com/a-r-j/graphein/pull/221) Adds a selection of structural metrics relevant to protein structures.
- [Tensor Operations] - [244](https://github.com/a-r-j/graphein/pull/244) Adds suite of utilities for working directly with tensor-based representations of proteins (graphein.protein.tensor).
- [Tensor Operations] - [244](https://github.com/a-r-j/graphein/pull/244) Adds suite of utilities for working with ESMfold (graphein.protein.folding_utils).

Improvements

- [Feature] = [277](https://github.com/a-r-j/graphein/pull/227) Adds support for pathlib paths for protein graph creation. [#269](https://github.com/a-r-j/graphein/issues/269)
- [Logging] - [221](https://github.com/a-r-j/graphein/pull/221) Adds global control of logging with `graphein.verbose(enabled=False)`.
- [Logging] - [242](https://github.com/a-r-j/graphein/pull/242) Adds control of protein graph construction logging. Resolves [#238](https://github.com/a-r-j/graphein/issues/238)

Protein

- [Bugfix] - [222]<https://github.com/a-r-j/graphein/pull/222)> Fixes entrypoint for user-defined `df_processing_funcs` ([#216](https://github.com/a-r-j/graphein/issues/216))
- [Feature] = [263](https://github.com/a-r-j/graphein/pull/263) Adds control of Alt Loc selection strategy. N.b. Default `ProteinGraphConfig` changed to include insertions by default (`insertions=True`) and `alt_locs="max_occupancy"`.
- [Feature] - [264](https://github.com/a-r-j/graphein/pull/264) Adds entrypoint to `graphein.protein.graphs.construct_graph` for passing in a BioPandas dataframe directly.
- [Feature] - [229](https://github.com/a-r-j/graphein/pull/220) Adds support for filtering KNN edges based on self-loops and chain membership. Contribution by anton-bushuiev.
- [Feature] - [234](https://github.com/a-r-j/graphein/pull/234) Adds support for aggregating node features over residues (`graphein.protein.features.sequence.utils.aggregate_feature_over_residues`).
- [Bugfix] - [234](https://github.com/a-r-j/graphein/pull/234) fixes use of nullcontext in silent graph construction.
- [Bugfix] - [234](https://github.com/a-r-j/graphein/pull/234) Fixes division by zero errors for edge colouring in visualisation.
- [Bugfix] - [254](https://github.com/a-r-j/graphein/pull/254) Fix peptide bond addition for all atom graphs.
- [Bugfix] - [223](https://github.com/a-r-j/graphein/pull/220) Fix handling of insertions in protein graphs. Insertions are now given IDs like: `A:SER:12:A`. Contribution by manonreau.
- [Bugfix] - [226](https://github.com/a-r-j/graphein/pull/226) Catches failed AF2 structure downloads [#225](https://github.com/a-r-j/graphein/issues/225)

- [Bugfix] - [229](https://github.com/a-r-j/graphein/pull/220) Fixes bug in KNN edge computation. Contribution by anton-bushuiev.
- [Bugfix] - [220](https://github.com/a-r-j/graphein/pull/220) Fixes edge metadata conversion to PyG. Contribution by manonreau.
- [Bugfix] - [220](https://github.com/a-r-j/graphein/pull/220) Fixes centroid atom grouping & avoids unnecessary edge computation where none are found. Contribution by manonreau.

- [Bugfix] - [268](https://github.com/a-r-j/graphein/pull/268) Fixes 'sequence' metadata feature for atomistic graphs, removing duplicate residues. Contribution by kamurani.

ML

- [Bugfix] - [234](https://github.com/a-r-j/graphein/pull/234) - Fixes bugs and improves `conversion.convert_nx_to_pyg` and `visualisation.plot_pyg_data`. Removes distance matrix (`dist_mat`) from defualt set of features converted to tensor.

Utils

- [Improvement] - [234](https://github.com/a-r-j/graphein/pull/234) - Adds `parse_aggregation_type` to retrieve aggregation functions.

RNA

- [Bugfix] - [281](https://github.com/a-r-j/graphein/pull/234) - Bugfix for nx->PyG conversion for graphs containing edges without "kind" attributes. Contribution by rg314.

Constants

- [Improvement] - [234](https://github.com/a-r-j/graphein/pull/234) - Adds 1 to 3 mappings to `graphein.protein.resi_atoms`.

Documentation

- [Tensor Module] - [244](https://github.com/a-r-j/graphein/pull/244) Documents new graphein.protein.tensor module.
- [CI] - [244](https://github.com/a-r-j/graphein/pull/244) Updates to intersphinx maps

Package

- [CI] - [244](https://github.com/a-r-j/graphein/pull/244) CI now runs for python 3.8, 3.9 and torch 1.12.0 and 1.13.0
- [CI] - [244](https://github.com/a-r-j/graphein/pull/244) Separate builds for core library and library with DL dependencies.
- [Licence] - [244](https://github.com/a-r-j/graphein/pull/244) Bump to 2023

Protein

- [Bugfix] - [206](https://github.com/a-r-j/graphein/pull/206) Fixes `KeyError` when using `graphein.protein.edges.distance.node_coords`
- [Bugfix] - Includes missing data files in `MANIFEST.in` 205

GRN

- [Bugfix] - [208](https://github.com/a-r-j/graphein/pull/208) - Resolves SSL issues with RegNetwork.

ML

- [Feature] - [208](https://github.com/a-r-j/graphein/pull/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](https://github.com/a-r-j/graphein/pull/208) explicitly installs `jupyter_contrib_nbextensions` in Docker.

Protein

- [Feature] - [186](https://github.com/a-r-j/graphein/pull/186) adds support for scaling node sizes in plots by a computed feature. Contribution by cimranm
- [Feature] - [189](https://github.com/a-r-j/graphein/pull/189/) adds support for parallelised download from the PDB.
- [Feature] - [189](https://github.com/a-r-j/graphein/pull/189/) adds support for: van der waals interactions, vdw clashes, pi-stacking interactions, t_stacking interactions, backbone carbonyl-carbonyl interactions, salt bridges
- [Feature] - [189](https://github.com/a-r-j/graphein/pull/189/) adds a `residue_id` column to PDB dfs to enable easier accounting in atom graphs.
- [Feature] - [189](https://github.com/a-r-j/graphein/pull/189/) refactors torch geometric datasets to use parallelised download for faster dataset preparation.

Bugfixes

- [Patch] - [187](https://github.com/a-r-j/graphein/pull/187) updates sequence retrieval due to UniProt API changes.
- [Patch] - [189](https://github.com/a-r-j/graphein/pull/189) fixes bug where chains and PDB identifiers were not properly aligned in `ml.ProteinGraphDataset`.
- [Patch] - [201](https://github.com/a-r-j/graphein/pull/201) Adds missing `MSE` to `graphein.protein.resi_atoms.RESI_NAMES`, `graphein.protein.resi_atoms.RESI_THREE_TO_1`. [#200](https://github.com/a-r-j/graphein/issues/200)
- [Patch] - [201](https://github.com/a-r-j/graphein/pull/201) Fixes bug where check for same-chain always evaluates as False. [#199](https://github.com/a-r-j/graphein/issues/199)
- [Patch] - [201](https://github.com/a-r-j/graphein/pull/201) Fixes bug where deprotonation would only remove hydrogens based on `atom_name` rather than `element_symbol`. [#198](https://github.com/a-r-j/graphein/issues/198)
- [Patch] - [201](https://github.com/a-r-j/graphein/pull/201) Fixes bug in ProteinGraphDataset input validation.

Breaking Changes

- [189](https://github.com/a-r-j/graphein/pull/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.

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](https://github.com/a-r-j/graphein/pull/170) Adds support for viewing edges in `graphein.protein.visualisation.asteroid_plot`. Contribution by avivko.
- [Patch] - [178](https://github.com/a-r-j/graphein/pull/178) Fixes [#171](https://github.com/a-r-j/graphein/pull/171) and optimizes `graphein.protein.features.nodes.dssp`. Contribution by avivko.
- [Patch] - [174](https://github.com/a-r-j/graphein/pull/174) prevents insertions always being removed. Resolves [#173](https://github.com/a-r-j/graphein/issues/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=...`.

- [Patch] - 158 changes the eigenvector computation method from `nx.eigenvector_centrality` to `nx.eigenvector_centrality_numpy`.
- [Feature] - 154 adds a way of checking that DSSP is executable before trying to use it. 154
- [Feature] - 157 adds support for small molecule graphs using RDKit. Resolves 155.
- [Feature] - 159 adds support for conversion to Jraph graphs for JAX users.

Breaking Changes

- 157 refactors config matching operators from `graphein.protein.config` to `graphein.utils.config`
- 157 refactors config parsing operators from `graphein.utils.config` to `graphein.utils.config_parser`