Graphein

- [Feature] - 141 adds edge construction based on sequence distance.
- [Feature] - 143 adds equality and isomorphism testing functions between graphs, nodes and edges ([142](https://github.com/a-r-j/graphein/issues/142))
- [Feature] - 144 adds support for chain-level and secondary structure-level graphs with associated visualisation tools and tutorial. Resolves [128](https://github.com/a-r-j/graphein/issues/128)
- [Feature] - 144 adds support for chord diagram visualisations.
- [Feature] - 144 adds support for automagically downloading new PDB files for obsolete structures.
- [Feature] - 150 adds support for hydrogen bond donor and acceptor counts node features. 145
- [Misc] - 144 makes visualisation functions accessible in the `graphein.protein` namespace. 138
- [Bugfix] - 147 fixes error in `add_distance_threshold` introduced in v1.2.1 that would prevent the edges being added to the graph. [146](https://github.com/a-r-j/graphein/issues/146)
- [Bugfix] - 149 fixes a bug in `add_beta_carbon_vector` that would cause coordinates to be extracted for multiple positions if the residue has an altloc. Resolves [148](https://github.com/a-r-j/graphein/issues/148)

- [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.

- [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.

- [Bugfix] - 107 improves robustness of removing insertions and hetatms, resolves 98
- [Packaging] - 108 fixes version mismatches in pytorch_geometric in docker install

- [Packaging] - 100 adds docker support.
- [Feature] - 96 Adds support for extracting subgraphs
- [Packaging] - 101 adds support for devcontainers for remote development.
- [Bugfixes] - 95 adds improved robustness for edge construction functions in certain edge cases. Insertions in the PDB were occasionally not picked up due to a brittle implementations. Resolves 74 and 98

- [Improvement] - 79 Replaces `Literal` references with `typing_extensions.Literal` for Python 3.7 support.