Add support for 3D RNA Graphs (#165)

[a-r-j]

• add RNA atomic edge funcs

• add RNA 3D constants

• add bpRNA parser

• add Ryan's Nussinov algo implementation

• add radius of gyration feature

• add positional encoding of sequence

• update docstrings and add interface subgraphs

• docstring

• rm unused import

• add rich as a base requirement

• update version string

• black

• add additional RNA tests

• update rna docs

• finalise RNA tutorial with 3D structures

• merge

• add edge funcs

• add RNA graphs

• add rna subgraphs

• add rna features

• update rna constants

• resolve circular import

• move edge funcs to submodule

• make subgraphs editable downstream

• set node size multiplier to a saner default

• add smiles test file

• use rich-click for cli, minor linting

• add distance edges

• add RNA visualisation

• add nussinov test

• use rich-click instead of click

• add rna test structure

• skip nussinov cell to avoid timeout

• simplify af2 structure retrieval #168

• add plddt colouring for AF2

• linting

• bugfixes for AF2

• add edge distance func

• add graph feats to docs

• add fully connected and distance window edges

• remove erroneous import

• add molecule features

• add conformer generation and fragment graphs

• update top level init with version and loguru logging

• update changelog

• black, isort

• add loguru as dependency

• fix edge construction funcs

• fix rdkit util tests

• fix tests

• fix tests

• try converting everything to tensor

• fix edge distance func

• fix conversion

• add zinc & chembl utils

• add molecule modelling tutorial.ipynb

• add smilite dependency

• fix notebook test

• remove tests for molecule tutorial

• update requirements

• isort

• add sequence homology splitting

• update docs

• rollback nx version

• fix blast

• fix blast

• add antibody tutorial

• update notebook for docs

• fix dataset readme tables

• add notebooks

• update notebooks and docs

• remove antibody_dev example

• add line graph

• update rna tests

• update CLI

• update ML utils

• add dynamics features

• add degree oh

• fix naming

• add naming changes to RNA

• update molecule utils

• update chain graph tutorial

• update intersphinx mappings

• isort

• black

• fix test

• skip inconsistent mol test

• skip zinc tests

• add skip to ppi graph test if HGNC unavailable

• remove debug cell

• pin nx version

• remove nx version pin

• pin mpl chord dependency

• proper HETATM handling

• add pyg visualisation

• resolve dataframe handling

• update to tutorial for df handling

• restore plddt vis

• pin scipy version for plots

• unpin scipy dependency

• skip API calls in tutorials

• update changelog

• update version to 1.5.0rc1

Reference Issues/PRs

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