v1.5.0rc1 #182

a-r-j · 2022-06-30T13:01:18Z

a-r-j
Jun 30, 2022
Maintainer

[Feature] - Add support for 3D RNA Graphs #165 adds support for direct AF2 graph construction.
[Feature] - Add support for 3D RNA Graphs #165 adds support for selecting model indices from PDB files.
[Feature] - Add support for 3D RNA Graphs #165 adds support for extracting interface subgraphs from complexes.
[Feature] - Add support for 3D RNA Graphs #165 adds support for computing the radius of gyration of a structure.
[Feature] - Add support for 3D RNA Graphs #165 adds support for adding distances to protein edges.
[Feature] - Add support for 3D RNA Graphs #165 adds support for fully connected edges in protein graphs.
[Feature] - Add support for 3D RNA Graphs #165 adds support for distance window-based edges for protein graphs.
[Feature] - Add support for 3D RNA Graphs #165 adds support for transformer-like positional encoding of protein sequences.
[Feature] - Add support for 3D RNA Graphs #165 adds support for plddt-like colouring of AF2 graphs
[Feature] - Add support for 3D RNA Graphs #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] - Add support for 3D RNA Graphs #165 Refactors HETATM selections.

[Feature] - Add support for 3D RNA Graphs #165 adds additional graph-level molecule features.
[Feature] - Add support for 3D RNA Graphs #165 adds support for generating conformers (and 3D graphs) from SMILES inputs
[Feature] - Update multiprocessing, CLI and molecular graph utils #163 Adds support for molecule graph generation from an RDKit.Chem.Mol input.
[Feature] - Update multiprocessing, CLI and molecular graph utils #163 Adds support for multiprocess molecule graph construction.

[Feature] - Add support for 3D RNA Graphs #165 adds support for 3D RNA graph construction.
[Feature] - Add support for 3D RNA Graphs #165 adds support for generating RNA SS from sequence using the Nussinov Algorithm.

[Patch] - Update multiprocessing, CLI and molecular graph utils #163 uses tqdm.contrib.process_map insteap of multiprocessing.Pool.map to provide progress bars in multiprocessing.
[Fix] - Add support for 3D RNA Graphs #165 makes returned subgraphs editable objects rather than views
[Fix] - Add support for 3D RNA Graphs #165 fixes global logging set to "debug".
[Fix] - Add support for 3D RNA Graphs #165 uses rich progress for protein graph construction.
[Fix] - Add support for 3D RNA Graphs #165 sets saner default for node size in 3d plotly plots
[Dependency] - Add support for 3D RNA Graphs #165 Changes CLI to use rich-click instead of click for prettier formatting.
[Package] - Add support for 3D RNA Graphs #165 Adds support for logging with loguru and rich
[Package] - Pin BioPandas version to 0.4.1 to support additional parsing features.

Add support for 3D RNA Graphs #165 adds RNA SS edges into graphein.protein.edges.base_pairing
Update multiprocessing, CLI and molecular graph utils #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=....

This discussion was created from the release v1.5.0rc1.