Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.5...v1.7.6
Published by a-r-j 12 months ago
graphein.protein.tensor.io.to_pdb
& prep for 1.7.5
release by @a-r-j in https://github.com/a-r-j/graphein/pull/352
Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.4...v1.7.5
Published by a-r-j almost 1 year ago
PDBManager
by @a-r-j in https://github.com/a-r-j/graphein/pull/346
add_sequence_neighbour_vector
by @anton-bushuiev in https://github.com/a-r-j/graphein/pull/336
1.7.4
release by @a-r-j in https://github.com/a-r-j/graphein/pull/351
Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.3...v1.7.4
Published by a-r-j about 1 year ago
Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.2...v1.7.3
Published by a-r-j about 1 year ago
Adds support for newer biopandas releases
Published by a-r-j about 1 year ago
PDBManager
- Bug fixes, adding necessary changes to export only first PDB model, and merging-in latest updates from master
by @a-r-j in https://github.com/a-r-j/graphein/pull/311
Protein
initialisation #317 by @a-r-j in https://github.com/a-r-j/graphein/pull/318
PDBManager
by @amorehead in https://github.com/a-r-j/graphein/pull/322
.requirements
reference for extras in setup.py by @AH-Merii in https://github.com/a-r-j/graphein/pull/330
Full Changelog: https://github.com/a-r-j/graphein/compare/v1.7.0...v1.7.1
Published by a-r-j over 1 year ago
PDBManager
Class (WIP) by @amorehead in https://github.com/a-r-j/graphein/pull/272
Full Changelog: https://github.com/a-r-j/graphein/compare/v1.6.0...v1.7.0
Published by a-r-j over 1 year ago
add_k_nn_edges
and add minor extension by @anton-bushuiev in https://github.com/a-r-j/graphein/pull/229
{'insertions': True}
by @manonreau in https://github.com/a-r-j/graphein/pull/223
initialise_graph_with_metadata
had duplicated residues) by @kamurani in https://github.com/a-r-j/graphein/pull/268
convert_nx_to_pyg
#280 by @rg314 in https://github.com/a-r-j/graphein/pull/281
Full Changelog: https://github.com/a-r-j/graphein/compare/v1.5.2...v1.6.0
Published by a-r-j about 2 years ago
KeyError
when using graphein.protein.edges.distance.node_coords
MANIFEST.in
#205ProteinGraphDataset
and InMemoryProteinGraphDataset
.by adding a params:
pdb_paths
and set theself.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 fromself.raw
.
If you wish to download from af2 or pdb, just setpdb_paths
toNone
and it goes back to the former version.
jupyter_contrib_nbextensions
in Docker.Published by a-r-j about 2 years ago
MSE
to graphein.protein.resi_atoms.RESI_NAMES
, graphein.protein.resi_atoms.RESI_THREE_TO_1
. #200
atom_name
rather than element_symbol
. #198
Published by a-r-j over 2 years ago
residue_id
column to PDB dfs to enable easier accounting in atom graphs.graphein.protein.visualisation.asteroid_plot
. Contribution by @avivko.graphein.protein.features.nodes.dssp
. Contribution by @avivko.ml.ProteinGraphDataset
.graphein.molecule.graphs.construct_graph
. Interface is simplified to simply path="some/path.extension"
instead of separate inputs like mol2_path=...
and sdf_path=...
.Published by a-r-j over 2 years ago
graphein.protein.visualisation.asteroid_plot
. Contribution by @avivko.graphein.protein.features.nodes.dssp
. Contribution by @avivko.graphein.molecule.graphs.construct_graph
. Interface is simplified to simply path="some/path.extension"
instead of separate inputs like mol2_path=...
and sdf_path=...
.Published by a-r-j over 2 years ago
Full Changelog: https://github.com/a-r-j/graphein/compare/v.1.3.0...v1.4.0
Published by a-r-j over 2 years ago
Full Changelog: https://github.com/a-r-j/graphein/compare/v1.2.1...v.1.3.0
Published by a-r-j over 2 years ago
[WIP][Protein] add vector node features. by @a-r-j in https://github.com/a-r-j/graphein/pull/124
[WIP] add PDB and PyMol utilities [utils] by @a-r-j in https://github.com/a-r-j/graphein/pull/121
fix edges functions adding nodes to graphs with chain selections #134 by @a-r-j in https://github.com/a-r-j/graphein/pull/136
[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.
graphein.protein.graphs.compute_rgroup_dataframe
and moves it to graphein.protein.utils
. All internal references have been moved accordingly.Full Changelog: https://github.com/a-r-j/graphein/compare/v1.2.0...v1.2.1
Published by a-r-j over 2 years ago
[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.
#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.
Published by a-r-j over 2 years ago
Published by a-r-j over 2 years ago
Adds subgraphing support, bugfixes as per changelog.