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Consistent conversion to undirected graphs #301

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merged 13 commits into from
Apr 16, 2023
Merged

Consistent conversion to undirected graphs #301

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167556e
Fix `convert_nx_to_pyg` to return undirected graph
anton-bushuiev Apr 10, 2023
bf9cf7c
Merge branch 'master' of https://github.com/anton-bushuiev/graphein
anton-bushuiev Apr 10, 2023
1e3b609
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 10, 2023
08bd1be
Fix symmetrization of edges of different kinds
anton-bushuiev Apr 10, 2023
e105a85
Merge
anton-bushuiev Apr 10, 2023
ddf8330
Clean
anton-bushuiev Apr 10, 2023
e156ade
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 10, 2023
93bbcdf
Fix case when `edge_index` is not desired
anton-bushuiev Apr 11, 2023
f4dc6e3
Test directed/undirected conversion consistency
anton-bushuiev Apr 11, 2023
27d082e
Merge branch 'master' of https://github.com/anton-bushuiev/graphein
anton-bushuiev Apr 11, 2023
55722c2
Update contributors
anton-bushuiev Apr 11, 2023
6d8c1f8
Merge branch 'a-r-j:master' into master
anton-bushuiev Apr 16, 2023
908c10e
Update CHANGELOG.md
anton-bushuiev Apr 16, 2023
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Update CHANGELOG.md
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@anton-bushuiev
anton-bushuiev authored Apr 16, 2023
commit 908c10ecc57e4ed1efde71ba164d70df0d4113cc
3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,9 @@
* [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)

#### Improvements
* [Bugfix] - [#301](https://github.com/a-r-j/graphein/pull/301) Fixes the conversion of undirected NetworkX graph to directed PyG data.

#### 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)
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