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Modify graphs.py to handle insertions when {'insertions': True} #223

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merged 12 commits into from
Dec 8, 2022
Merged

Modify graphs.py to handle insertions when {'insertions': True} #223

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8845e85
update conversion
Oct 18, 2022
f9bfc95
fix coord issues
Oct 18, 2022
b4e150a
update graphs.py to handle insertions
Oct 24, 2022
ade2cb2
Merge branch 'master' into insertion
a-r-j Oct 31, 2022
a75b207
fix affedcted test
a-r-j Nov 2, 2022
d807dd8
accomodate insertion in hbond donor and acceptor
a-r-j Nov 2, 2022
2aeeaa4
update changelog
a-r-j Nov 2, 2022
707e6e5
Merge branch 'master' into insertion
a-r-j Nov 9, 2022
98dbe17
Merge branch 'master' into insertion
a-r-j Dec 7, 2022
cec18d6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 7, 2022
a45316e
Add control flow for insertion labelling
a-r-j Dec 7, 2022
2693ecd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 7, 2022
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Merge branch 'master' into insertion
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@a-r-j
a-r-j authored Nov 9, 2022
commit 707e6e575f27487b25502e5e0dd832bcf5dc5fbc
2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -6,6 +6,8 @@
#### Protein

* [Bugfix] - [#223](https://github.com/a-r-j/graphein/pull/220) Fix handling of insertions in protein graphs. Insertions are now given IDs like: `A:SER:12:A`. Contribution by @manonreau.
* [Feature] - [#229](https://github.com/a-r-j/graphein/pull/220) Adds support for filtering KNN edges based on self-loops and chain membership. Contribution by @anton-bushuiev.
* [Bugfix] - [#229](https://github.com/a-r-j/graphein/pull/220) Fixes bug in KNN edge computation. Contribution by @anton-bushuiev.
* [Bugfix] - [#220](https://github.com/a-r-j/graphein/pull/220) Fixes edge metadata conversion to PyG. Contribution by @manonreau.
* [Bugfix] - [#220](https://github.com/a-r-j/graphein/pull/220) Fixes centroid atom grouping & avoids unnecessary edge computation where none are found. Contribution by @manonreau.

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7 changes: 2 additions & 5 deletions graphein/protein/edges/distance.py
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Expand Up @@ -496,11 +496,8 @@ def add_aromatic_sulphur_interactions(
condition2 = resi1 in PI_RESIS and resi2 in SULPHUR_RESIS

if (condition1 or condition2) and resi1 != resi2:
if G.has_edge(resi1, resi2):
G.edges[resi1, resi2]["kind"].add("aromatic_sulphur")
else:
G.add_edge(resi1, resi2, kind={"aromatic_sulphur"})

add_edge(G, resi1, resi2, "aromatic_sulphur")


def add_cation_pi_interactions(
G: nx.Graph, rgroup_df: Optional[pd.DataFrame] = None
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