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fix peptide bonds for all atom graphs #254

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merged 3 commits into from
Jan 26, 2023
Merged

fix peptide bonds for all atom graphs #254

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856b44d
fix peptide bonds for all atom graphs
a-r-j Jan 26, 2023
0b3aa00
update changelog
a-r-j Jan 26, 2023
5fc75c2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 26, 2023
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
### 1.5.3 - UNRELEASED


#### Improvements
* [Logging] - [#221](https://github.com/a-r-j/graphein/pull/221) Adds global control of logging with `graphein.verbose(enabled=False)`.
* [Logging] - [#242](https://github.com/a-r-j/graphein/pull/242) Adds control of protein graph construction logging. Resolves [#238](https://github.com/a-r-j/graphein/issues/238)

#### Protein

* [Bugfix] - [#254](https://github.com/a-r-j/graphein/pull/254) Fix peptide bond addition for all atom graphs.
* [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.
* [Bugfix] - [#226](https://github.com/a-r-j/graphein/pull/226) Catches failed AF2 structure downloads [#225](https://github.com/a-r-j/graphein/issues/225)
* [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.
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9 changes: 9 additions & 0 deletions graphein/protein/edges/distance.py
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Expand Up @@ -190,6 +190,15 @@ def add_sequence_distance_edges(
(n, v) for n, v in G.nodes(data=True) if v["chain_id"] == chain_id
]

# Subset to only N and C atoms in the case of full-atom
# peptide bond addition
if G.graph["config"].granularity == "atom" and name == "peptide_bond":
chain_residues = [
(n, v)
for n, v in chain_residues
if v["atom_type"] in {"N", "C"}
]

# Iterate over every residue in chain
for i, residue in enumerate(chain_residues):
try:
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