fix peptide bonds for all atom graphs (#254)

* fix peptide bonds for all atom graphs

* update changelog

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

CHANGELOG.md

@@ -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.

graphein/protein/edges/distance.py

@@ -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: