From a28c4fe6bafdd3e016dab753e806011b2728d956 Mon Sep 17 00:00:00 2001
From: Josh Mitchell <yoshanuikabundi@gmail.com>
Date: Tue, 21 Jan 2025 19:03:08 +1100
Subject: [PATCH] Simplify _add_to_molecules signature

---
 openff/pablo/_pdb.py            | 4 +---
 openff/pablo/_tests/test_pdb.py | 1 -
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/openff/pablo/_pdb.py b/openff/pablo/_pdb.py
index b5f23ed..c3a53fd 100644
--- a/openff/pablo/_pdb.py
+++ b/openff/pablo/_pdb.py
@@ -291,7 +291,6 @@ def topology_from_pdb(
             this_molecule = _add_to_molecule(
                 molecules,
                 this_molecule,
-                res_atom_idcs,
                 chemical_data,
                 data,
                 use_canonical_names,
@@ -382,7 +381,6 @@ def _set_box_vectors(topology: Topology, data: PdbData):
 def _add_to_molecule(
     molecules: MutableSequence[Molecule],
     this_molecule: Molecule,
-    res_atom_idcs: tuple[int, ...],
     residue_match: ResidueMatch,
     data: PdbData,
     use_canonical_names: bool,
@@ -406,7 +404,7 @@ def _add_to_molecule(
         "pdb_idx_to_mol_atom_idx",
         {},
     )
-    for pdb_index in res_atom_idcs:
+    for pdb_index in sorted(residue_match.res_atom_idcs):
         atom_def = residue_match.atom(pdb_index)
 
         if data.alt_loc[pdb_index] != "":
diff --git a/openff/pablo/_tests/test_pdb.py b/openff/pablo/_tests/test_pdb.py
index 9c7eda7..acc5e3b 100644
--- a/openff/pablo/_tests/test_pdb.py
+++ b/openff/pablo/_tests/test_pdb.py
@@ -115,7 +115,6 @@ def test_add_to_molecule_when_empty(cys_data: PdbData, cys_match: ResidueMatch):
         molecules=molecules,
         this_molecule=this_molecule,
         residue_match=cys_match,
-        res_atom_idcs=tuple(cys_match.res_atom_idcs),
         use_canonical_names=False,
     )
     assert mol_out is this_molecule