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RDKit GetSSSR Non-determinism Fix #2920

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RDKit GetSSSR Non-determinism Fix #2920

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81b03d3
RDKit `GetSSSR` Non-determinism Fix
JacksonBurns Apr 9, 2026
590a472
fix test collection failure
JacksonBurns Apr 9, 2026
f69ef81
reorder property cache update
JacksonBurns Apr 9, 2026
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16 changes: 12 additions & 4 deletions rmgpy/molecule/molecule.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2681,13 +2681,21 @@ def get_smallest_set_of_smallest_rings(self, symmetrized=False):
return_mapping=False,
save_order=True,
ignore_bond_orders=True)

rdkit_mol.UpdatePropertyCache(strict=False)
ranks = list(Chem.CanonicalRankAtoms(rdkit_mol, breakTies=True))
rank_to_idx = {rank: idx for idx, rank in enumerate(ranks)}
new_order = [rank_to_idx[i] for i in range(rdkit_mol.GetNumAtoms())]
canonical_mol = Chem.RenumberAtoms(rdkit_mol, new_order)
if symmetrized:
ring_info = Chem.GetSymmSSSR(rdkit_mol)
ring_info = Chem.GetSymmSSSR(canonical_mol)
else:
ring_info = Chem.GetSSSR(rdkit_mol)
ring_info = Chem.GetSSSR(canonical_mol)

for ring in ring_info:
atom_ring = [self.atoms[idx] for idx in ring]
# Map the new canonical indices back to the original RMG atom indices
original_idx_ring = [new_order[idx] for idx in ring]
atom_ring = [self.atoms[idx] for idx in original_idx_ring]

sorted_ring = self.sort_cyclic_vertices(atom_ring)
sssr.append(sorted_ring)
if symmetrized:
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