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Cover errors in fragmentation.py #27

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Cover errors in fragmentation.py #27

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4 changes: 2 additions & 2 deletions src/ms_pred/magma/fragmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ def __init__(
self.smiles = mol_str
self.mol = Chem.MolFromSmiles(self.smiles)
if self.mol is None:
return
raise RuntimeError(f"Invalid molecule encountered. SMILES: {self.smiles}")
self.inchi = Chem.MolToInchi(self.mol)
if not mol_str_canonicalized:
self.mol = common.canonical_mol_from_inchi(self.inchi)
Expand All @@ -60,7 +60,7 @@ def __init__(
self.inchi = mol_str
self.mol = common.canonical_mol_from_inchi(self.inchi) # inchi must be canonicalized
if self.mol is None:
return
raise RuntimeError(f"Invalid molecule encountered. InChI: {self.inchi}")
self.smiles = Chem.MolToSmiles(self.mol)
self.mol = Chem.MolFromSmiles(self.smiles) # always use canonical smiles for mols
else:
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