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Optional ignore stereo when construction routes #39

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Merged
SGenheden merged 1 commit into from
Apr 13, 2026
Merged

Optional ignore stereo when construction routes #39

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18 changes: 14 additions & 4 deletions rxnutils/routes/readers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -110,14 +110,20 @@ def reaction_dataframe2routes(subdata):
return grouped.apply(reaction_dataframe2routes)


def reactions2route(reactions: Sequence[str], metadata: Sequence[Dict[str, Any]] = None) -> SynthesisRoute:
def reactions2route(
reactions: Sequence[str],
metadata: Sequence[Dict[str, Any]] = None,
ignore_stereo: bool = True,
) -> SynthesisRoute:
"""
Convert a list of reactions into a retrosynthesis tree

This is based on matching partial InChI keys of the reactants in one
reaction with the partial InChI key of a product.

:params reactions: list of reaction SMILES
:params metadata: optional list of metadata dictionaries for each reaction
:params ignore_stereo: whether to ignore stereochemistry when matching reactants and products
:returns: the created trees
"""

Expand All @@ -126,7 +132,7 @@ def make_dict(product_smiles):
"type": "mol",
"smiles": product_smiles,
}
product_inchi = smiles2inchikey(product_smiles, ignore_stereo=True)
product_inchi = smiles2inchikey(product_smiles, ignore_stereo=ignore_stereo)
reaction = product2reaction.get(product_inchi)
if reaction is not None:
metadata = dict(reaction["metadata"])
Expand All @@ -147,14 +153,18 @@ def make_dict(product_smiles):
for reaction, meta in zip(reactions, metadata):
reactants_smiles, _, product_smiles = split_rsmi(reaction)
product_smiles = Chem.CanonSmiles(product_smiles)
partial_product_inchi = smiles2inchikey(product_smiles, ignore_stereo=True)
partial_product_inchi = smiles2inchikey(
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product_smiles, ignore_stereo=ignore_stereo
)
inchi_map[partial_product_inchi] = product_smiles
reactants = split_smiles_from_reaction(reactants_smiles)
try:
reactants = [Chem.CanonSmiles(smi) for smi in reactants]
except:
raise ValueError(f"Cannot canonicalize SMILES: {reactants_smiles}")
all_reactants = all_reactants.union([smiles2inchikey(smi, ignore_stereo=True) for smi in reactants])
all_reactants = all_reactants.union(
[smiles2inchikey(smi, ignore_stereo=ignore_stereo) for smi in reactants]
)
product2reaction[partial_product_inchi] = {
"smiles": reaction,
"product": product_smiles,
Expand Down