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optional smile conversion for DeNovo eval #33

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optional smile conversion for DeNovo eval #33

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1 change: 1 addition & 0 deletions src/xlm/configs/lightning_train/post_hoc_evaluator/denovo.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,3 +5,4 @@ compute_validity: True
compute_uniqueness: True
compute_qed: True
compute_sa: True
convert_to_smile: True
4 changes: 3 additions & 1 deletion src/xlm/tasks/molgen.py
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Original file line number Diff line number Diff line change
Expand Up @@ -502,13 +502,15 @@ def __init__(
compute_uniqueness: bool = True,
compute_qed: bool = True,
compute_sa: bool = True,
convert_to_smile: bool = True
):
self.use_bracket_safe = use_bracket_safe
self.compute_diversity = compute_diversity
self.compute_validity = compute_validity
self.compute_uniqueness = compute_uniqueness
self.compute_qed = compute_qed
self.compute_sa = compute_sa
self.convert_to_smile = convert_to_smile

# Lazy-loaded TDC oracles (to avoid import overhead)
self._oracle_qed = None
Expand Down Expand Up @@ -575,7 +577,7 @@ def eval(
all_smiles = []
for pred in predictions:
safe_str = pred.get("text", "")
smiles = self._safe_to_smiles_with_bracket_handling(safe_str)
smiles = self._safe_to_smiles_with_bracket_handling(safe_str) if self.convert_to_smile else safe_str
pred["smiles"] = smiles # Add SMILES to prediction dict
if (
smiles is not None
Expand Down