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fix(rdkit): avoid deprecated explicit valence API #969

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fix(rdkit): avoid deprecated explicit valence API #969

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e03f63d
fix(rdkit): avoid deprecated explicit valence API
njzjz-bot Apr 18, 2026
f1cf0be
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 18, 2026
d64c08c
test(rdkit): strengthen explicit valence compatibility checks
njzjz-bot Apr 18, 2026
31c12f3
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 18, 2026
53ce12e
test(rdkit): drop explicit valence compatibility test
njzjz-bot Apr 18, 2026
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11 changes: 9 additions & 2 deletions dpdata/rdkit/sanitize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,11 +10,18 @@ def get_explicit_valence(atom, verbose=False):
sum([bond.GetBondTypeAsDouble() for bond in atom.GetBonds()])
)
try:
exp_val = atom.GetExplicitValence()
try:
from rdkit import Chem

exp_val = atom.GetValence(Chem.ValenceType.EXPLICIT)
valence_method = "GetValence(Chem.ValenceType.EXPLICIT)"
except (ImportError, AttributeError, TypeError):
exp_val = atom.GetExplicitValence()
valence_method = "GetExplicitValence()"
if exp_val != exp_val_calculated_from_bonds:
if verbose:
print(
f"Explicit valence given by GetExplicitValence() and sum of bond order are inconsistent on {atom.GetSymbol()}{atom.GetIdx() + 1}, using sum of bond order."
f"Explicit valence given by {valence_method} and sum of bond order are inconsistent on {atom.GetSymbol()}{atom.GetIdx() + 1}, using sum of bond order."
)
return exp_val_calculated_from_bonds
except Exception:
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