Hi,
I was surprised to see that a (dubious) structure that goes through
SanitizeMol OK can fail a subsequent sanitization call:
print("Start")
mol = Chem.MolFromSmiles('C1=n(C)-c=Cn1', sanitize=False)
print("Before first sanitization")
Chem.SanitizeMol(mol)
print("Before second sanitization")
Chem.SanitizeMol(mol)
print("Done")
The output is:
Start
Before first sanitization
Before second sanitization
[16:54:20] Explicit valence for atom # 1 N, 4, is greater than permitted
Traceback (most recent call last):
File "./san.py", line 9, in <module>
Chem.SanitizeMol(mol)
ValueError: Sanitization error: Explicit valence for atom # 1 N, 4, is
greater than permitted
Is this an unavoidable aspect of the way SanitizeMol works, since it does
several operations (Kekulize, check valencies, set aromaticity, conjugation
and hybridization) in a certain order, or should this be considered a bug?
Best,
Ivan
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