Dear all,
There are several questions I want to ask for help.
1. When I read a molecular by MolFromSmiles and MolFromSmarts,it throw an
exception，As shown below , the molecule “n1c(=O)nc(=O)cc1” can’t be read by
MolFromSmiles while MolFromSmarts work well.So what the difference between
MolFromSmiles and MolFromSmarts when read a molecular smiles?( I still expect
MolFromSmarts is compatible with MolFromSmile and more advanced.)
2.The smiles “n1c(=O)nc(=O)cc1” and “N1C(=O)NC(=O)C=C1” is two kinds of ways to
write the structure,when I use the HasSubStructureMatch test it ,I expect the
one is contained within the other,but the result is inconsistent with my
expect, I just want to know why? Did I misunderstand this function?
>>> mfsmi = AllChem.MolFromSmiles
>>> mfsma = AllChem.MolFromSmarts
>>> asub = mfsma("n1c(=O)nc(=O)cc1")
>>> a = mfsmi("n1c(=O)nc(=O)cc1")
>>> a1 = mfsma("n1c(=O)nc(=O)cc1")
>>> a.HasSubstructureMatch(asub)
Traceback (most recent call last):
File "<input>", line 1, in <module>
a.HasSubstructureMatch(asub)
AttributeError: 'NoneType' object has no attribute 'HasSubstructureMatch'
>>> a1.HasSubstructMatch(asub)
True
>>> bsub = mfsma("N1C(=O)NC(=O)C=C1")
>>> b = mfsmi("N1C(=O)NC(=O)C=C1")
>>> b1 = mfsma("N1C(=O)NC(=O)C=C1")
>>> b.HasSubstructMatch(bsub)
False
>>> b1.HasSubstructMatch(bsub)
True
>>> a1.HasSubstructMatch(bsub)
False
>>> b.HasSubstructMatch(asub)
True
>>> b1.HasSubstructMatch(asub)
False
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