SMILES that can't be round tripped through RDKit #1228

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coleb opened this Issue Dec 22, 2016 · 2 comments

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@coleb
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coleb commented Dec 22, 2016 edited

image

Ya, it's a crazy molecule, but if RDKit can write it, shouldn't it be able to read it?

mol = Chem.MolFromSmiles('OS(=O)(=O)C1=CC2=C(C=C1)\C1=N\C3=C4C=C(C=CC4=C4\N=C5/N=C(/N=C6\N([Al](Cl)N34)\C(=N/C2=N1)C1=CC=C(C=C61)S(=O)=O)C1=C5C=C(C=C1)S(O)(=O)=O)S(O)(=O)=O')
smi = Chem.MolToSmiles(mol)
print(smi) # O=[SH](=O)c1ccc2c(c1)c1nc3c4ccc(S(=O)(=O)O)cc4c(nc4c5ccc(S(=O)(=O)O)cc5c5nc6c7ccc(S(=O)(=O)O)cc7c(nc2n1[al](Cl)n54)=n-6)-n=3
Chem.MolFromSmiles(smi)

The problem is the Aluminum: going from '[Al]' to '[al]'.

@gedeck
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gedeck commented Dec 22, 2016
@proteneer

Aromatic Aluminums are a thing?

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