CHEMBL1185048 triggers an interesting RDKit behavior.
If I strip salts from it, generate a SMILES string, and try to re-parse the
SMILES string, I get the error message "Can't kekulize mol".
That is, RDKit won't read its own output SMILES.
Here's a reproducible. I'll start with the parts that work.
>>> from rdkit import Chem
>>> from rdkit.Chem import SaltRemover
>>> remover = SaltRemover.SaltRemover()
>>>
>>> import urllib2
>>> chembl1185048 =
>>> urllib2.urlopen("https://www.ebi.ac.uk/chembldb/download_helper/getmol/658998";)
>>> for mol in Chem.ForwardSDMolSupplier(chembl1185048):
... break
...
>>> Chem.MolToSmiles(mol)
'COCCOCCOCCOC(C1(C(OCCOCCOCCOC)=O)C23C11C4=c5c6c7c8c5c2c2c5c3c3c9c%10c%11c%12c%13c9c9c%14c%15c(c1c93)C4C1c3c4c9c%16c%17c(c7c7c%18c%19c%20c(c%21c%12C%12%22CN(CCOCCOCCN)CC%12(c9c(c3-%15)C%14C%13%22)C%16C%21c%20c7%17)c%11c(c%19c2c8%18)c%105)c4c61)=O'
>>> Chem.MolFromSmiles(Chem.MolToSmiles(mol))
<rdkit.Chem.rdchem.Mol object at 0x101da3d70>
>>>
Now I'll strip salts and generate the SMILES. Again, this works as expected:
>>> mol2 = remover.StripMol(mol)
>>> Chem.MolToSmiles(mol2)
'COCCOCCOCCOC(C1(C(OCCOCCOCCOC)=O)C23C11C4=c5c6c7c8c5c2c2c5c3c3c9c%10c%11c%12c%13c%14c%15c%11c(c%11c%16c(c8c2%11)c2c7c7c8c2c(c%15%16)C%14C2c8c8c%11c%14c%15c%16c8C22CN(CCOCCOCCN)CC%132C2C%16c8c(c3c1c(c8=%15)C4C%14c6c7%11)c9c%122)c%105)=O'
However, this SMILES string isn't parseable, which I didn't expect.
>>> Chem.MolFromSmiles(Chem.MolToSmiles(mol2))
[16:42:13] Can't kekulize mol
Yet another thing to stack on Greg's desk while he's on holiday. :)
Andrew
[email protected]
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