I'm desalting the ChEMBL data set and generating the corresponding de-salted SD and SMILES files. I found a problem in the conversion step, and found that the problem has nothing to do with the de-salting.
My code failed with CHEMBL1269997, which is record ~750,200 out of 1,142,974.
(In other words, it took a while to get to this point.) Here's a reproducible:
>>> from rdkit import Chem
>>> writer = Chem.SDWriter("/dev/stdout")
>>> for mol in Chem.ForwardSDMolSupplier("CHEMBL1269997.sdf"):
... writer.write(mol)
...
[22:11:05]
****
Invariant Violation
Violation occurred on line 388 in file
/tmp/homebrew-rdkit-HEAD-Ebdo/Code/GraphMol/FileParsers/MolFileStereochem.cpp
Failed Expression: pick >= 0
****
Traceback (most recent call last):
File "<stdin>", line 2, in <module>
RuntimeError: Invariant Violation
>>> Chem.MolToSmiles(mol)
'OCC1=CC2OC(CC(C)C)(CC(C)C)C3C4CCCC56C(OC(C)(C)O5)C1(O)C46C23'
>>> Chem.MolToSmiles(mol, isomericSmiles=True)
'OCC1=C[C@@H]2OC(CC(C)C)(CC(C)C)[C@@H]3[C@H]4CCC[C@@]56[C@@H](OC(C)(C)O5)[C@]1(O)[C@]46[C@H]23'
>>>
You can see that the molecule was read in, is not None, and can be used to
generate a SMILES.
The CHEMBL1269997.sdf is attached.
This error was previously reported in the thread JP started, titled "Invariant
violation...", dated July 6, 2011. Greg replied:
> Wow that is certainly an error I never expected to see. From the code,
> I guess the molecule has a stereocenter that is surrounded by other
> stereocenters and something extremely unfortunate is happening with
> the way decisions are being made about which bonds to wedge. As Eddie
> requested in an earlier message, it would be helpful to have the input
> that produced the error so that it can be added to the test cases (and
> so that I can be sure the problem is fixed once I figure out how to).
but I see no posting of a failing structure. I hope the attached structure
helps resolve this problem.
Andrew
da...@dalkescientific.com
CHEMBL1269997.sdf
Description: Binary data
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