On Sep 7, 2012, at 12:34 PM, Fabian Dey wrote:
> 1) I might be getting something wrong here, but it seems as if
> SmilesMolSupplier misses the very first Smiles:
Chem.SmilesMolSupplier by default assumes there is a title line.
(I think most other toolkits don't support title lines.) You
can disable this with a parameter to the constructor:
suppl = Chem.SmilesMolSupplier('test.smi', titleLine=True)
> It turned out that for the corresponding SD-file the atom elements were
> written in all captial letters (e.g. CL) - if these were changed to
> the proper format (Cl) RDKIT passed without throwing an error. Although
> I can preprocess the SD-files with a script, it would be nice if RDKIT
> could handle these cases internally.
Where does the SD file come from? Shouldn't the upstream code be fixed
so it doesn't generate a "CL"?
Andrew
[email protected]
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