Hi David,
thanks for your answer and yes, this seems to be the case.
It could be solved by either using raw strings or escaping with
smiles = smiles.encode('string-escape')
However, I thought that it might be something that could be done by the
toolkit to avoid errors that could go unnoticed for a long time :-)
Best,
Michael
On Mon, Oct 12, 2015 at 10:42 PM, David Hall <[email protected]> wrote:
> That behavior appears to all be in python; as you’ve written it, your
> smiles string has a newline before rdkit ever sees it:
>
> >>> print 'C/C=C\n1nc(nn1)C'
> C/C=C
> 1nc(nn1)C
> >>> print 'C/C=C\\n1nc(nn1)C'
> C/C=C\n1nc(nn1)C
>
>
> On Oct 12, 2015, at 4:37 PM, Michael Reutlinger <[email protected]> wrote:
>
> Hi all,
>
> I just found an unexpected behaviour in the current RDKit. My input is a
> perfectly valid smiles with explicitly specified double bond configuration.
> Actually, similar smiles were obtained using the RDKit.
>
> The problem is, when submitting the smiles string containing an \n to
> MolFromSmiles only the part before the \n is used and the rest is
> disregarded. The \ needs to be quoted to a \\ in order to work correct.
>
> Is this a desired / expected behaviour?
>
> Best,
> Michael
>
> <Screen Shot 2015-10-12 at 22.04.57.png>
>
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