It looks like you are using some type of smarts extension ( I believe it to
be CACTVS ), as far as I know "{" is not a valid SMARTS. I switched it to
what I assume is correct:
[R{0-1}:8] becomes [!R,R1:8]
Which means this is not in a ring or in exactly one ring. Basically, this
is not a valid daylight SMIRKS, it may be a valid CACTVS SMIRKS.
Here is some documentation for CACTVS extensions:
http://xemistry.net/Documentation/html/tcl_reference-45.htm
Cheers,
Brian
On Fri, May 13, 2016 at 3:40 PM, Soren <soeren...@gmail.com> wrote:
> Hi,
>
> I took a molecule and a reaction pattern from
> Guasch, Laura, Markus Sitzmann, and Marc C. Nicklaus. 2014. “Enumeration
> of Ring-Chain Tautomers Based on SMIRKS Rules.” *Journal of Chemical
> Information and Modeling* 54 (9): 2423–32.
>
> CODE:
>
> TestMol = 'c1cccc(O)c1C(=O)CC(=O)' # (C)C(O)C(N)C(=C)C(=N)C(=O)O'
>
> rx =
> AllChem.ReactionFromSmarts('[O,N,S,Se,Te:2]=[C;!R:3][!R:4]~[!R:7]~[R{0-1}:8]~'
>
> '[R{0-1}:6][O,N,S,Se,Te;!R:5][#1:1]>>[#1:1][O,N,S,Se,Te:2]'
>
> '[#6R1;!c:3]1[*;R1:4]~[*;R1:7]~[*:8]~[R:6][O,N,S,Se,Te;R1:5]1')
>
> rx.GetNumProductTemplates()
> tmp = rxn.RunReactants((TestMol,))
>
> RESULT:
>
> ValueError: ChemicalReactionParserException: Problems constructing reactant
> from SMARTS:
> [O,N,S,Se,Te:2]=[C;!R:3][!R:4]~[!R:7]~[R{0-1}:8]~[R{0-1}:6][O,N,S,Se,Te;!R:5][#1:1]
>
>
> Any idea what goes wrong? Is there something wrong with the string?
>
> RDKit : 2015.03.1
>
>
>
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