Re: [Rdkit-devel] smiles parsing - rings

[Jonas B. <dr....@gm...>]

Hi Andrew,
Good to hear from you, and thanks for the info. I might go for a
quick-n-dirty fix then. The reason I am asking is that I am rewriting an
OEChem script to RDkit to share with a collaborator, and this way of doing
it (with parentheses) works fine in OEChem, with the OESmilesToMol
function.
Cheers
Jonas

tis 20 nov. 2018 kl. 17:04 skrev Andrew Dalke <da...@da...>:

> Hi Jonas,
>
> > On Nov 20, 2018, at 16:36, Jonas Boström <dr....@gm...>
> wrote:
> > not_ok_smiles = "C%43CCC%42.CC%42.CC(%43)C"
>
> The error message from RDKit is the not-very-helpful:
>
>    SMILES Parse Error: syntax error for input: 'C%43CCC%42.CC%42.CC(%43)C'
>
> If you try out my 'smiview' (available via 'pip install smiview' for
> Python):
>
>   % python smiview.py 'C%43CCC%42.CC%42.CC(%43)C'
>   Cannot parse --smiles: Unexpected term
>     C%43CCC%42.CC%42.CC(%43)C
>                         ^ Tokenizing stopped here
>   An open branch must be followed by an atom, bond, or dot.
>
> In Daylight and OpenSMILES, the ring closures must occur immediately after
> the atom symbol. More specifically, quoting
> http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html :
>
>   The bonds are numbered in any order, designating ring opening (or ring
> closure)
>   bonds by a digit immediately following the atomic symbol at each ring
> closure.
>
>
> RDKit also allows ring closures after a ')', which is connected to the
> atom symbol before the matching '('.
>
> Cheers,
>
>                                 Andrew
>                                 da...@da...
>
>
>
>
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