Hi Jonas,
> On Nov 20, 2018, at 16:36, Jonas Boström <dr.jonas.bost...@gmail.com> 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...@dalkescientific.com
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