Yes, by design and matches the InChI behaviour.
CC1=C(C)C=C1
InChI=1S/C6H8/c1-5-3-4-6(5)2/h3-4H,1-2H3
InChIKey=QNZUSULCBOVZRK-UHFFFAOYSA-N
CC1=CC=C1C
InChI=1S/C6H8/c1-5-3-4-6(5)2/h3-4H,1-2H3
InChIKey=QNZUSULCBOVZRK-UHFFFAOYSA-N
Instead of looking at aromaticity (a whole can of worms) conjugated double
bonds in rings are allowed to move irrespective of their aromatic
status (conjugate
equivalence). Since SMILES/InChI are primarily meant for information
retrieval it's useful to get one from the other. If you need further
refinement you can do a post match check. We *could* add an option that
only allows bonds marked as aromatic to migrate. A better example is
something like this:
If you want to force differences, define the stereochemistry on the double
bonds. This says "don't move this double bond", again matching the InChI.
- John
On 8 March 2018 at 10:37, Christoph Steinbeck <
christoph.steinb...@uni-jena.de> wrote:
> I was looking at whether RandomGenerator covers all of constitutional
> isomer space that it is supposed to do (it seems to do) and used CDK unique
> smiles as a hash. In this test code, RandomGenerator found only 4308 of the
> 4315 compounds that Molgen (http://www.molgen.de/literature.html)
> predicted.
>
> Turned out that the reason was that the CDK unique smiles implementation
> generates identical ‘unique’ smiles for non-identical molecules. They are
> all mesomeric cyclobutadiens. See attached graphics and SDF file.
>
> Both RDKIT and Openbabel generate the right number 4315 non-identical
> unique smiles.
>
> Kind regards,
>
> Chris
>
> —
> Prof. Dr. Christoph Steinbeck
> Analytical Chemistry - Cheminformatics and Chemometrics
> Friedrich-Schiller-University Jena, Germany
> Phone Secretariat: +49-3641-948171
> http://cheminf.uni-jena.de
> http://orcid.org/0000-0001-6966-0814
>
> What is man but that lofty spirit - that sense of enterprise.
> ... Kirk, "I, Mudd," stardate 4513.3..
>
>
>
>
>
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