Just to add on - if you really want to use InChI (don't) then you could
store the AuxInfo but the CDK doesn't have a conversion method that accepts
it when turning it back into an AtomContainer.
I also notice you're using unique SMILES (default by old APIs), you
probably want isomeric that a non-canonical but store stereochemistry.
IAtomContainer mol = SmilesGenerator.isomeric().create(container);
John
Regards,
John W May
john.wilkinson...@gmail.com
On 2 September 2015 at 19:54, John M <john.wilkinson...@gmail.com> wrote:
> Hi Martin,
>
> The InChI is an identifier and not a structure representation it should
> never be used as such. For maximum preservation you should store compounds
> as Kekulé SMILES or Molfile. You can store additional data such as
> coordinates supplementary to the SMILES.
>
> You might find a recent presentation by Noel (O Babel) and Rajarshi (CDK)
> useful:
>
> http://baoilleach.blogspot.co.uk/2015/08/the-whole-of-cheminformatics-best.html
>
> John
>
>
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