Re: [OpenBabel-scripting] InChI and SMILES

[Noel O'B. <bao...@gm...>]

The InChI key is available as an option of the InChI format:
http://baoilleach.blogspot.com/2008/10/generating-inchis-mini-me-inchikey.html

So no need for SMILES...

BTW, it's handier for me if you send OB questions to the mailing list
rather than directly to me. It gives someone else a chance to
answer..:-)

- Noel

On 7 December 2010 15:47, Ken Smith <k.w...@qu...> wrote:
> Hi Noel
>
> Just a quick (probably stupid) question.
>
> I need to create a table of InChIs and InChIKeys for all the elements and
> their common isotopes.  I couldn't see an easy way of using OpenBabel
> (python) to generate the keys from hand-cranked InChIs, so I tried using
> SMILES (which means I need to learn the SMILES format, and I'm then
> constrained by its limitations).  When I use it though, I get some
> disconnected metal errors that (as a non-chemist) I don't understand, and
> the InChI I get has a hydrogen added.  Can you point me in the right
> direction?  My preference is to avoid having to go via SMILES, but if not, a
> SMILES workaround suffice for the time being.
>
> Cheers,
>
> Ken
>
>
> E.g. below is some trivial python code to generate the InChI(Keys) from
> SMILES.
>
>
> python getInchiFromSmiles.py [Na]
>
> ==============================
> *** Open Babel Warning  in InChI code
>  #0 :Metal was disconnected
> ==============================
> *** Open Babel Warning  in InChI code
>  #0 :Metal was disconnected
> InChI=1S/Na.H
> MPMYQQHEHYDOCL-UHFFFAOYSA-N
>
>
>
>
> import openbabel as ob
> import sys
>
> def getInChIAndInChIKey(smilesString):
>   conv = ob.OBConversion()
>   conv.SetInAndOutFormats("smi", "inchi")
>
>   mol = ob.OBMol()
>   conv.ReadString(mol, smilesString)
>   inchi = conv.WriteString(mol).rstrip()
>   conv.SetOptions("K", conv.OUTOPTIONS)
>   inchikey = conv.WriteString(mol).rstrip()
>   return(inchi, inchikey)
>
>
> def main(argv = None):
>   if argv is None:
>      argv = sys.argv
>
>   if len(argv) != 2:
>      sys.exit("Usage: getInchiFromSmiles.py <SMILES format>")
>
>   smiles = argv[1]
>   inchi, inchikey = getInChIAndInChIKey(smiles)
>
>   print inchi
>   print inchikey
>
>   return 0
>
>
>
> if __name__ == '__main__':
>   main()
>
>
> P.S.  I'd also like to be able to represent protonated hydrogen (H3+), but
> I've no idea how to represent that in SMILES.  Presumably in InChI I use the
> protonation layer if I want to hand-crank the InChI...
>
>
>