Or more succintly, with obabel 2.3.1 I have:
C:\Users\Noel>obabel -:[Al]C#N -oinchi -xK -xX Recmet
==============================
*** Open Babel Warning in InChI code
#1 :Metal was disconnected
♥
1 molecule converted
...which is rather sweet, but probably not the desired outcome. :-)
Do you have time to take a look Chris?
- Noel
On 9 December 2011 19:51, Ken Smith <k.w.sm...@qub.ac.uk> wrote:
> Folks
>
> I'm trying to use Openbabel to generate a non-standard InChIKey for a few of
> my metal cyanides and isocyanides (because configurations produce the same
> Standard InChIKey).
>
> Below is my code. Execution of the code leaving the comments intact yields
> the Standard InChI and Standard InChIKey (with the expected disconnected
> metal warnings).
>
> ==============================
> *** Open Babel Warning in InChI code
> #0 :Metal was disconnected
> ==============================
> *** Open Babel Warning in InChI code
> #0 :Metal was disconnected
> InChI: InChI=1S/CN.Al/c1-2;
> InChIKey: HWKFKJIIRKPLHF-UHFFFAOYSA-N
>
>
> Removing the comments to add the RecMet option (to reconnect the metal and
> therefore end up with different InChIs and InChIKeys for my cyanide and
> isocyanide species) seems to break the InChIKey part of the code (it's not
> generated).
>
>
> ==============================
> *** Open Babel Warning in InChI code
> #0 :Metal was disconnected
> ==============================
> *** Open Babel Warning in InChI code
> #0 :Metal was disconnected
> InChI: InChI=1/CN.Al/c1-2;/rCAlN/c2-1-3
> InChIKey:
>
>
>
> Any ideas? Note that I get similar behaviour if I try to use obabel
> directly.
>
>
>
> Cheers,
>
> Ken
>
>
>
>
> def getInChIAndInChIKey(smilesString):
>
> inchi = None
> inchikey = None
>
> mol = ob.OBMol()
>
> conv = ob.OBConversion()
>
> conv.SetInAndOutFormats("smi", "inchi")
> conv.ReadString(mol, smilesString)
>
> conv.AddOption("X", conv.OUTOPTIONS, "DoNotAddH")
> # conv.AddOption("X", conv.OUTOPTIONS, "RecMet")
>
> inchi = conv.WriteString(mol).rstrip()
>
> conv.SetOptions("K", conv.OUTOPTIONS)
> conv.AddOption("X", conv.OUTOPTIONS, "DoNotAddH")
> # conv.AddOption("X", conv.OUTOPTIONS, "RecMet")
>
> inchikey = conv.WriteString(mol).rstrip()
>
> return(inchi, inchikey)
>
>
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This white paper is intended to serve as a reference, checklist and point of
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