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I am trying to convert a standard InChI string to a non-standard InChI string with fixed-hydrogen-layer:

Standard InChI for Uracil: InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)

Desired outcome: InChI=1/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)/f/h5-6H

My question is if this is at all theoretically possible without further information and if not, are there other ways to achieve this goal, e.g. using an existing database?

The ultimate goal is to convert the InChI string with hydrogen layer into a mol file to be able to map chromatogram peaks against it, so I installed OpenBabel which can do the trick, but it can not solve the aforementioned conversion between the InChIs.

I already found the cactus website which allows to convert from InChIKey (which I can generate from the standard InChI that I have) to the correct non-standard InChI (with hydrogen layer) via this URL: http://cactus.nci.nih.gov/chemical/structure/{INCHIKEY_HERE}/inchi. The problem here is that it returns multiple correct non-standard InChI strings (with fixed hydrogen layer). One of them is the one I am looking for but I don't see a way to figure out how to pick the correct one. As you can imagine I want to run this in an automated fashion for hundreds of conversions.

Thank you very much for your input.

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  • $\begingroup$ First off, I'm not sure why you didn't ask your Open Babel question on the mailing lists. It certainly should be able to do what you want. $\endgroup$ – Geoff Hutchison Mar 5 '15 at 16:52
  • $\begingroup$ But I think you're trying to pick a particular tautomer. That should be your focus. There are multiple tautomers possible, so why are you singling out one? $\endgroup$ – Geoff Hutchison Mar 5 '15 at 16:53
  • $\begingroup$ Geoff, for the example above, I am looking to get the specific tautomer that is Uracil. I am starting my search with a keyword like Uracil and by this I get the standard InChI string for it, which I then want to use to convert to the one with hydrogen layer but specific to the initial search term. That is why I single one out. $\endgroup$ – Loddi Mar 7 '15 at 9:23
  • $\begingroup$ I don't think you understand. There are multiple tautomeric forms of uracil. You would have to have some sort of "standardization" procedure, generate all tautomers, etc. $\endgroup$ – Geoff Hutchison Mar 7 '15 at 12:19
  • $\begingroup$ Geoff, is there a way to calculate the most common tautomer? This could be the solution. Thanks $\endgroup$ – Loddi Mar 9 '15 at 17:48

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