I don't think Fixed-H InChIs will help here. The InChI was never intended as a way to store chemical information, but just to be an index, so that several tautomeric forms will all give the same InChI. If you use it to store structures, then you have to accept that the original structure will be normalised, and it may be normalised to a tautomer which is unexpected. The classic case is the amide which you have observed.
As I see it, you have two solutions: either to convert the database to SMILES (for example) and alter the structures so that all amides are 'correctly' represented, or else to alter the queries to the unusual amide tautomer before doing the substructure search. OBChemTsfm may be able to help (http://baoilleach.blogspot.co.uk/2012/08/transforming-molecules-intowellother.html). - Noel On 4 April 2013 13:21, Fredrik Wallner <fred...@wallner.nu> wrote: > Hi, > > I have a database with standard InChI's that I would like to do substructure > matches on with openbabel/pybel. My problem is that the InChI's are given > with non-intuitive tautomers (eg. amides have the double bond to the nitrogen > instead of the oxygen if possible), leading to confusion when my users are > searching. > > Does anyone have any suggestions as to how this can be solved, preferably > without creating Fixed-H InChI's. > > Kind regards, > Fredrik > ------------------------------------------------------------------------------ > Minimize network downtime and maximize team effectiveness. > Reduce network management and security costs.Learn how to hire > the most talented Cisco Certified professionals. Visit the > Employer Resources Portal > http://www.cisco.com/web/learning/employer_resources/index.html > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Minimize network downtime and maximize team effectiveness. Reduce network management and security costs.Learn how to hire the most talented Cisco Certified professionals. Visit the Employer Resources Portal http://www.cisco.com/web/learning/employer_resources/index.html _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
