From: Egon W. <ego...@gm...> - 2012-09-24 15:27:08
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On Mon, Sep 24, 2012 at 5:16 PM, John May <joh...@gm...> wrote: > I looked into this a bit more and unfortunately the InChI does need 4 neighbours… but this can be resolved. You can move the implicit hydrogen generation to the InChI code conversion - that way it never gets added to container but the inchi is still calculated correctly. I tested it and it worked (phew). Indeed! > It's simply a matter of adding a null check for at3 (4th ligand) and if it's null add a new JniInChIAtom "H" and JniInChIBond to the 'input' structure. > > Here's the line: > >> JniInchiAtom at3 = (JniInchiAtom) atomMap.get(surroundingAtoms[3]); That might actually be the easiest fix... I'll give that a try in the train home... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |