> I just got this message, and I am pretty sure the CDK does this wrong > too... the original problem was that InChI generation failed, because > a SDF was read wrongly...
To be more accurate, and according to Wolf-D.Ihlenfeldt, It's not much that the SDF was read wrongly (if I understood well what you said), on the contrary: the inchi software 1.02 is making use of the strict bond type definition of the MDL format, in which bond type values ranging from 4 to 8 should be used for SSS query ONLY. That's the reason why inchi calculation failed when the aromatic bond type 4 is used in the actual structure definition. Now the weird thing is that the inchi calculation does not fail for all aromatic structures having bond types set to 4 (see the rest of the discussion on the inchi user list on sourceforge), but (based on my own observations) only fail when the molecules contains aromatic heterocycle having at least one nitrogen... As the CDK makes use of the inchi toolkit recompiled to be run as java program, I'm guessing these issues are the same. Vincent ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
