On Thu, Apr 23, 2009 at 10:12 AM, Vincent Le Guilloux <vincent.le-guill...@univ-orleans.fr> wrote: > Quoting Rajarshi Guha <rg...@indiana.edu>: >> More practically, the CDK did not recognize the atom type of the >> oxygen... this can, for example, be the results of it being negative >> and have three neighbors... > > The weired thing here is that the CDK does not recognizes the atom type > while it still display the right element symbol...
That is what I have been trying to explain: element type != atom type > The thing is that i've tested here my code on a dataset of 3000 molecules, > and I had at least a hundred of compounds for which the CDK complains with > this same error. Feel free to email me structures that fail... > I guess the structures may be corrupted in most cases, but still. Possibly... Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------------ Register Now & Save for Velocity, the Web Performance & Operations Conference from O'Reilly Media. Velocity features a full day of expert-led, hands-on workshops and two days of sessions from industry leaders in dedicated Performance & Operations tracks. Use code vel09scf and Save an extra 15% before 5/3. http://p.sf.net/sfu/velocityconf _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
