On Apr 22, 2009, at 11:24 AM, Vincent Le Guilloux wrote: > Hi, > > I'm currenty using CDK to read SDF files using an IteratingMDLReader, > and I've many errors of the same type during the execution. The > exception message is the following: > org.openscience.cdk.exception.CDKException: IAtom is not typed! O > at > org > .openscience > .cdk > .tools.CDKHydrogenAdder.addImplicitHydrogens(CDKHydrogenAdder.java: > 125) > at > org > .openscience > .cdk > .tools.CDKHydrogenAdder.addImplicitHydrogens(CDKHydrogenAdder.java: > 110) > at > sa2.gui.dbimport.ImportWorker.cleanMolecule(ImportWorker.java:157)
On converting to SMILES via OpenBabel and viewing it in the Daylight depict service, it looks weird. You have a negatively charged oxygen with 3 bonds. Is this mean to be a TS? ------------------------------------------------------------------- Rajarshi Guha <[email protected]> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Q: What's polite and works for the phone company? A: A deferential operator. ------------------------------------------------------------------------------ Stay on top of everything new and different, both inside and around Java (TM) technology - register by April 22, and save $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. 300 plus technical and hands-on sessions. Register today. Use priority code J9JMT32. http://p.sf.net/sfu/p _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
