On Tue, Nov 22, 2011 at 10:18 AM, Jochen Schreiber <[email protected]> wrote: > If i try this command i get the following error: > > java.lang.NullPointerException > at org.openscience.cdk.io.MDLReader.readMolecule(MDLReader.java:327) > at org.openscience.cdk.io.MDLReader.readChemFile(MDLReader.java:201) > at org.openscience.cdk.io.MDLReader.read(MDLReader.java:150) > at net.guha.apps.sim3d.MomentSimilarity.main(MomentSimilarity.java:158) > org.openscience.cdk.exception.CDKException: Error while parsing line 3: null > -> null > at org.openscience.cdk.io.MDLReader.readMolecule(MDLReader.java:501) > at org.openscience.cdk.io.MDLReader.readChemFile(MDLReader.java:201) > at org.openscience.cdk.io.MDLReader.read(MDLReader.java:150) > at net.guha.apps.sim3d.MomentSimilarity.main(MomentSimilarity.java:158)
While I do not expect this to fix your problem, but can you please try using the MDLV2000Reader instead? The MDLReader is for a very old MDL molfile format, one without a "V2000" mention on the fourth line... I would also appreciate if you would file a bug report, attaching the SDF from PubChem that causes the error... even if the MDLReader is probably not the right reader, it should fail from informatively... thanx. Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) 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 ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
