Hello, i could try MDLV2000 Reader cause i didn't do this in java.
I call this command: java -jar momsim.jar --sdfile Compound_000000001_000025000.sdf.sdf --qfile query.sdf And i don't know how i could say to momsim.jar use the MDLV2000Reader. Jochen Am 22.11.2011 um 10:28 schrieb Egon Willighagen: > 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
