I've put up a new version on that web page. It's changed a bit from the old version as I couldn't find the old sources. Uses the latest CDK master so quite a bit faster. Usage is now
java -jar momsim.jar -q query.sdf Compound_000000001_000025000.sdf.sdf etc On Tue, Nov 22, 2011 at 4:18 AM, Jochen Schreiber <[email protected]> wrote: > Helly everbody, > > i want to calculate the similarity with: > > java -jar momsim.jar --sdfile Compound_000000001_000025000.sdf.sdf --qfile > query.sdf > > The query.sdf is the Strucutre form PubChem with the Compound ID = 1 and > saved as 3D-SDF. > > 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) > Caused by: java.lang.NullPointerException > at org.openscience.cdk.io.MDLReader.readMolecule(MDLReader.java:327) > ... 3 more > Exception in thread "main" java.lang.NullPointerException > at net.guha.apps.sim3d.MomentSimilarity.main(MomentSimilarity.java:162) > > Where is my fault? > > With best, > > Jochen Schreiber > ------------------------------------------------------------------------------ > 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 > -- Rajarshi Guha NIH Chemical Genomics Center ------------------------------------------------------------------------------ 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
