Hi,
I have a problem reading an SDF file (namely:
http://test.powdermania.de/CID_16078.sdf)
I get a java.lang.NullPointerException in the last line of this code
snippet:
URL url = fileURI.toURL();
InputStream in = url.openStream();
MDLV2000Reader sdfreader = new MDLV2000Reader(new
InputStreamReader(in));
ChemFile chemFile = (ChemFile)sdfreader.read((ChemObject)new
ChemFile());
Other SDFiles seem to work. Looking at the stack trace there seems to be
a problem with line 3 of the file. The stack trace is:
java.lang.NullPointerException
at
org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:358)
at
org.openscience.cdk.io.MDLV2000Reader.readChemFile(MDLV2000Reader.java:229)
at
org.openscience.cdk.io.MDLV2000Reader.read(MDLV2000Reader.java:178)
at
opentox.algorithm.descriptorcalculation.CDKPhysChemDescriptorsResource.calculateAllDesc(CDKPhysChemDescriptorsResource.java:235)
at
opentox.algorithm.descriptorcalculation.CDKPhysChemDescriptorsResource.acceptRepresentation(CDKPhysChemDescriptorsResource.java:127)
at org.restlet.resource.Resource.post(Resource.java:689)
at org.restlet.resource.Resource.handlePost(Resource.java:538)
at org.restlet.Finder.handle(Finder.java:357)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:504)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at
com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)
at
com.noelios.restlet.application.ApplicationHelper.handle(ApplicationHelper.java:112)
at org.restlet.Application.handle(Application.java:341)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:504)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:504)
at org.restlet.Filter.doHandle(Filter.java:150)
at
com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)
at org.restlet.Component.handle(Component.java:673)
at org.restlet.Server.handle(Server.java:331)
at com.noelios.restlet.ServerHelper.handle(ServerHelper.java:68)
at
com.noelios.restlet.http.HttpServerHelper.handle(HttpServerHelper.java:147)
at
com.noelios.restlet.ext.simple.SimpleProtocolHandler.handle(SimpleProtocolHandler.java:75)
at simple.http.Dispatcher.run(Dispatcher.java:83)
at simple.util.process.Daemon.execute(Daemon.java:121)
at simple.util.process.Daemon.run(Daemon.java:106)
org.openscience.cdk.exception.CDKException: Error while parsing line 3:
null -> null
at
org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:721)
at
org.openscience.cdk.io.MDLV2000Reader.readChemFile(MDLV2000Reader.java:229)
at
org.openscience.cdk.io.MDLV2000Reader.read(MDLV2000Reader.java:178)
at
opentox.algorithm.descriptorcalculation.CDKPhysChemDescriptorsResource.calculateAllDesc(CDKPhysChemDescriptorsResource.java:235)
at
opentox.algorithm.descriptorcalculation.CDKPhysChemDescriptorsResource.acceptRepresentation(CDKPhysChemDescriptorsResource.java:127)
at org.restlet.resource.Resource.post(Resource.java:689)
at org.restlet.resource.Resource.handlePost(Resource.java:538)
at org.restlet.Finder.handle(Finder.java:357)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:504)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at
com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)
at
com.noelios.restlet.application.ApplicationHelper.handle(ApplicationHelper.java:112)
at org.restlet.Application.handle(Application.java:341)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:504)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Router.handle(Router.java:504)
at org.restlet.Filter.doHandle(Filter.java:150)
at
com.noelios.restlet.StatusFilter.doHandle(StatusFilter.java:130)
at org.restlet.Filter.handle(Filter.java:195)
at org.restlet.Filter.doHandle(Filter.java:150)
at org.restlet.Filter.handle(Filter.java:195)
at com.noelios.restlet.ChainHelper.handle(ChainHelper.java:124)
at org.restlet.Component.handle(Component.java:673)
at org.restlet.Server.handle(Server.java:331)
at com.noelios.restlet.ServerHelper.handle(ServerHelper.java:68)
at
com.noelios.restlet.http.HttpServerHelper.handle(HttpServerHelper.java:147)
at
com.noelios.restlet.ext.simple.SimpleProtocolHandler.handle(SimpleProtocolHandler.java:75)
at simple.http.Dispatcher.run(Dispatcher.java:83)
at simple.util.process.Daemon.execute(Daemon.java:121)
at simple.util.process.Daemon.run(Daemon.java:106)
Caused by: java.lang.NullPointerException
at
org.openscience.cdk.io.MDLV2000Reader.readMolecule(MDLV2000Reader.java:358)
... 42 more
Any suggestions?
Regards,
Tobias Girschick
--
Dipl.-Bioinf. Tobias Girschick
Technische Universität München
Institut für Informatik
Lehrstuhl I12 - Bioinformatik
Bolzmannstr. 3
85748 Garching b. München, Germany
Room: MI 01.09.042
Phone: +49 (89) 289-18002
Email: tobias.girsch...@in.tum.de
Web: http://wwwkramer.in.tum.de/people/girschic
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