From: Thomas K. <tho...@we...> - 2007-06-27 06:46:49
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Hi everybody, after an update of my cdk version to the current trunk I recognized an inc= rease of the number of tests which throw errors within the cdk-taverna pro= ject. (From 3 to 19 errors). Has anybody an idea what this increase caused= =3F=20 I found errors while using the following classes: org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor org.openscience.cdk.qsar.descriptors.molecular.IPMolecularDescriptor org.openscience.cdk.qsar.descriptors.bond.ResonancePositiveChargeDescripto= r org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor The error messages are all nearly identical and like: --------------------------------------------------------------------------= ----- Test set: org.openscience.cdk.applications.taverna.qsar.descriptors.molecu= lar.IPMolecularTest --------------------------------------------------------------------------= ----- Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.03 sec <= << FAILURE! test=5FLocalWorkerIPMolecular(org.openscience.cdk.applications.taverna.qsar.= descriptors.molecular.IPMolecularTest) Time elapsed: 0.02 sec <<< ERROR!= java.lang.NoSuchMethodError: org.openscience.cdk.interfaces.IAtom.getForma= lCharge()I at org.openscience.cdk.reaction.type.RearrangementCation1Reaction.setActi= veCenters(RearrangementCation1Reaction.java:265) at org.openscience.cdk.reaction.type.RearrangementCation1Reaction.initiat= e(RearrangementCation1Reaction.java:160) at org.openscience.cdk.tools.StructureResonanceGenerator.getAllStructures= (StructureResonanceGenerator.java:188) at org.openscience.cdk.charges.GasteigerPEPEPartialCharges.assignGasteige= rPiPartialCharges(GasteigerPEPEPartialCharges.java:125) at org.openscience.cdk.qsar.descriptors.atomic.PartialPiChargeDescriptor.= calculate(PartialPiChargeDescriptor.java:173) at org.openscience.cdk.qsar.descriptors.bond.IPBondDescriptor.calculateCo= jugatedPiSystDescriptor(IPBondDescriptor.java:666) at org.openscience.cdk.qsar.descriptors.bond.IPBondDescriptor.calculate(I= PBondDescriptor.java:160) at org.openscience.cdk.qsar.descriptors.molecular.IPMolecularDescriptor.c= alculatePlus(IPMolecularDescriptor.java:175) at org.openscience.cdk.qsar.descriptors.molecular.IPMolecularDescriptor.c= alculate(IPMolecularDescriptor.java:128) at org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.Ab= stractMolecularDescriptor.execute(AbstractMolecularDescriptor.java:101) at org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.IP= MolecularTest.test=5FLocalWorkerIPMolecular(IPMolecularTest.java:82) Can somebody give me a hint what's worng=3F Cheers, Thomas ------------------------------------------------------- Thomas Kuhn =20 Institut f=FCr biologische und chemische Informatik / Institute for Bioinfor= matics and Chemoinformatics Fachhochschule Gelsenkirchen / University of Applied Sciences of Gelsenkir= chen Fachbereich Angewandte Naturwissenschaften / Department of Applied Natural= Sciences August-Schmidt-Ring 10 D-45665 Recklinghausen Fon +49-(0)2361-4970053 Mobile +49-(0)177-8085663 =20 E-Mail tho...@fh... |
From: Egon W. <ego...@gm...> - 2007-06-27 07:53:51
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On Wednesday 27 June 2007, Thomas Kuhn wrote: > after an update of my cdk version to the current trunk I recognized an > increase of the number of tests which throw errors within the cdk-taverna > project. (From 3 to 19 errors). Has anybody an idea what this increase > caused? Yes, the 'upgrade' of the core classes, to work with Class-es instead of natives. This give a lot of NullPointerExceptions, where CDK code does not realize that fields (like implicit hydrogen count) might be UNSET. Those bits of code have now to test if the field == NULL (aka UNSET) and then make a reasonable assumption, or deal with it otherwise. > I found errors while using the following classes: > > org.openscience.cdk.qsar.descriptors.atomic.PartialTChargePEOEDescriptor > org.openscience.cdk.qsar.descriptors.molecular.IPMolecularDescriptor > org.openscience.cdk.qsar.descriptors.bond.ResonancePositiveChargeDescriptor > org.openscience.cdk.qsar.descriptors.bond.BondPartialTChargeDescriptor > > The error messages are all nearly identical and like: > > --------------------------------------------------------------------------- >---- Test set: > org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.IPMolec >ularTest > --------------------------------------------------------------------------- >---- Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.03 > sec <<< FAILURE! > test_LocalWorkerIPMolecular(org.openscience.cdk.applications.taverna.qsar.d >escriptors.molecular.IPMolecularTest) Time elapsed: 0.02 sec <<< ERROR! > java.lang.NoSuchMethodError: > org.openscience.cdk.interfaces.IAtom.getFormalCharge()I at Indeed, the method getFormalCharge() that returns an 'int' no longer exists, and it now returns an Integer. Egon -- ego...@gm... Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |