From: Nina J. <jel...@gm...> - 2011-10-30 07:24:21
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Hello All, I've run into the following problem. Instantiating AminoAcidCountDescriptor() fails with NPE, likely for the reason of not finding "org/openscience/cdk/templates/data/list_aminoacids.cml" resource. This CML file is not included in qsar-pdb jar, where the AminoAcid class calling it is, nor in cdk-qsarprotein, where the descriptor class is. Which cdk-* jar it is expected to be within? A minor issue - should org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor be in qsar-molecular package , instead of package qsar-protein, as it accepts IAtomContainer on input as other IMolecularDescriptors? Thanks, Nina |
From: Egon W. <ego...@gm...> - 2011-10-30 08:00:45
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On Sun, Oct 30, 2011 at 8:24 AM, Nina Jeliazkova <jel...@gm...> wrote: > I've run into the following problem. > Instantiating AminoAcidCountDescriptor() fails with NPE, likely for the > reason of not > finding "org/openscience/cdk/templates/data/list_aminoacids.cml" resource. > This CML file is not included in qsar-pdb jar, where the AminoAcid class > calling it is, nor in cdk-qsarprotein, where the descriptor class is. It is in the cdk-pdb.jar. > Which cdk-* jar it is expected to be within? That is defined by one of the src/META-INF/*.datafiles files. Now, it is indeed in a different jar, so depending on the system you are using, you could experience classpath issues... however, Maven should be fine. > A minor issue - should > org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptor be > in qsar-molecular package , instead of package qsar-protein, as it accepts > IAtomContainer on input as other IMolecularDescriptors? Dunno... I leave that to the community... I guess this is one of those descriptors that can be interesting to both... (some small molecules are peptides or peptide-like) 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 |