[Biojava-dev] #bug: pdb file parse error,

Fico wuuter at gmail.com
Thu Nov 8 03:02:23 UTC 2012


Hi, all
I got an error when I parsing the pdb file "1FNX.pdb", the error
information as following:

*Exception in thread "main"
org.biojava3.core.exceptions.CompoundNotFoundError: Compound not found for:
Cannot find compound for: U
    at
org.biojava3.core.sequence.storage.ArrayListSequenceReader.setContents(ArrayListSequenceReader.java:201)
    at
org.biojava3.core.sequence.template.AbstractSequence.<init>(AbstractSequence.java:88)
    at org.biojava3.core.sequence.DNASequence.<init>(DNASequence.java:64)
    at
org.biojava.bio.structure.io.SeqRes2AtomAligner.alignNucleotideGroups(SeqRes2AtomAligner.java:416)
    at
org.biojava.bio.structure.io.SeqRes2AtomAligner.align2NucleotideChains(SeqRes2AtomAligner.java:199)
    at
org.biojava.bio.structure.io.SeqRes2AtomAligner.align(SeqRes2AtomAligner.java:145)
    at
org.biojava.bio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2745)
    at
org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2644)
    at
org.biojava.bio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2485)
    at
org.biojava.bio.structure.io.PDBFileReader.getStructure(PDBFileReader.java:892)
    at
org.biojava.bio.structure.io.PDBFileReader.getStructure(PDBFileReader.java:884)
    at PDBTest.main(PDBTest.java:24)*

my biojava version is 3.0.4



More information about the biojava-dev mailing list