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

[Andreas Prlic]

Hi Fico,

I think this is the same as

https://redmine.open-bio.org/issues/3371

which is already resolved in trunk. Are you using Maven? Then you could
just point to 3.0.5-SNAPSHOT to get the updated libraries.


Andreas




On Wed, Nov 7, 2012 at 7:02 PM, Fico <wuuter at gmail.com> wrote:

> 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
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>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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