[Biojava-l] PDBFileParser Error for PDB files without ATOM part for some chains defined in the header

[Guoying Qi]

HI Andreas,

I am trying to read a local copy of PDB file.

Here is the code.

Thanks.

Guoying

        String pdbFileName = "testdata/test/pdb/pdb2ja5.ent";

        FileParsingParameters fileParsingParameters = new FileParsingParameters();
        fileParsingParameters.setStoreEmptySeqRes(true);
        fileParsingParameters.setLoadChemCompInfo(false);
        fileParsingParameters.setHeaderOnly(true);

        PDBFileParser parser = new PDBFileParser();
        parser.setFileParsingParameters(fileParsingParameters);
        
        BufferedReader pdbFileReader = new BufferedReader(new FileReader(pdbFileName));
        Structure structure1 = parser.parsePDBFile(pdbFileReader);
        
        System.out.println("***\n" + structure1 + "****\n");

        PDBFileReader pdbreader = new PDBFileReader();
        pdbreader.setFileParsingParameters(fileParsingParameters);
        Structure structure2 = pdbreader.getStructure(pdbFileName);

        System.out.println("***\n" + structure2 + "****\n");


> On 16 Sep 2015, at 01:52, Andreas Prlic <andreas at sdsc.edu> wrote:
> 
> Hi Guoying,
> 
> Can you share the code and the exact FileParsingParameters that you are using to parse your file? 
> 
> 2JA5 does not have coordinates for chain N. The following code still can parse out a structure object. BioJava complains, but with a different error message than you reported. The error message that I get seems like over-reporting from BioJava and it probably should be a warning, rather than an error. 
> 
> Having said that, your exception is a NullpointerException and at least with the code below I don't get that...
> 
> FileParsingParameters params = new FileParsingParameters();
> params.setStoreEmptySeqRes(true);
> 
> AtomCache cache = new AtomCache();
> cache.setUseMmCif(false);
> cache.setFileParsingParams(params);
> 
> StructureIO.setAtomCache(cache);
> 
> Structure bioAssembly = StructureIO.getBiologicalAssembly("2ja5",1);
> 
> Andreas
> 
> 
> 
> 
> On Tue, Sep 15, 2015 at 3:21 AM, Guoying Qi <gqi at ebi.ac.uk <mailto:gqi at ebi.ac.uk>> wrote:
> Hi there,
> 
> I am using BioJava 4.1.0 and got the following error message for PDB 2ja5 when no ATOM for chain N, P and T when StoreEmptySeqRes is on.
> 
> I am sure the parser should cope with this kind of issues.
> 
> Could somebody have a look?
> 
> Thanks.
> 
> Guoying
> 
> 
> Exception in thread "main" java.lang.NullPointerException
> 
> at org.biojava.nbio.structure.io.PDBFileParser.storeUnAlignedSeqRes(PDBFileParser.java:3026)
> 
> at org.biojava.nbio.structure.io.PDBFileParser.triggerEndFileChecks(PDBFileParser.java:2973)
> 
> at org.biojava.nbio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2769)
> 
> 
> 
> 

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