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

[Andreas Prlic]

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> 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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