[Biojava-l] NullPointerException with toMMCIF method

[Jose Duarte]

Thanks for reporting. It looks like this was introduced recently with the
fix for this issue: https://github.com/biojava/biojava/issues/1116

I can submit a patch soon, it should be an easy fix.

Jose

On Mon, 13 Apr 2026 at 07:38, Enrico Morelli <morelli at cerm.unifi.it> wrote:

> Dear all,
>
> I'm having trouble with a CIF that give me a NullPointerException using
> toMMCIF method:
>
>  public static void main(String[] args) throws StructureException,
> IOException {
>         Structure structure = StructureIO.getStructure("2G10");
>         System.out.println(StructureTools.getNrAtoms(structure));
>         System.out.println(structure.toMMCIF());
> }
>
>
> Exception in thread "main" java.lang.NullPointerException: Cannot invoke
> "org.biojava.nbio.structure.EntityInfo.getType()" because the return value
> of "org.biojava.nbio.structure.Chain.getEntityInfo()" is null
>         at org.biojava.nbio.structure.io
> .cif.AbstractCifFileSupplier$AtomSiteCollector.accept(AbstractCifFileSupplier.java:312)
>         at
> java.base/java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
>         at
> java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1709)
>         at
> java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:556)
>         at
> java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:546)
>         at
> java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)
>         at
> java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:265)
>         at
> java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:702)
>         at org.biojava.nbio.structure.io
> .cif.AbstractCifFileSupplier.getInternal(AbstractCifFileSupplier.java:39)
>         at org.biojava.nbio.structure.io
> .cif.CifStructureSupplierImpl.get(CifStructureSupplierImpl.java:17)
>         at org.biojava.nbio.structure.io
> .cif.CifStructureConverter.toCifFile(CifStructureConverter.java:230)
>         at org.biojava.nbio.structure.io
> .cif.CifStructureConverter.toText(CifStructureConverter.java:205)
>         at org.biojava.nbio.structure.io
> .FileConvert.toMMCIF(FileConvert.java:599)
>         at
> org.biojava.nbio.structure.StructureImpl.toMMCIF(StructureImpl.java:697)
>         at BioJavaTest.main(BioJavaTest.java:15)
>
> Is there a reason for that?
>
> Thanks
>
> --
> -----------------------------------------------------------
>   Enrico Morelli
>   System Administrator | Programmer | Web Developer
>
>   CERM - Polo Scientifico
>   via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY
> ------------------------------------------------------------
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at biojava.org
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>
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