[Biojava-l] NullPointerException with toMMCIF method

[Enrico Morelli]

On Mon, 13 Apr 2026 09:31:17 -0700
Jose Duarte <jose.duarte at rcsb.org> wrote:

> 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

Thank you very much. Can you send an email when the new release is available on Maven?

Thanks again
> 
> 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
> > https://mailman.open-bio.org/mailman/listinfo/biojava-l
> >  



-- 
-----------------------------------------------------------
  Enrico Morelli
  System Administrator | Programmer | Web Developer

  CERM - Polo Scientifico
  via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY
------------------------------------------------------------