From morelli at cerm.unifi.it  Mon Apr 13 10:28:36 2026
From: morelli at cerm.unifi.it (Enrico Morelli)
Date: Mon, 13 Apr 2026 16:28:36 +0200
Subject: [Biojava-l] NullPointerException with toMMCIF method
Message-ID: <20260413162836.3ea58981@python.cerm.unifi.it>

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
------------------------------------------------------------

From jose.duarte at rcsb.org  Mon Apr 13 12:31:17 2026
From: jose.duarte at rcsb.org (Jose Duarte)
Date: Mon, 13 Apr 2026 09:31:17 -0700
Subject: [Biojava-l] NullPointerException with toMMCIF method
In-Reply-To: <20260413162836.3ea58981@python.cerm.unifi.it>
References: <20260413162836.3ea58981@python.cerm.unifi.it>
Message-ID: <CAHhO=JFE=2Hc8XEhUpSB_SvxXFjNwm+7iJD=u0kRGD1FuCr14A@mail.gmail.com>

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
> https://mailman.open-bio.org/mailman/listinfo/biojava-l
>
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From morelli at cerm.unifi.it  Tue Apr 14 03:01:37 2026
From: morelli at cerm.unifi.it (Enrico Morelli)
Date: Tue, 14 Apr 2026 09:01:37 +0200
Subject: [Biojava-l] NullPointerException with toMMCIF method
In-Reply-To: <CAHhO=JFE=2Hc8XEhUpSB_SvxXFjNwm+7iJD=u0kRGD1FuCr14A@mail.gmail.com>
References: <20260413162836.3ea58981@python.cerm.unifi.it>
 <CAHhO=JFE=2Hc8XEhUpSB_SvxXFjNwm+7iJD=u0kRGD1FuCr14A@mail.gmail.com>
Message-ID: <20260414090137.20bc12d0@python.cerm.unifi.it>

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
------------------------------------------------------------