On Mon, 13 Apr 2026 09:31:17 -0700 Jose Duarte <[email protected]> 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 <[email protected]> > 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 - [email protected] > > 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 ------------------------------------------------------------ _______________________________________________ Biojava-l mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biojava-l
