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 <[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 >
_______________________________________________ Biojava-l mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biojava-l
