Bug: column label_comp_id is undefined

[luk27official]

Hello,
the structure taken from the 2.5.1 release (updated 4gqq) seems to be still failing: https://wwwdev.ebi.ac.uk/pdbe/entry-files/download/4gqq_updated.cif

This is the PrankWeb log:

2025-08-07T21:28:46 [DEBUG] : Executing '/opt/java-tools/bin/java-tools structure-info --input=/data/prankweb/predictions/v4-user-upload/2025-08-07-21-28-38-947964BF-5CFE-4398-B534-B1333D5297DC/working/structure-raw.cif --output=/data/prankweb/predictions/v4-user-upload/2025-08-07-21-28-38-947964BF-5CFE-4398-B534-B1333D5297DC/working/structure-information.json' ...
21:28:47 [main] ERROR cusbg.prankweb.pjtools.Executor - Command execution failed.
org.rcsb.cif.EmptyColumnException: column label_comp_id is undefined
	at org.rcsb.cif.model.Column$EmptyColumn.getStringData(Column.java:111) ~[ciftools-java-7.0.1.jar:?]
	at org.rcsb.cif.schema.DelegatingStrColumn.get(DelegatingStrColumn.java:17) ~[ciftools-java-7.0.1.jar:?]
	at org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl.addSites(CifStructureConsumerImpl.java:1509) ~[biojava-structure-7.2.2.jar:7.2.2]
	at org.biojava.nbio.structure.io.cif.CifStructureConsumerImpl.finish(CifStructureConsumerImpl.java:1231) ~[biojava-structure-7.2.2.jar:7.2.2]
	at org.biojava.nbio.structure.io.cif.CifStructureConverter.fromCifFile(CifStructureConverter.java:160) ~[biojava-structure-7.2.2.jar:7.2.2]
	at org.biojava.nbio.structure.io.cif.CifStructureConverter.fromInputStream(CifStructureConverter.java:83) ~[biojava-structure-7.2.2.jar:7.2.2]
	at org.biojava.nbio.structure.io.CifFileReader.getStructure(CifFileReader.java:43) ~[biojava-structure-7.2.2.jar:7.2.2]
	at cusbg.prankweb.pjtools.structure.StructureAdapter.loadCifFile(StructureAdapter.java:57) ~[prankweb-java-tools.jar:?]
	at cusbg.prankweb.pjtools.structure.StructureAdapter.loadStructure(StructureAdapter.java:38) ~[prankweb-java-tools.jar:?]
	at cusbg.prankweb.pjtools.structure.StructureAdapter.fromFile(StructureAdapter.java:27) ~[prankweb-java-tools.jar:?]
	at cusbg.prankweb.pjtools.command.info.InfoCommand.loadStructure(InfoCommand.java:77) ~[prankweb-java-tools.jar:?]
	at cusbg.prankweb.pjtools.command.info.InfoCommand.execute(InfoCommand.java:60) ~[prankweb-java-tools.jar:?]
	at cusbg.prankweb.pjtools.Executor.executeCommand(Executor.java:39) [prankweb-java-tools.jar:?]
	at cusbg.prankweb.pjtools.ApplicationEntry.run(ApplicationEntry.java:37) [prankweb-java-tools.jar:?]
	at cusbg.prankweb.pjtools.ApplicationEntry.main(ApplicationEntry.java:22) [prankweb-java-tools.jar:?]

Full log: https://prankweb.cz/analyze?database=v4-user-upload&code=2025-08-07-21-28-38-947964BF-5CFE-4398-B534-B1333D5297DC

Thanks.

[rdk]

The bug is happening in prankweb-java-tools, java-tools project under PrankWeb separate from P2Rank. prankweb-java-tools is using standard BioJava library while in P2Rank I'm using forked build fixing the bug.

The bug with PDBe updated cif structures (like 4gqq_updated.cif) is still not fixed in latest BioJava 7.2.2, but the bug #77 is.
My fork of BioJava fixing the bug is here https://github.com/rdk/biojava/tree/updated-cif-parsing-bug-7.2.2

I'm not sure why we are still/again using prankweb-java-tools in PrankWeb. That's the question to ask Peter.
In any case, BioJava version in prankweb-java-tools should at least be updated to 7.2.2 or I can give you build of my fork.

I will try to get the fix into upstream BioJava but I'm not sure how fast it will go.

[luk27official]

Thanks for the clarification, I forgot that we are using BioJava directly in PrankWeb as well!

I think that it is not critical, so we can wait for the official BioJava release. I will just create an issue in the PrankWeb repository so we do not forget to update it later.

[rdk]

Note for myself: looking at https://github.com/cusbg/prankweb/blame/4066f6e2d1bc2d6d7d6ed360b359c75a2aaae9a8/java-tools/src/main/java/cusbg/prankweb/pjtools/command/info/InfoCommand.java#L188 it is not certain the fix in my fork will work.

This is something they probably should fix at PDBe since label_comp_id seems to be required but they are not providing it in some updated structures.