mmCIF writer emits no entry identifier: getPdbId() is lost on a write-then-read round trip #1143

Summary

AbstractCifFileSupplier writes the PDB identifier only as the name of the data_ block. It emits neither _entry.id nor _struct.entry_id, so the identifier is lost for every consumer that reads it as a data item rather than from the block header.

Two independent consumers are affected:

Steps to reproduce

Structure s = CifStructureConverter.fromInputStream(
        new GZIPInputStream(...open 4hhb.cif.gz...));
System.out.println(s.getPdbId());                 // 4HHB

String cif = CifStructureConverter.toText(s);
System.out.println(cif.contains("_entry.id"));        // false
System.out.println(cif.contains("_struct.entry_id")); // false

Structure back = CifStructureConverter.fromInputStream(
        new ByteArrayInputStream(cif.getBytes()));
System.out.println(back.getPdbId());              // null   <-- expected 4HHB

Actual output of the block header and identifier items as written today:

data_4HHB
(no _entry.id, no _struct.entry_id)

Expected

Structure.getPdbId() should survive a toText() / fromInputStream() round trip, and the written file should carry the identifier where mmCIF consumers look for it.

Why both items matter

_entry.id is the canonical place for the identifier and is what Jmol reads. BioJava's own reader (CifStructureConsumerImpl.consumeStruct) only looks at _struct.entry_id. Writing just one of the two leaves the other consumer broken, so both should be written.

Measured with Jmol, loading the identical structure inline with one item added at a time:

as written today (block header only)  ->  _M.pdbID = []
plus  _entry.id         3ALB          ->  _M.pdbID = [3ALB]
plus  _struct.entry_id  3ALB          ->  _M.pdbID = []
plus  both                            ->  _M.pdbID = [3ALB]

A practical consequence downstream: Jmol's isosurface ... eds fetches an electron-density box around the selection, but it needs an entry to ask about. With load =3alb it renders; with the same structure pushed inline via toMMCIF() it renders nothing, purely because the identifier was lost.

Location

biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/AbstractCifFileSupplier.java, in getInternal(...) — the identifier appears only in the enterBlock(...) call.

Version

Reproduced on master (5b29945). The behaviour is long-standing, not a recent regression.