NPE when parsing certain PDB structures with "params.setCreateAtomBonds(true)" #943
Description
Hi,
thank you a lot providing and updating BioJava continuously.
I encountered a problem with the legacy pdb file parsing in the latest 6.0.0-alpha4 version of BioJava. When creating creating bonds an NPE is thrown.
Minimal (not)working example:
PDBFileReader reader = new PDBFileReader();
FileParsingParameters params = new FileParsingParameters();
params.setCreateAtomBonds(true);
reader.setFileParsingParameters(params);
reader.getStructureById("1v9i");throws
java.lang.NullPointerException: Cannot invoke "org.biojava.nbio.structure.Chain.getGroupByPDB(org.biojava.nbio.structure.ResidueNumber)" because "chain" is null
at org.biojava.nbio.structure.io.BondMaker.getAtomFromRecord(BondMaker.java:475)
at org.biojava.nbio.structure.io.BondMaker.formLinkRecordBond(BondMaker.java:336)
at org.biojava.nbio.structure.io.PDBFileParser.formBonds(PDBFileParser.java:2775)
at org.biojava.nbio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2700)
at org.biojava.nbio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2557)
at org.biojava.nbio.structure.io.PDBFileReader.getStructure(PDBFileReader.java:140)
at org.biojava.nbio.structure.io.LocalPDBDirectory.getStructureById(LocalPDBDirectory.java:334)
at ...
I think there is a problem with the legacy chain id format where authId:C is requested but only asymId:A and asymId:B are present.
All the Best
Christoph
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