[Biojava-dev] [BioJava - Bug #3355] (New) DNA chain from PDB file missing residue numbers and atoms

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Issue #3355 has been reported by Steven Darnell.

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Bug #3355: DNA chain from PDB file missing residue numbers and atoms
https://redmine.open-bio.org/issues/3355

Author: Steven Darnell
Status: New
Priority: High
Assignee: biojava-dev list
Category: structure
Target version: 
URL: 


When opening 1REP, the nucleotide groups for the DNA in chain B lack residues numbers and atoms. Looking at the PDB file, chain B does contain ATOM for most of the residues. The expected behavior is that the atoms should be associated with the appropriate nucleotide groups in chain B.

It would also be helpful for the toString method for NucleotideImpl to be stylized more like AminoAcidImpl, which provides more clear content regarding the group, record, and residue types. For example, the label "PDB:" is not indicative of nucleotides.

@PDBFileReader reader = new PDBFileReader();
reader.setAutoFetch(false);
FileParsingParameters params = new FileParsingParameters();
params.setParseSecStruc(true);
params.setAlignSeqRes(true);
params.setParseCAOnly(false);
params.setLoadChemCompInfo(true);
reader.setFileParsingParameters(params);
try {
	Structure structure = reader.getStructure("1REP.pdb");
	System.out.println();
	for( Chain c : structure.getChains() ) {
		System.out.println(String.format("Chain %s: %s", c.getChainID(), 
				c.getHeader().getMolName()));
		for( Group g : c.getSeqResGroups() ) {
			System.out.println(String.format("%s: %s", g.getClass().getSimpleName(),
					g.toString()));
		}
		System.out.println();
	}
} catch (Exception e) {
	System.out.println(e);
}@

_Code output:_

@Chain B: DNA (5'- D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP *GP*GP*T)-3')
NucleotideImpl: PDB: DC null false
NucleotideImpl: PDB: DT null false
NucleotideImpl: PDB: DG null false
NucleotideImpl: PDB: DA null false
NucleotideImpl: PDB: DG null false
NucleotideImpl: PDB: DG null false
NucleotideImpl: PDB: DG null false
NucleotideImpl: PDB: DC null false
NucleotideImpl: PDB: DA null false
NucleotideImpl: PDB: DA null false
NucleotideImpl: PDB: DT null false
NucleotideImpl: PDB: DT null false
NucleotideImpl: PDB: DT null false
NucleotideImpl: PDB: DG null false
NucleotideImpl: PDB: DT null false
NucleotideImpl: PDB: DC null false
NucleotideImpl: PDB: DA null false
NucleotideImpl: PDB: DC null false
NucleotideImpl: PDB: DA null false
NucleotideImpl: PDB: DG null false
NucleotideImpl: PDB: DG null false
NucleotideImpl: PDB: DT null false@


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