[Biojava-l] PDBFileParser and identifying atoms in ligands

[Andy Thomas-Cramer]

>From a PDB file, I can identify which atoms are in ligands, and which
are in residues in the chain. The chain atoms end with the TER record.

 

>From the BioJava API, I can distinguish as well -- if it's an amino
sequence and the automatic alignment between SEQRES and ATOM sequences
is successful. 

 

Is there a way through the API to identify atoms in ligands, when the
chain is not an amino sequence or alignment fails? It looks like the TER
record is ignored by PDBFileParser.