Hi Andy, You don't need to process TERs to build up the representation of a structure. The BioJava data model will work fine even if the file does not contain any amino acids. (e.g. check 2KQO )
Ligands will get represented as Hetatom groups in the datamodel. Check the Hetatom or Group javadocs for how to access their atoms. For your last question: Check out the Chain.getAtomGroups() and Chain.getSeqResGroups() methods... If it does not work the way you expect for a particular PDB ID, please let me know the ID, so I can take a look at the details. Andreas On Thu, May 6, 2010 at 9:50 AM, Andy Thomas-Cramer <[email protected]> wrote: > >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. > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
