[Cdk-user] Handling PDB files

[Tim D. <tdu...@gm...>]

I'm looking at how CDK can handle PDB files and have got the basic 
reading working:

InputStream is = ...
PDBReader reader =new PDBReader(is);
ChemFile file = reader.read(new ChemFile());
IPDBPolymer structure = (IPDBPolymer)ChemFileManipulator
         .getAllAtomContainers(file).get(0);

But I'm struggling with a couple of things:

1. How to extract out the ligand information - all I can find is the 
protein chains, but that clearly doesn't include all the atoms. I was 
expecting that there would be a way to get each "fragment" as an 
IAtomContainer so that I could extract the bound ligands.

2. How to convert to chains to protein/nucleic acid sequences e.g. in 
FASTA format.

Thanks

Tim