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
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