On 21/06/2016 19:11, John M wrote:
Don't really use that functionality but...
1. Aren't there no bonds in a PDBFile so getting separate fragments
isn't clear cut? If you have a sample file would help.
You are correct that PDB files do not contain bond info. This has always
been an issue as bond information has to be guessed. But it does contain
"chain" and "monomer" information so the different "fragments" can be
inferred (though there can of course be bonds between the fragments e.g.
disulphide bonds).
I was thinking (hoping) that CDKs various abstractions for monomer,
polymer etc. already handled this, but if so I can't figure it out.
An example would be 1CX2 (http://files.rcsb.org/view/1cx2.pdb) where you
would be able to access the 4 separate polypeptide chains (A-D) as well
as the ligands (S58 in this case).
2. For the residue information you can cast the atoms to PDBAtom and
access info from there.
that doesn't help much. But I did find that from the IPDBPolymer you can
get the IPDBStructures and the IStrands. But I'm still struggling to
work out whether that really helps me :-(
Tim
Regards,
John W May
john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>
On 21 June 2016 at 17:25, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
I asked this question a while ago about reading PDB files but
didn't get
any response.
https://sourceforge.net/p/cdk/mailman/message/35110892/
Hoping someone might know the answer?
Tim
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