[BioRuby] bio.pdb doubt
K. Shameer
shameer at ncbs.res.in
Mon Feb 18 05:16:03 UTC 2008
Dear Naohisa and Alex,
Thanks for the links and the sample code.
I have one more doubt :) .
Is there any method to check whether a protein is multichain/single chain
using BioRuby. I checked in BioRuby in Anger document and wiki, but I
couldnt find it (May be am missing something important)
Thanks,
K. Shameer
NCBS - TIFR
> You can use Bio::PDB#find_atom or Bio::PDB#find_residue methods.
>
> require 'bio'
>
> # reading PDB data
> pdb = Bio::FlatFile.open("pdb1a0d.ent") { |f| f.next_entry }
>
> # using Bio::PDB#find_atom
> atoms = pdb.find_atom do |atom|
> (atom.chainID == "A" and atom.resSeq >= 22) or
> (atom.chainID == "B" and atom.resSeq <= 50)
> end
> print atoms.to_s
>
> print "\n"
>
> # the same thing can be done by using Bio::PDB#find_residue
> residues = pdb.find_residue do |residue|
> (residue.chain.id == "A" and residue.resSeq >= 22) or
> (residue.chain.id == "B" and residue.resSeq <= 50)
> end
> print residues.to_s
>
>
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