[BioRuby] bio.pdb doubt
Naohisa GOTO
ngoto at gen-info.osaka-u.ac.jp
Wed Feb 20 13:53:53 UTC 2008
Dear Shameer,
Information of chains for each macromolecule is described in
'COMPND' record. In BioRuby, Bio::PDB#record method can be used.
Because the information obtained by the method is sometimes
naive, processing of the data would be needed.
Below is a sample program:
require 'bio'
def parse_COMPND(pdb)
molecules = []
current_molecule = nil
pdb.record('COMPND')[0].compound.each do |a|
case a[0]
when 'MOL_ID'
current_molecule = {}
molecules.push current_molecule
when 'CHAIN'
chains = a[1].split(/\s*\,\s*/)
current_molecule[:chains] = chains
end
current_molecule[a[0]] = a[1]
end
molecules
end
pdb1 = Bio::FlatFile.open('pdb1fjg.ent') { |f| f.next_entry }
pdb2 = Bio::FlatFile.open('pdb1a0d.ent') { |f| f.next_entry }
[ pdb1, pdb2 ].each do |pdb|
compounds = parse_COMPND(pdb)
compounds.each do |c|
p c['MOLECULE']
p c[:chains]
end
end
The meanings of the 'COMPND' record is described in
PDB file format document:
http://www.wwpdb.org/documentation/format23/sect2.html#COMPND
--
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp /ng at bioruby.org
On Mon, 18 Feb 2008 10:46:03 +0530 (IST)
"K. Shameer" <shameer at ncbs.res.in> wrote:
> 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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