branch-1-6/examples/structure/structure-io.pl

   1 #!/bin/perl -w
   2 # Getting  Entry, Chain, Residue, and Atom objects given a PDB file
   3
   4 use Bio::Structure::IO;
   5 use strict;
   6
   7 my $file = shift or die "No PDB file\n";
   8 my $structio = Bio::Structure::IO->new(-file => $file);
   9 my $struc = $structio->next_structure;
  10
  11 for my $chain ($struc->get_chains) {
  12    my $chainid = $chain->id;
  13    # one-letter chaincode if present, 'default' otherwise
  14    for my $res ($struc->get_residues($chain)) {
  15       my $resid = $res->id;
  16       # format is 3-lettercode - dash - residue number, e.g. PHE-20
  17       my $atoms = $struc->get_atoms($res);
  18       # actually a list of atom objects, used here to get a count
  19       print join "\t", $chainid,$resid,$atoms,"\n";
  20    }
  21 }