bioinformatics - Perl program to calculate neibouring residues from a pdb file -

this program extract neighboring residues within 4.5 angstrom. have resolved program atom numbers. these want extract

• the residue numbers,
• residue name,
• atom № and
• atom name.

i output data in tabular form can directly copy results. i'm stuck , require extract fields atom numbers obtained in $close_atomno, , how use program multiple pdb files , different catalytic residues in 1 go.

any appreciated.

#!/usr/bin/perl use list::util qw(sum); use data::dumper qw(dumper); use 5.010;  "enter residue no."; chomp(my $r_no = <stdin>);  (@all_pos, @all_data, @matching_pos, @matching_data);  $residue_file = "neighbouring_residues.txt"; open $out_fh1, '>', $residue_file or die "can't open $residue_file: $!";  "enter file name"; chomp(my $infile_name = <stdin>); open in, '<', $infile_name or die "can't open $infile_name: $!";  line: while (<in>) {    chomp;     /^atom/ or next line;    @fields = split;    push @all_pos,  [ @fields[6 .. 8]    ];    push @all_data, [ @fields[1 .. 3, 5] ];     if( $fields[6] eq $r_no) {        $_;       push @matching_pos,  [ @fields[6 .. 8]    ];       push @matching_data, [ @fields[1 .. 3, 5] ];    }  }  $out_fh1 "neighbouring residues @ position $r_no in 4.5a region are:"; %close_atoms;  matching_atom: $i1 ( 0 .. $#matching_pos ) {    $matching_atom = $matching_data[$i1][1];    $matching_atom eq $_ , next matching_atom qw/n ca o c/;    $i2 ( 0 .. $#all_pos ) {       ($close_atomno, $close_residueno) = @{$all_data[$i2]}[0, 3];       $dist = distance($matching_pos[$i1], $all_pos[$i2]);       if($dist < 4.5 , $close_residueno != $r_no) {          $close_atoms{$close_atomno} = 1;       }    } }  sub distance { sqrt sum map {$_**2} map {$_[0][$_] - $_[1][$_]} 0 .. $#{$_[0]} };  @close_atoms = keys %close_atoms;  $out_fh1 "@close_atoms"; $m (0 .. $#close_atoms) {     $out_fh1 $all_pos[$m];# here problem want residue details according $close_atomno  }  "result in $residue_file"; 

this typical input file:

atom 9   n glu 1 35.540 1.925 27.662 1.00 19.70 n atom 10 ca glu 1 35.626 1.018 28.802 1.00 20.96 c atom 11  c glu 1 34.264 0.794 29.444 1.00 20.22 c 

with columns in order:

• atom
• atom number
• atom name
• residue name
• chain
• residue number
• x coord
• y coord
• z coord
• irrelevant
• irrelevant
• irrelevant

use warnings; use strict;  $base_r_no = $argv[0]; open in, "<$argv[1]" or die;  @atoms_data = map {[split]} grep {/^atom/} <in>;  foreach $base_atom (grep {($$_[2] !~ /^n|ca|o|c$/) && ($$_[5] eq $base_r_no)} @atoms_data) {     foreach $matched_atom (grep {dist($base_atom,$_) < 4.5} @atoms_data) {         print join("\t",@{$matched_atom})."\n";     } }  sub dist {     return sqrt( ($$_[1][5]-$$_[0][5])**2 + ($$_[1][6]-$$_[0][6])**2 + ($$_[1][7]-$$_[0][7])**2 ); } 

as multiple pdb files - cat files 1 file , hand script.