Question

I have a PDB file. Now it has two parts separated by TER. Before TER I call it part 1. I want to take x,y,z of ATOM 1 of first part i.e before TER and find distance to all x,y,z co ordinates after TER and then second ATOM of part one to all ATOMS of part second. This has to be repeated for all ATOMS of first part= to all ATOMS of second part. I have to automate it for 20 files. names of my files begin like 1_0.pdb,2_0.pdb….20_0.pdb.
This is a distance calculation. I have tried something in PERL but its very rough. Can someone help a bit.
The File looks like:

—-long file (I truncated it)—-

ATOM   1279 C    ALA    81      -1.925 -11.270   1.404
ATOM   1280 O    ALA    81      -0.279   9.355  15.557
ATOM   1281 OXT  ALA    81      -2.188  10.341  15.346
TER   
ATOM   1282 N    THR    82      29.632   5.205   5.525
ATOM   1283 H1   THR    82      30.175   4.389   5.768
ATOM   1284 H2   THR    82      28.816   4.910   5.008

The code is: In the end it finds the maximum distance and its co ordinates

my @points = (); 
open(IN, @ARGV[0]) or die "$!"; 
while (my $line = <IN>) { 

  chomp($line); 
  my @array = (split (/\s+/, $line))[5, 6, 7]; 
  print "@array\n"; 
  push @points, [ @array ]; 
} 
close(IN); 


 $max=0;
 for my $i1 ( 0 .. $#points  )

{ 
    my ( $x1, $y1, $z1 ) = @{ $points[$i1] };  
    my $dist = sqrt( ($x1+1.925)**2 + ($y1+11.270)**2 + ($z1-1.404)**2 ); 
    print "distance from (-1.925 -11.270 1.404) to ( $x1, $y1, $z1 ) is $dist\n"; 

    if ( $dist > $max )
     { $max = $dist;
       $x=$x1;
       $y=$y1;
       $z=$z1; 
      }}
    print "maximum value is : $max\n";
print "co ordinates are : $x $y $z\n";        

Answer 1

Not sure I clearly understand what you want, but how about:

#!/usr/local/bin/perl 
use strict;
use warnings;

my (@refer, @points);
my $part = 0;
while (my $line = <DATA>) { 
    chomp($line);
    if ($line =~ /^TER/) {
        $part++;
        next;
    }
    my @array = (split (/\s+/, $line))[5, 6, 7]; 
    if ($part == 0) {
        push @refer, [ @array ]; 
    } else {
        push @points, [ @array ]; 
    }
} 
my %max = (val=>0, x=>0, y=>0, z=>0);
foreach my $ref(@refer) {
    my ($x1, $y1, $z1) = @{$ref};
    foreach my $atom(@points) {
        my ($x, $y, $z) = @{$atom};
        my $dist = sqrt( ($x-$x1)**2 + ($y-$y1)**2 + ($z-$z1)**2 );
        if ($dist > $max{val}) {
            $max{val} = $dist;
            $max{x} = $x;
            $max{y} = $y;
            $max{z} = $z;
        }
    }
}
print "max is $max{val}; coord: x=$max{x}, y=$max{y}, z=$max{z}\n";

__DATA__
ATOM   1279 C    ALA    81      -1.925 -11.270   1.404
ATOM   1280 O    ALA    81      -0.279   9.355  15.557
ATOM   1281 OXT  ALA    81      -2.188  10.341  15.346
TER   
ATOM   1282 N    THR    82      29.632   5.205   5.525
ATOM   1283 H1   THR    82      30.175   4.389   5.768
ATOM   1284 H2   THR    82      28.816   4.910   5.008

output:

max is 35.9813670807545; coord: x=30.175, y=4.389, z=5.768