#!/usr/bin/perl -w
use strict;

use constant {
    		RAD => 9,
    		X => 5,
    		Y => 6,
    		Z => 7,
    		NB => 1,
    		REST => 10,
};

my $file;
print "Please type the filename with the solvent: ";
chomp($file = <STDIN>);
die "File \"$file\" doesn\'t seem to exist!!\n" unless -e $file;
open(SOLVFILE, $file) or die("Couldn't open file  $file\n");

print "Please type the filename with the structure: \n";
chomp($file = <STDIN>);
die "File \"$file\" doesn\'t seem to exist!!\n" unless -e $file;
open(STRUCTFILE, $file) or die("Couldn't open file  $file\n");

open(PDB, ">Solvent.pdb") or die "$!";
open(OVERL, ">OverL.txt") or die "$!";

my @solv;
my $line;
while ($line=<SOLVFILE>)
{
    chomp $line;
    push @solv, [split /\s+/, $line];
    push @{$solv[-1]}, $line;
}
close SOLVFILE;
print "Number of atoms in solvent file is ",$#solv+1," \n";

my @struct;
while ($line=<STRUCTFILE>)
{
    chomp($line);
    push @struct, [split /\s+/, $line];
    push @{$struct[-1]}, $line;
}
close STRUCTFILE;
print "Number of atoms in structure file is ",$#struct+1," \n";

for (my $i = 0; $i <= $#solv; $i++)
{
    my $v = $solv[$i];
    for my $t (@struct)
    {
    	
    	if (	# Sum of radius is greater than distance
                # between the atoms
    		($v->[RAD] + $t->[RAD])
    		> 
    		sqrt(
    		  ($v->[X] - $t->[X])**2
    		+ ($v->[Y] - $t->[Y])**2
    		+ ($v->[Z] - $t->[Z])**2
    		))
    	{
    		print OVERL "Overlap for atoms ",
                   $v->[NB]," and ",$t->[NB],"\n";
        } else {
                print PDB $v->[REST],"\n";
    	}
    }
}
close OVERL;
close PDB;
exit;