Hi,
I want to check for overlap of two files.
In both files the lines look this way:
ATOM 1 K+ K+ 1 27.261 7.934 32.141 1.0000 1.000
ATOM 1 N ALA 1 -12.149 -11.899 13.144 0.1414 1.550
Columns 6-8 contain the x.y,z coordinates, and the last column
contains the radius. I want to remove from <SOLVFILE> all the entries that
overlap with the <STRUCTFILE>. The overlap criteria is that
the distance between entries in SOLVFILE and entries in STRUCTFILE
should be larger than the sum of the radii. If d<R1+R2 consider an overlap and remove the line from the <SOLVFILE>
Here is the code

 #!/usr/bin/perl -w

@desBooli = ();
@ATOM = ();
@atmnb1 = ();
@atmname1 = ();
@resname1 = ();
@resnb1 = ();
@rest1 = ();
@x1 = ();
@y1 = ();
@z1 = ();
@q1 = ();
@rad1 = ();

@atmnb2 = ();
@atmname2 = ();
@resname2 = ();
@resnb2 = ();
@x2 = ();
@y2 = ();
@z2 = ();
@q2 = ();
@rad2 = ();

print "Please type the filename with the solvent: ";
$file1 = <STDIN>;
chomp $file1;
#Does the file exist?
unless ( -e $file1) {
        print "File \"$file1\" doesn\'t seem to exist!!\n";
        exit;
}

#Can we open the file?
open(SOLVFILE, $file1) || die("Couldn't open file  $file1\n");

print "Please type the filename with the structure: ";
$file2 = <STDIN>;
chomp $file2;
#Does the file exist?
unless ( -e $file2) {
        print "File \"$file2\" doesn\'t seem to exist!!\n";
        exit;
}
#Can we open the file?
open(STRUCTFILE, $file2) || die ("Couldn't open file $file2\n");

open(test1, ">Solvent.pdb");
open(test2, ">OverL.txt");

$i=0;
while ($line=<SOLVFILE>)
        {
chop($line);
$rest1[$i] = $line;
($ATOM, $atomnb1[$i], $atmname1[$i],$resname1[$i],$resnb1[$i],$x1[$i],
+$y1[$i],$z1[$i],$q1[$i],$rad1[$i])= split(/\s+/, $line);
$i++;
        }
$Nsolv = $i;
print "Number of atoms in solvent file is $Nsolv \n";

$i = 0;
while ($line=<STRUCTFILE>)
        {
chop($line);
($ATOM, $atomnb2[$i], $atmname2[$i],$resname2[$i],$resnb2[$i],$x2[$i],
+$y2[$i],$z2[$i],$q2[$i],$rad2[$i])= split(/\s+/, $line);
$i++;
        }
$Nstruct = $i;
print "Number of atoms in structure file is $Nstruct \n";

for ($i = 0; $i <=$Nsolv-1; $i++)
{
$desBooli[$i] = 0;
}

for ($i = 0; $i <=$Nsolv-1; $i++)
{
  for ($j = 0; $j <=$Nstruct-1; $j++)
  {
$dist = sqrt(($x1[$i]-$x2[$j])*($x1[$i]-$x2[$j])+($z1[$i]-$z2[$j])*($z
+1[$i]-$z2[$j])+($z1[$i]-$z2[$j])*($z1[$i]-$z2[$j]));
$radSum = $rad1[$i] +$rad2[$j];
if($dist < $radSum) {
print test2 "Overlap for atoms $atomnb1[$i] and $atomnb2[$j]\n";
$desBooli[$i] = 1;
 }
  }
}

$i = 0;

for ($i = 0; $i <=$Nsolv-1; $i++)
{
if ($desBooli[$i] == 0){
print test1 "$rest1[$i]\n"
}
}

close STRUCTFILE;
close SOLVFILE;
close test1;
close test2;
exit;
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