program to calculate distance between 5 atoms

Shell Programming and Scripting
1

Hello,

I am a beginner with perl. I have a perl program to calculate the distance between 5 atoms or more.

i have an array which looks like this:
6.324 32.707 50.379
5.197 32.618 46.826
4.020 36.132 46.259
7.131 38.210 45.919
6.719 38.935 42.270
2.986 39.221 41.892
-0.269 37.184 41.565

I want to assign these values with Xi(column 1), Yi(column 2)and Zi(column 3). Suppose the first row values are (Xi,Yi,Zi), then the second row values will be (Xj, Yj, Zj) I want to calculate the distance using the formula

$dist = sqrt(($Xi-$Xj)**2+($Yi-$Yj)**2+($Zi-$Zj)**2) between row1/row2, row1/row3, row1/row4 ......so on.... till row6/row7

so its an iterative calculation. probably i shud us a for loop, and another forloop within the previous for loop. i am totally stuck.

till now my perl program looks like this:

open(IN, "/Users/anu/out.pl") or die "$!";
while (my $line = <IN>) {
chomp($line);
my @array = (split (/\s+/, $line))[6, 7, 8];
print "@array\n";
}
close(IN);

I dnt know wat to do..please help

Thank you

2

I use PHP, you can convert to Perl easily

<?php
$file = "file";
$handle = fopen($file,"r");
$base = explode(" ",trim(fgets($handle))); #get first line, put them into array

# get the rest of the line
while( !feof($handle)){
  $line = explode(" ",trim(fgets($handle,4096))); #put them to array 
  # do the formula
  $formula = sqrt(  sqrt( abs($base[0] - $line[0] ) ) +  sqrt( abs($base[1] - $line[1]))  + sqrt ( abs($base[2] - $line[2] ) ) );
  echo "formula $formula\n";  
}
fclose($handle);
?>