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distance calculation for XYZ coordiantes

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Join Date: Sep 2008

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annie_singh annie_singh is offline

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distance calculation for XYZ coordiantes

Oct 1st, 2008

Hello,

I am a beginner in perl. I am stuck with a problem. 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

These are the X, Y and Z coordinates from a pdb file. I want to calculate the distance using these three coordinate values. First i want to know how to assign variable names to these values in the array. I have to use this formula to calculate the distance:

$dist = sqrt(($x1-$x2)**2+($y1-$y2)**2+($z1-$z2)**2);

Till now I have written the script shown below to obtain the three columns which is shown above. I am stuck. I need help to calculate distance using 'for loop' or i guess its two for loops within which would look something like this:

for($AAi = 1; $AAi<= 7; $AAi++){ #here $AAi shud take the first three values(x1, y1, z1)
for ($AAj = 2; $AAj<= 7; $AAj++){ #similarly $AAj shud take 2nd 3 values(x2, y2, z2)
my $dist = sqrt(($x1-$x2)**2+($y1-$y2)**2+($z1-$z2)**2);

and do an iterative distance calculation. am stuck....

my exiting code:

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);

Thank you..

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Join Date: Dec 2005

Posts: 5,850

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Salem

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Void main'ers are DOOMed

Re: distance calculation for XYZ coordiantes

Oct 1st, 2008

> my exiting code:
Really....
http://www.daniweb.com/forums/post702120-2.html
Try to reply to existing threads which cover basically the same topic as before.

In your loop, having worked out the distance between
6.324 32.707 50.379
5.197 32.618 46.826
ie, lines 1 and 2

Would you then need to work out the distance between
5.197 32.618 46.826
4.020 36.132 46.259
ie, lines 2 and 3

Something like

 Help with Code Tags 
 Perl Syntax (Toggle Plain Text) 
my @old;
open (IN, "filename.pdb") or die "$!";
while (my $line = <IN>) {
   chomp($line);
   my @array = (split(/\s+/,$line))[6,7,8];
   print "@array\n";
   if ( $. > 1 ) {
      # now work out distance between @old and @array
   }
   @old = @array;
}
close (IN);
my @old;
open (IN, "filename.pdb") or die "$!";
while (my $line = <IN>) {
   chomp($line);
   my @array = (split(/\s+/,$line))[6,7,8];
   print "@array\n";
   if ( $. > 1 ) {
      # now work out distance between @old and @array
   }
   @old = @array;
}
close (IN);

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Join Date: Sep 2008

Posts: 6

Reputation: annie_singh is an unknown quantity at this point

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annie_singh annie_singh is offline

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Re: distance calculation for XYZ coordiantes

Oct 1st, 2008

hi,

Well, I did get extract the three columns with the script, but i wanted to know how to calculate the distance and put them in an output file.

The distance calculation is between row1_row2, then row1_row3, row1_row4, row1_row5.... so on... till row6_row7.

This was the problem. I do not know how to do this iterative distance calcultion.

Thank you,