Distance between xyz coordinates in pdb files

[stellaparallax]

Hi,

I am creating a program that calculates the distance between the x, y, z coordinates of atoms listed in a pdb file.

So far i have this:

#!/usr/bin/perl -w


$num = 0;
$count = 0;

while (<>) {

# Find x, y, z coordinates and store in separate arrays

if ($_ =~ /^ATOM/) {
@line = $_ =~ m/^(.....).(.....).(....).(...)..(....)....(........)(........)(........)/;

$x = $line[5];
$arrayx[$num] = $x;

$y = $line[6];
$arrayy[$num] = $y;

$z = $line[7];
$arrayz[$num] = $z;

++$num;
}

# Count number of atoms

if ($_ =~ /^ATOM/) {
++$count;
}
}

# Calculate distance between all atom coordinates

foreach $i (0..$count) {

foreach $j ($i + 1..$count) {

$dist = sqrt(
($arrayx[$i] - $arrayx[$j])**2 +
($arrayy[$i] - $arrayy[$j])**2 +
($arrayz[$i] - $arrayz[$j])**2
);

print "$dist\n"

}
}

When I run the program i get this message popping up for some of the lines and I don't know what to do to fix it:

"Use of uninitialized value in subtraction (-) at ./gas.pl line 42, <> line 14368"

The line that it states is the last line of the pdb file, however i don't see why this line is involved in my calculations as this is not present in any of my arrays.

The pdb file I'm using is located here :

http://www.rcsb.org/pdb/explore.do?structureId=3PBL

Any help would be much appreciated as I am VERY new to Perl.
Thanks

 

[prex1]

Please enclose code between [ignore]

[/ignore][i]your code here[/i][ignore]

[/ignore] tags.
There are at least two errors in your code:
- [tt]$count[/tt] will contain the number of counts + 1 . You should initialize it like so [tt]$count=-1[/tt] instead of [tt]$count=0[/tt]
- the first [tt]foreach[/tt] is incorrect, it should go to [tt]$count-1[/tt] ; also, if you have thousands of lines, you should write it like so

foreach($i=0;$i<$count;$i++){
  foreach($j=$i+1;$j<=$count;$j++){

Franco

http://www.xcalcs.com

: Online engineering calculations

http://www.megamag.it

: Magnetic brakes for fun rides

http://www.levitans.com

: Air bearing pads

 

[duncdude]

[tt]#!/usr/bin/perl

$num = 0;

while ( <DATA> ) {

# Find x, y, z coordinates and store in separate arrays

if ( $_ =~ s/^ATOM__(.....).(.....).(....).(...)..(....)....(........)(........)(........)/$arrayx[ $num ] = $6; $arrayy[ $num ] = $7; $arrayz[ $num ] = $8/e ) {

print "num is $num\n";
print '=' x ( 7 + ( length $num ) );
print "\n";

print $arrayx[ $num ] . "\n";
print $arrayy[ $num ] . "\n";
print $arrayz[ $num ] . "\n\n";

$num++;
}

}

foreach( $i = 0; $i < $num; $i++ ) {

foreach( $j = $i + 1; $j <= $num; $j++ ) {

print $arrayx[$i] . " \$arrayx[$i]\n";
print $arrayy[$i] . " \$arrayx[$i]\n";
print $arrayz[$i] . " \$arrayx[$i]\n";
print $arrayx[$j] . " \$arrayx[$j]\n";
print $arrayy[$j] . " \$arrayx[$j]\n";
print $arrayz[$j] . " \$arrayx[$j]\n\n";

if ( $arrayx[$i] > 0 && $arrayy[$i] > 0 && $arrayz[$i] > 0 &&
$arrayx[$j] > 0 && $arrayy[$j] > 0 && $arrayz[$j] > 0 ) {

$dist = sqrt(
( $arrayx[$i] - $arrayx[$j] ) ** 2 +
( $arrayy[$i] - $arrayy[$j] ) ** 2 +
( $arrayz[$i] - $arrayz[$j] ) ** 2
);

print "distance = $dist\n\n";
}
}
}

__DATA__
ATOM__123456789123456789123456789123456789123456789123456789
ATOM__234567891234567891234567891234567891234567891234567891
ATOM__345678912345678912345678912345678912345678912345678912[/tt]

Kind Regards
Duncan

 

[duncdude]

coloring in regex shows (...) mapping to $6, $7 * $8 respectively

[tt]#!/usr/bin/perl

$num = 0;

s/^ATOM__(.....).(.....).(....).(...)..(....)....[green](........)[/green][blue](........)[/blue](........)/$arrayx[ $num ] = [green]$6[/green]; $arrayy[ $num ] = [blue]$7[/blue]; $arrayz[ $num++ ] = $8/e while ( <DATA> );

foreach( $i = 0; $i < $num; $i++ ) {

foreach( $j = $i + 1; $j <= $num; $j++ ) {

if ( $arrayx[$i] > 0 && $arrayy[$i] > 0 && $arrayz[$i] > 0 && $arrayx[$j] > 0 && $arrayy[$j] > 0 && $arrayz[$j] > 0 ) {

$dist = sqrt(( $arrayx[$i] - $arrayx[$j] ) ** 2 + ( $arrayy[$i] - $arrayy[$j] ) ** 2 + ( $arrayz[$i] - $arrayz[$j] ) ** 2 );

print "distance = $dist\n";
}
}
}

__DATA__
ATOM__123456789123456789123456789123456789123456789123456789
ATOM__234567891234567891234567891234567891234567891234567891
ATOM__345678912345678912345678912345678912345678912345678912[/tt]

Kind Regards
Duncan