Performing a function on each combination of variables in two arrays - perl

Question

I am trying to take one set of data and subtract each value in that data by another set of data.
For example:
Data set one (1, 2, 3)
Data set two (1, 2, 3, 4, 5)
So I should get something like (1 - (1 .. 5)) then (2 - (1..5)) and so on.
I currently have:
#!/usr/bin/perl
use strict;
use warnings;
my $inputfile = $ARGV[0];
open( INPUTFILE, "<", $inputfile ) or die $!;
my #array = <INPUTFILE>;
my $protein = 'PROT';
my $chain = 'P';
my $protein_coords;
for ( my $line = 0; $line <= $#array; ++$line ) {
if ( $array[$line] =~ m/\s+$protein\s+/ ) {
chomp $array[$line];
my #splitline = ( split /\s+/, $array[$line] );
my %coordinates = (
x => $splitline[5],
y => $splitline[6],
z => $splitline[7],
);
push #{ $protein_coords->[0] }, \%coordinates;
}
}
print "$protein_coords->[0]->[0]->{'z'} \n";
my $lipid1 = 'MEM1';
my $lipid2 = 'MEM2';
my $lipid_coords;
for ( my $line = 0; $line <= $#array; ++$line ) {
if ( $array[$line] =~ m/\s+$lipid1\s+/ || $array[$line] =~ m/\s+$lipid2\s+/ ) {
chomp $array[$line];
my #splitline = ( split /\s+/, $array[$line] );
my %coordinates = (
x => $splitline[5],
y => $splitline[6],
z => $splitline[7],
);
push #{ $lipid_coords->[1] }, \%coordinates;
}
}
print "$lipid_coords->[1]->[0]->{'z'} \n";
I am trying to take every value in $protein_coords->[0]->[$ticker]->{'z'} minus each value in $lipid_coords->[1]->[$ticker]->{'z'}.
My overall objective is to find (z2-z1)^2 in the equation d = sqrt((x2-x1)^2+(y2-y1)^2-(z2-z1)^2). I think that if I can do this once then I can do it for X and Y also. Technically I am trying to find the distance between every atom in a PDB file against every lipid atom in the same PDB and print the ResID for distance less than 5A.

Answer 1

To iterate on all combinations of two arrays, just embed two for loops:
use strict;
use warnings;
my #dataone = (1, 2, 3);
my #datatwo = (1, 2, 3, 4, 5);
for my $one (#dataone) {
for my $two (#datatwo) {
print "$one - $two\n";
}
}
Outputs:
1 - 1
1 - 2
1 - 3
1 - 4
1 - 5
2 - 1
2 - 2
2 - 3
2 - 4
2 - 5
3 - 1
3 - 2
3 - 3
3 - 4
3 - 5

Answer 2

This will give you the result of subtracting each element of set 2 from each element of set 1 in what I believe is the manner you were asking.
#!/usr/bin/perl
use strict;
use warnings;
my #set1 = (1, 2, 3);
my #set2 = (1, 2, 3, 4, 5);
my #set3 = ();
for my $val (#set1) {
push #set3, map { $val - $_ } #set2;
}
local $" = ', ';
print "#set3\n";
system 'pause';
The result will be an array containing (1 - (1..5), 2 - (1..5), 3 - (1..5)).
Contents of #set3 after script runs:
0, -1, -2, -3, -4, 1, 0, -1, -2, -3, 2, 1, 0, -1, -2
All the other protein and lipid stuff is way over my head, but I hope this at least helps a little. You should now have an array containing the subtracted elements that you can work with to get the rest of your results!
Edit:
Can replace the loop with this one liner :)
my #set3 = map { my $v = $_; map { $v - $_ } #set2 } #set1;
map is a pretty nifty function!

Answer 3

The easiest way to do this is to do your calculations while you're going through file two:
for (my $line = 0; $line <= $#array; ++$line) {
if (($array[$line] =~ m/\s+$lipid1\s+/) | ($array[$line] =~ m/\s+$lipid2\s+/)) {
chomp $array[$line];
my #splitline = (split /\s+/, $array[$line]);
my %coordinates = (x => $splitline[5],
y => $splitline[6],
z => $splitline[7],
);
push #{$lipid_coords->[1]}, \%coordinates;
# go through each of the sets of protein coors in your array...
for my $p (#{$protein_coords->[0]}) {
# you can store this value however you want...
my $difference = $protein_coords->[0][$p]{z} - $coordinates{z};
}
}
}
If I were you, I would use some form of unique identifier to allow me to access the data on each combination -- e.g. build a hash of the form $difference->{<protein_id>}{<lipid_id>} = <difference>.