[gmx-users] perl script for g_hbond

[leila karami]

Dear Justin

thank you very much.

what I used as HB.pl exactly is as follows:

is there problem in that?

#!/usr/bin/perl
#
# plot_hbmap.pl - plot the probability of finding a particular hydrogen bond
# based on several input files:
#   1. coordinate file (for atom naming) - MUST be a .pdb file with NO CHAIN
IDENTIFIERS
#   2. hbmap.xpm
#   3. hbond.ndx (modified to contain only the atom numbers in the
[hbonds...]
section, nothing else)
#
use strict;
unless(@ARGV) {
     die "Usage: perl $0 -s structure.pdb -map hbmap.xpm -index
hbond.ndx\n";
}
# define input hash
my %args = @ARGV;
# input variables
my $map_in;
my $struct;
my $ndx;
if (exists($args{"-map"})) {
     $map_in = $args{"-map"};
} else {
     die "No -map specified!\n";
}
if (exists($args{"-s"})) {
     $struct = $args{"-s"};
} else {
     die "No -s specified!\n";
}
if (exists($args{"-index"})) {
     $ndx = $args{"-index"};
} else {
     die "No -index specified!\n";
}
# open the input
open(MAP, "<$map_in") || die "Cannot open input map file!\n";
my @map = <MAP>;
close(MAP);
open(STRUCT, "<$struct") || die "Cannot open input coordinate file!\n";
my @coord = <STRUCT>;
close(STRUCT);
open(NDX, "<$ndx") || die "Cannot open input index file!\n";
my @index = <NDX>;
close(NDX);
# determine number of HB indices and frames
my $nres = 0;
my $nframes = 0;
for (my $i=0; $i<scalar(@map); $i++) {
     if ($map[$i] =~ /static char/) {
         my $res_line = $map[$i+1];
         my @info = split(" ", $res_line);
         $nframes = $info[0];
         my @nframes = split('', $nframes);
         shift(@nframes);    # get rid of the "
         $nframes = join('', @nframes);
         $nres = $info[1];
     }
}
print "Processing the map file...\n";
print "There are $nres HB indices.\n";
print "There are $nframes frames.\n";
# initialize hashes for later output writing
# counter $a holds the HB index from hbond.ndx
my %hbonds;
for (my $a=0; $a<$nres; $a++) {
     $hbonds{$a+1} = 0;
}
# donor/acceptor hashes for bookkeeping purposes
my %donors;
for (my $b=1; $b<=$nres; $b++) {
     $donors{$b} = 0;
}
my %acceptors;
for (my $c=1; $c<=$nres; $c++) {
     $acceptors{$c} = 0;
}
# clean up the output - up to 18 lines of comments, etc.
splice(@map, 0, 18);
# remove any "x-axis" or "y-axis" lines
for (my $n=0; $n<scalar(@map); $n++) {
     if (($map[$n] =~ /x-axis/) || ($map[$n] =~ /y-axis/)) {
             shift(@map);
             $n--;
     }
}
# There should now be $nres lines left in the file
# The HB map for the last index is written first (top-down in .xpm file)
#   * Element 0 is index $nres, element 1 is $nres-1, etc.
for (my $i=$nres; $i>=1; $i--) {
     # There will be $nframes+2 elements in @line (extra two are " at
beginning
     # and end of the line)
     # Establish a conversion factor and split the input lines
     my $j = $nres - $i;
     my @line = split('', $map[$j]);
     # for each index, write to hash
     for (my $k=1; $k<=($nframes+1); $k++) {
         if ($line[$k] =~ /o/) {
             $hbonds{$i}++;
         }
     }
}
print "Processing the index file...\n";
# Open up the index file and work with it
for (my $n=0; $n<$nres; $n++) {
     my @line = split(" ", $index[$n]);
     $donors{$n+1} = $line[0];
     $acceptors{$n+1} = $line[2];
}

# some arrays for donor and acceptor atom names
my @donor_names;
my @donor_resn;
my @acceptor_names;
my @acceptor_resn;
# Open up the structure file and work with it
print "Processing coordinate file...\n";
foreach $_ (@coord) {
     my @line = split(" ", $_);
     my $natom = $line[1];
     my $name = $line[2];
     my $resn = $line[3];
     my $resnum = $line[4];
     if ($line[0] =~ /ATOM/) {
         unless ($resn =~ /SOL/) {
             for (my $z=1; $z<=$nres; $z++) {
                 if ($donors{$z} == $natom) {
                     $donor_names[$z] = $name;
                     $donor_resn[$z] = join('', $resn, $resnum);
                 } elsif ($acceptors{$z} == $natom) {
                     $acceptor_names[$z] = $name;
                     $acceptor_resn[$z] = join('', $resn, $resnum);
                 }
             }
         }
     }
}
# open a single output file for writing
open(OUT, ">>summary_HBmap.dat") || die "Cannot open output file!\n";
printf(OUT "%10s\t%10s\t%10s\t%10s\%10s\n", "#    Donor", " ", "Acceptor", "
",
"% Exist.");
for (my $o=1; $o<=$nres; $o++) {
     printf(OUT "%10s\t%10s\t%10s\t%10s\t%10.3f\n", $donor_resn[$o],
$donor_names[$o], $acceptor_resn[$o], $acceptor_names[$o],
(($hbonds{$o}/$nframes)*100));
}
close(OUT);
exit;


-- 

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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