File Coverage

blib/lib/Bio/Water.pm

Criterion	Covered	Total	%
statement	12	64	18.7
branch	0	12	0.0
condition	0	6	0.0
subroutine	4	6	66.6
pod	0	2	0.0
total	16	90	17.7

package Bio::Water;

use 5.012003;
use strict;
use warnings;

require Exporter;

#Intially the module Named as Water now its moved to Bio::Water

our @ISA = qw(Exporter);

our %EXPORT_TAGS = ( 'all' => [ qw(

) ] );

our @EXPORT_OK = ( @{ $EXPORT_TAGS{'all'} } );

our @EXPORT = qw(wbridge);

our $VERSION = '0.02';

sub wbridge{
    my ($v,$file,$dstart,$dend)=@_;
chomp($file);
chomp($dstart);
chomp($dend);
my @h=();
my @tmp=();
my @result=();
open(RD,"$file") or die "Cannot open the file";
while(){
push(@h,$_),if($_=~/^HETATM.*HOH/);
}
my $len=$#h;
for(my $i=0;$i<$len;$i++){
    my $flag=0;
    my @tmp=();
    my $val='';
	my $tmp1=$h[$i];
	for(my $j=0;$j<$len;$j++){
		my $di=calc($tmp1,$h[$j]);
		if($di >=$dstart && $di <=$dend){if($flag==0){push(@tmp,$h[$i]);delete $h[$i];$flag++;}else{
		push(@tmp,$h[$j]);delete $h[$j];
			}
		}
	}
for(my $k=0;$k
	for(my $j=0;$j
		my $di=calc($tmp[$k],$h[$j]);
        if($di >=$dstart && $di <=$dend){
		push(@tmp,$h[$j]);delete $h[$j];
		}
	}
}
foreach my $dd (@tmp){
	$val.=substr($dd,21,5).",";$val=~s/\s//g;
}
chop $val;
#print($val."\n")if($val);
push(@result,$val."\n")if($val);
}
return @result;
}
sub calc{
       no warnings;
       my ($tmpv,$hv)=@_;
	   my $x1=substr($tmpv,30,8);$x1=~s/\s//g;
       my $x2=substr($hv,30,8);$x2=~s/\s+//;
       my $y1=substr($tmpv,38,8);$y1=~s/\s+//;
       my $y2=substr($hv,38,8);$y2=~s/\s+//;
       my $z1=substr($tmpv,46,8);$z1=~s/\s+//;
       my $z2=substr($hv,46,8);$z2=~s/\s+//;
       my $dis=sqrt((($x2-$x1)**2)+(($y2-$y1)**2)+(($z2-$z1)**2));
       return $dis;
}


1;
__END__