Thanks @Darren, will the code look like this? and also i want the output to be printed for respective files as different files in different directory

my $dir = '/path/to/dir';

# read only pd files:

opendir DIR, $dir or die "read dir $dir - $!";

my @pdb_files = grep /\.pdb/, readdir DIR;


closedir DIR;

foreach my $file (@pdb_files)

{

open( FH,"$dir\\$file")

while(<FH>) 

{

$output_from_my_precompiled_tool = `/path/to/my/tool $file`;

}
close(FH);

}
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Well, no. Probably not.

I'm not exactly clear whether you want to pass each entire file to your external tool, or whether you want to open each file and then pass it line by line. I guess probably the former. If that's the case, then perhaps this example will help.

$ echo 'some text' > 1.pdb
$ echo 'some more text' > 2.pdb
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Lets say for example your external tool is /bin/cat, and you want to cat each file and capture the output.

$ cat foo.pl
#!/usr/bin/perl
use strict;
use warnings;

my $dir = '.';
my $cat = '/bin/cat';
opendir DIR, $dir or die "Cannot open directory $dir:$!\n";
my @pdb_files = grep { -f $_ && $_ =~ /\.pdb$/ } readdir DIR;
closedir DIR;

for my $file (@pdb_files) {
    my $content = `$cat "$dir/$file"`;
    chomp $content;
    print "Content of $file is $content\n";

}
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$ perl foo.pl
Content of 1.pdb is some text
Content of 2.pdb is some more text
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That should be enough to get you going?

Sorry @Darren the program doesn't seems to work because its asking for two input files first input file is the exterior script(written already)and the second input is the PDB files. So,i think incorporating a function which calls the script file first followed by the PDB files will help. So, could you please tell me how to do this?

will the code look like this? after embedding the external script ?

#!/usr/bin/perl

use strict;
use warnings;


my $dir = '.';

#for embeding the mcsearch percompile version
my $mcsearch = '/bin/mcsearch';

#to read the PDB files from the directory
opendir DIR, $dir or die "Cannot open directory $dir:$!\n";

my @pdb_files = grep { -f $_ && $_ =~ /\.pdb$/ } readdir DIR;

closedir DIR;

print "Enter the script file";
$a=<>;

open(IN,$a) or die;


#giving each file as a input to mcsearch
for my $file (@pdb_files)

 {
while(<>)

{
    my $content = `$mcsearch "$dir/$file"`;

    chomp $content;

    print "Content of $file is $content\n";

}
}
[download]

http://www.major.iric.ca/MajorLabEn/MC-Tools_files/MC-Annotate.zip here is the tool, i want to embed this tool and give the inputs to the tool, the web version of this tool looks like http://www.major.iric.ca/MC-Search/

So looking at the web version i was trying to provide two inputs