I would like my output to be:

$individual[0]=
-OECHEM 658567-

1 2 0000 V2000
4 \t 5 8.7 7.655 3
2 \t 55 6 4 5
M END
$$$$

$individual1=
-OECHEM 35343-

3 6 0000 V2000
1 \t 7 6 4.6 9
2 \t 45 0 3 5
M END
$$$$

i.e. having 2 seperate regex groups (or array elements) of just everything up to M END. and then add $$$$ to the next line.

I have so far tried:

my @individual;
@individual = split (/\$\$\$\$/,$file);
[download]

The split works but doesnt include the token used to split on, i.e. i end up with

$individual[0] =
-OECHEM 658567-

1 2 0000 V2000
4 \t 5 8.7 7.655 3
2 \t 55 6 4 5
M END
> <compound id>
665765765
> <source>
db1

$individual[1] =
-OECHEM 35343-

3 6 0000 V2000
1 \t 7 6 4.6 9
2 \t 45 0 3 5
M END
> <compound id>
3546789
> <source>
db1

I tried a regex like /(.*)?M END/ig May have to do two steps to do grouping and then substitution.

Thanks.

split removes the token it matched, but since you know what it is (here: $$$$ you can simply add it again.

Instead of slurping the whole file and then slipping, you can set the input record separator accordingly:

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my @records;
{
    local $/ = '$$$$' . "\n";
    while (my $record = <DATA>) {
        my ($stripped) = split /\nM END\n/, $record, 2;
        push @records, "$stripped\nM END\n$/";
    }
}
print Dumper \@records;

__DATA__
-OECHEM 658567-

1 2 0000 V2000
4 \t 5 8.7 7.655 3
2 \t 55 6 4 5
M END
> <compound id>
665765765
> <source>
db1

$$$$
-OECHEM 35343-

3 6 0000 V2000
1 \t 7 6 4.6 9
2 \t 45 0 3 5
M END
> <compound id>
3546789
> <source>
db1

$$$$
[download]

thank you thats great - it works. Just out of interest, does __DATA__ act as an "in file" file handler? thanks