You could split using a character class containng space characters and left and right parentheses, see perlre.

$ perl -Mstrict -Mwarnings -E '
my $line = q{25 ((18 25 4) (3 12 1))};
my @nums = split m{[\s()]+}, $line;
say qq{@nums};'
25 18 25 4 3 12 1
$
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I hope this is helpful.