Alternate version without intermediate parse tree, just building the C code directly.

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1139915

use strict; # recursive descent parser using /\G/gc and C generator
use warnings;

my $had = $_ = @ARGV ? "@ARGV" : '.not.foo(1,bar(2)+1,3).and.baz(4,5)'
+;
my $want = '! foo[2][bar[1]][0] && baz[4][3]';

my $answer = expr();
/\G\s* \z /gcx or error(); # verify complete parse

print "had  $had\nwant $want\ngot  $answer\n";

sub expr # left associative => term (.and. term)*
  {
  my $left = term();
  $left = "(($left) && (" . term() . '))' while /\G\s* \.and\. /gcx;
  return $left;
  }

sub term # left associative => item ([+] item)*
  {
  my $left = item();
  $left = "(($left)+(" . item() . '))' while /\G\s* \+ /gcx;
  return $left;
  }

sub list
  {
  my $left = '[(' . expr() . ')-1]';
  $left = '[(' . expr() . ")-1]$left"  while /\G\s* , /gcx;
  return $left;
  }

sub item # number, .not. minus, array, or (expr)
  {
  /\G\s* (\d+) /gcx and return $1;
  /\G\s* \.not\. /gcx and return '!(' . item() . ')';
  /\G\s* (\w+) \s* \( /gcx and do{ # array
    my $arr = $1;
    my $value = list();
    /\G\s* \) /gcx or error();
    return $arr . $value;
    };
  /\G\s* \( /gcx and # parens
    do{ my $value = expr(); /\G\s* \) /gcx or error(); return $value }
+;
  error();
  }

sub error { die s/\G/ SYNTAX ERROR->/r, "\n" }
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