BTW I hate java...
The actual java code I'm using is:

for (j = 0; j < split_compounds_2.length; j++)
{
//System.out.println(split_compounds_2[j] + "\n");
//regular_expression = "(\\b" + split_compounds_2[j].trim() + "\\b\\W?
+)";
//(?:\W|^)\Q$term\E(?:(?=\W)|\z)
regular_expression = "(?:\\W|^)\\b"+ split_compounds_2[j].trim() + "\\
+b\\W?(?:(?=\\W?))";
System.out.println(regular_expression + "\n");
new_reaction_2 = new_reaction_2.replaceAll(regular_expression , " [" +
+ compound_id[0] + "] ");
}
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