Is it possible to have two sets of labels for numbering compounds throughout the document? Currently I'm using chemnum to make labels like 1, 2, 3a and so on. I want to introduce a new sequence of numbers, say, TS1, TS2... The only idea I have is to reset the counter right before I introduce new labels like this:
\documentclass[b5paper,12pt]{article}
\usepackage{chemnum}
\cmpdinit[init-sub = true]{1,2,3.{a,b}}
\newcommand*{\cmpdTS}[1]{\cmpd[cmpd-prefix=\bfseries{TS},cmpd-space={}]{#1}}
\begin{document}
Here are two compounds: \cmpd{1} and \cmpd{2}.
\cmpdreset
Here are two transition states: \cmpdTS{TS1.a} and \cmpdTS{TS2}.
Which of these two transition states is involved in transformation of \cmpd{1} to \cmpd{2}?
What about \cmpd{3.a}? It is formed from \cmpd{2} via \cmpdTS{TS3.a}.
\end{document}
But it's a bad idea because in the output I get: "What about 3a? It is formed from 2 via TS4a." instead of: "What about 3a? It is formed from 2 via TS3a." because of the resetting the counter.

\cmpdinit. Change it to\cmpdinit[init-sub = true]{1,2,3.{a,b}}. – cgnieder Sep 17 '12 at 20:03