If what you need is to build (synthesize) a Petri Net from a digital logic (a circuit?), you should take a look to the workcraft tool (www.workcraft.org).

If not, please clarify your question

Thank you, Hernán Ponce de León! I will give this tool a try.

What I need is the following - I know how to go from a Moore-type finite state machine graph to a real circuit using for example D-type flip-flops. I can implement this in FPGA. Now I want to get acquainted with a structural approach to do the same with Petri nets. It seems to me not so easy because we don't have a well known 0-state, but it should be feasible.

I found a book: "FSM-based Digital Design using Verilog HDL " by Peter Minns and Ian Elliott. Chapter 10/p.321 includes guidelines for practical implementation of Petri Nets.