Table 7.

Adding molecules to a term of the DSD compiler. We start by adding molecules D to an empty compiler term (ø,ø,ø,ø), written D ⊕ (ø,ø,ø,ø). The result is a compiler term containing the set of all strands S, segments G and reactions R that are generated from the initial molecules D. The rules assume that all molecules D and segments G are in standard form.

rule	conditions	before	def	after
CR		{θ1, … , θN} ⊕T	≜	θ1⊕ … ⊕ θN ⊕T
CU		(G, r,<S>, G′) ⊕ T	≜	<S>⊕G′ ⊕ T
CB		(<S>, G, r, G′) ⊕ T	≜	G′ ⊕ T
CN		(new N D) ⊕ (N, S, G, R)	≜	D ⊕ ({N} ∪ N, S, G, R)
CP		(D1 | D2) ⊕ T	≜	D1 ⊕ D2 ⊕ T
CSZ	<S> ∈ S	<S>⊕T	≜	T
CGZ	G ∈ G	G ⊕ T	≜	T
CS		<S>⊕ (N, S, G, R)	≜	R′ ⊕ (N,{<S>}∪ S, G, R ∪ R′)
CG		G ⊕ (N, S, G, R)	≜	R′ ⊕ (N, S, {G} ∪ G, R ∪ R′)