The nupack package in its latest version (3.2.2) has added
multi-tube design capabilities. This feature allows the user to design a reaction path. To write a multi-tube script, the user needs to determine the on-target and off-target complexes. In the nupack script, the on-target complex codes can be easily written while the off-target code cannot be easily written. I studied software manual several times, but I could not find out the principle behind the writing off-target code. Can anyone help me write the off-target code?
An example: off-target code are shown in bold letters.
tube Step__0 = C X B A
Step__0.C.conc[M] = 1e-08
Step__0.X.conc[M] = 1e-08
Step__0.B.conc[M] = 1e-08
Step__0.A.conc[M] = 1e-08
Step__0.offtargets = {maxsize = 2} - {X__A, I_s B_s}
tube Step__1 = X__A
Step__1.X__A.conc[M] = 1e-08
Step__1.offtargets = {maxsize = 2} + {X, A}
tube Step__2 = X__A__B
Step__2.X__A__B.conc[M] = 1e-08
Step__2.offtargets = {maxsize = 2} + {B, X__A}
tube Step__3a = X__A__B__C
Step__3a.X__A__B__C.conc[M] = 1e-08
Step__3a.offtargets = {maxsize = 2} + {C, X__A__B}
tube Step__3b = X A__B__C
Step__3b.X.conc[M] = 1e-08
Step__3b.A__B__C.conc[M] = 1e-08
Step__3b.offtargets = {maxsize = 2} + {X__A__B__C}