.. _class: RSD_sim Class ============= RSD_sim is a Python class that gives access to all of the simulator's built-in functions found :ref:`here `. To have access to the features of the class you must first instantiate an object of the class, directions for this can be found :ref:`here `. This page gives info about the input of the object instantiation, and the initiaizations made for the class. Class Object ------------ __init__(*domains=5*) **Parameters:** domains: *int*, *if NONE, default=5* The highest input or output index of the species indicated in *molecular_species()*. For example, if G{5,9} is specified, *domains* needs to be 9 or greater. This can be higher than the highest index in the system but it cannot be lower than the highest index in the system. .. _initials_defaults: Initializations --------------- All DNA template concentrations and initial conditions are initialized at 0. Rate Constants: self.ktxnO = 0.013 (1/s) self.ktxnG = 0.013 (1/s) self.ktxnTG = 0.013 (1/s) self.ktxnF = 0.013 (1/s) self.ktxnAG = 0.013 (1/s) self.ktxnCG = 0.013 (1/s) self.leak = 0.03 self.krz = 0.00417 (1/s) self.krsd = 1e3/1e9 (1/nM-s) self.krev = 270/1e9 (1/nM-s), 0 for inputs self.krep = 1e4/1e9 (1/nM-s) self.krepr = 0 (1/s) self.kth = 1e5/1e9 (1/nM-s) self.krzTG = 0.00417 (1/s) self.krsdF = 1e3/1e9 (1/nM-s) self.krevF = 1e3/1e9 (1/nM-s) self.krzA = 0.00417 (1/s) self.krsdA = 1e3/1e9 (1/nM-s) self.leakA = 0.06 self.krzCG = 0.00417 (1/s) self.krsdCGa = 1e5/1e9 (1/nM-s) self.krsdCGb = 1e5/1e9 (1/nM-s) self.krevCG = 1 (1/s) self.kssdO = 0 (1/s) self.kssdF = 0 (1/s) self.kdsduG = 0 (1/s) self.kdsdG = 0 (1/s) self.kdsdGO = 0 (1/s) self.kdsdGF = 0 (1/s) self.kdsduTG = 0 (1/s) self.kdsdTG = 0 (1/s) self.kdsduAG = 0 (1/s) self.kdsdAG = 0 (1/s) self.kdsdAGOa = 0 (1/s) self.kdsdAGOb = 0 (1/s) self.kdsdAGFb = 0 (1/s) self.kdsduCG = 0 (1/s) self.kdsdCG = 0 (1/s) self.kdsdCGOa = 0 (1/s) self.kdsdCGOb = 0 (1/s) self.kdrd = 0 (1/s) self.khybO = 1e6/1e9 (1/nM-s) self.khybR = 1e6/1e9 (1/nM-s)