package affectors; import main.Node; import main.Globals; /** This is one half of an affector that cleaves a single node into two other nodes under the influence of an inhibitor. Use this affector in each of the product species. Use the A version in the uncleaved species. This one is opposite to the Cleavage_IC affectors in that the regulator inhibits cleavage rather than activates it. Otherwise they are identical.

Formula
dNODEX/dt = CMax * SUBSTRATE * ( 1 - (INHIBITOR ^ nu) / ( K ^ nu + INHIBITOR ^ nu) )

Parameters
Substrate [SUBSTRATE] The uncleaved Node
Inhibitor [INHIBITOR] The regulator Node which is inhibiting cleavage
Kappa [K_INHIBITOR_SUBSTRATE] The level of the inhibitor at which it acts half-maximally.
nu [nu_INHIBITOR_SUBSTRATE] Cooperativity of the inhibitory term.
CMax [CMax_SUBSTRATE] Maximal rate of cleavage.

Usage
&CLEAVED_NODE

&Cleavage2B_IC SUBSTRATE INHIBITOR K_INHIBITOR_SUBSTRATE nu_INHIBITOR_SUBSTRATE C_SUBSTRATE
&endCLEAVED_NODE */ public class Cleavage2B_ICAff extends Affector { /** The level of inhibitor at which the cleavage reaction proceeds half-maximally. */ int kappaParam; /** The "cooperativity" exponent for the reaction. */ int nuParam; /** The maximal rate of cleavage. */ int cMaxParam; static final String desc = "Intracellular cleavage of a substrate, regulated by an inhibitor; version B for product"; static final String [] nodeDescriptions = {"Uncleaved substrate", "Inhibitor of cleavage"}; static final String [] paramDescriptions = {"Kappa: half-maximal activity of the inhibitor of cleavage", "nu: cooperativity of inhibitory term", "Cmax: maximal rate of cleavage"}; public Cleavage2B_ICAff() {} protected void setLabelsAndTypes() { setDescriptions(this.desc, nodeDescriptions, paramDescriptions); this.Type[GUI_CAPABLE] = 1; this.Type[CERTIFICATION] = Affector.RETURNS_DERIV; this.Type[MATHTYPE] = Affector.FF; this.Type[TERMTYPE] = Affector.CONVERSION; } public void setParameterNumbers(int [] param_nums) { kappaParam = param_nums[0]; nuParam = param_nums[1]; cMaxParam = param_nums[2]; } public float getValue(Node which_node) { float total_inhibitor = Nodes[1].getIntegrationValue(); float source = Nodes[0].getIntegrationValue(); float theTerm = params[cMaxParam] * source * Psi(total_inhibitor, params[kappaParam], params[nuParam]); return Globals.characteristicTime * theTerm; } }