package affectors; import main.Globals; import main.Node; /** This is the third half of a heterodimerization between a membrane-bound and a cytoplasmic protein, leading to a cytoplasmic complex. Use this affector in the dimerized species. Use the A and B versions in the undimerized ones. Be careful to put the membrane and cytoplasmic species in the right order in the initializer. The node_scale you use for the dimer should be the scale for the undimerized protein least similar to the dimer (i.e. for ligand/receptor binding, you might use ligand0).

Formula
dDIMER/dt = r * max * MEMBRANE_NODE * CYTO_NODE

Parameters
Membrane Node [MEMBRANE_NODE] The undimerized Node that is on the membrane
Cytoplasmic Node [CYTO_NODE] The undimerized Node that is in the cytoplasm
Dimerization rate [r_DIMER] The rate of the dimerization reaction.
Maximum Cyto [max] The maximum relative concentration of the undimerized Node less similar to the dimer.

Usage
&DIMER

&DimerizeMemCyto_CAff MEMBRANE_NODE CYTO_NODE r_DIMER max
&endDIMER */ public class DimerizeMemCyto_CAff extends Affector { /** The rate of the dimerization reaction. */ int kParam; /** The scaling factor of the other undimerized node in this reaction (i.e. max for second input node). */ int nodeScaleParam; static final String desc = "Dimerize membrane-bound & cytoplasmic node; version C for dimer"; static final String [] nodeDescriptions = {"Membrane-bound node", "Cytoplasmic node"}; static final String [] paramDescriptions = {"Second-order reaction rate constant", "Scale factor (max value) for least-similar node"}; static final int [] whichSides = {-1, -1}; public DimerizeMemCyto_CAff() {} protected void setLabelsAndTypes() { setDescriptions(this.desc, nodeDescriptions, paramDescriptions); setSided(true, whichSides); 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) { kParam = param_nums[0]; nodeScaleParam = param_nums[1]; } public float getValue(Node which_node) { return Globals.characteristicTime * params[kParam] * params[nodeScaleParam] * Nodes[0].getIntegrationValue() * Nodes[1].getIntegrationValue(); } }