affectors
Class PhosphorylationA_ICAff

java.lang.Object
  affectors.Affector
      affectors.PhosphorylationA_ICAff

All Implemented Interfaces:

java.lang.Cloneable

public class PhosphorylationA_ICAff

extends Affector

This is one half of an affector that phosphorylates a single node. Use this affector in the unphosphorylated species. Use the B version in the product species. For either membrane-bound or cytoplasmic kinases, as long as target is cytoplasmic.

Formula
dSUBSTRATE/dt = -Pmax * SUBSTRATE * (KINASE^nu / (K_KINASE^nu + KINASE^nu))

Parameters

Substrate [SUBSTRATE]	The unphosphorylated Node
Kinase [KINASE]	The kinase Node.
Half-max activation [K_KINASE_SUBSTRATE]	The concentration of kinase at which it phosphorylates at half its maximum rate.
Cooperativity [nu_KINASE_SUBSTRATE]	The non-linearity in kinase activity as kinase concentration increases.
Max reaction rate [P_KINASE]	The maximum reaction rate.

Usage
&SUBSTRATE

&PhosphorylationA_ICAff SUBSTRATE KINASE K_KINASE_SUBSTRATE nu_KINASE_SUBSTRATE P_KINASE

&endSUBSTRATE

@see PhosphorylationB_ICAff
@see DephosphorylationB_ICAff

Field Summary

Fields inherited from class affectors.Affector

ADesc, affectorType, CC, CERTIFICATION, CONVERSION, copyNumber, DEGRADATION, FF, firstFreeParam, GG, GUI_CAPABLE, HH, KK, MATHTYPE, NDesc, PDesc, PRODUCTION, RETURNS_DERIV, RETURNS_PARTIALS, TERMTYPE, TT, Type, UNSPECIFIED

Constructor Summary

PhosphorylationA_ICAff()

Method Summary

float	getNCValue(Node which_node)
float	getValue(Node which_node)
protected void	setLabelsAndTypes()
void	setParameterNumbers(int[] param_nums)

Methods inherited from class affectors.Affector

addDefaultParam, Chi, clearStatic, copy_, copy, doesContainTarget, findOrCreateParam, findParam, fixNodes, getNodes, getNumNodes, getNumParameters, getOtherSide, getParameter, getParameter, getParamName, getParamPos, getParamValue, getParamValue, getParamVariationMode, init, isLinearInTarget, Phi, Psi, setContainsTarget, setDescriptions, setParameter, setParamRange, setParamRange, setParamValue, setParamValue, setSide, setSided

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PhosphorylationA_ICAff

public PhosphorylationA_ICAff()

Method Detail

setLabelsAndTypes

protected void setLabelsAndTypes()

Specified by:

setLabelsAndTypes in class Affector

setParameterNumbers

public void setParameterNumbers(int[] param_nums)

Specified by:

setParameterNumbers in class Affector

getValue

public float getValue(Node which_node)

Overrides:

getValue in class Affector

getNCValue

public float getNCValue(Node which_node)

Overrides:

getNCValue in class Affector