affectors
Class PhosphorylateA_Aff

java.lang.Object
  affectors.Affector
      affectors.PhosphorylateA_Aff

All Implemented Interfaces:

java.lang.Cloneable

public class PhosphorylateA_Aff

extends Affector

This is one half of an affector that phosphorylates a single node based on a kinase activity. Use this affector in the unphosphorylated species. Use PhosphorylateB_Aff in the product (phosphorylated) species. For cytoplasmic proteins.

Formula
dNODE/dt = -PMax * NODE Phi(KINASE,K_kinase,nu_kinase)

Parameters

Node [NODE]	The unphosphorylated Node
Kinase [KINASE]	The kinase Node
Pmax [Pmax]	Maximal rate of phosporylation.
k_kinase [K_Kinase]	Concentration of kinase where activity is half maximal.
nu_kinase [nu_Kinase]	Apparent cooperativity of kinase activity.

Usage
&Node

&PhosphorylateA_Aff Node Kinase Pmax k_kinase nu_kinase

&endNode

See Also:

PhosphorylateB_Aff

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

PhosphorylateA_Aff()

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

PhosphorylateA_Aff

public PhosphorylateA_Aff()

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