affectors
Class DimerizeAllMembrane_AAff

java.lang.Object
  affectors.Affector
      affectors.DimerizeAllMembrane_AAff

All Implemented Interfaces:

java.lang.Cloneable

Direct Known Subclasses:

HeterodimerizeA_EC_XAff

public class DimerizeAllMembrane_AAff

extends Affector

This is one half of a dimerization where the ligand and receptor can bind within the same membrane as well as across different faces. All Nodes, including the dimer, must be membrane-bound. Use the A version of this affector for the undimerized species. Use the B version for the dimer. The node_scale (max) for each of the singleton proteins is the scaling factor for the >other< singleton.

Formula
dSINGLE_NODE1/dt = - r * max * SINGLE_NODE1 * SINGLE_NODE2

Parameters

Membrane Node [SINGLE_NODE1]	One undimerized Node
Cytoplasmic Node [SINGLE_NODE2]	The other undimerized Node
Dimerization rate [r_DIMER]	The rate of the dimerization reaction.
Maximum Cyto [max]	The maximum relative concentration of the >other< undimerized Node.

Usage
&SINGLE_NODE

&DimerizeAllMembrane_AAff SINGLE_NODE1 SINGLE_NODE2 r_DIMER max

&endSINGLE_NODE

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

DimerizeAllMembrane_AAff()

Method Summary

void	fixNodes(Cell cell, java.lang.String[] node_names) Overridden because this affector uses the same node in two places.
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, 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

DimerizeAllMembrane_AAff

public DimerizeAllMembrane_AAff()

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

fixNodes

public void fixNodes(Cell cell,
                     java.lang.String[] node_names)
              throws java.lang.Exception

Overridden because this affector uses the same node in two places.

Overrides:

fixNodes in class Affector

Throws:

java.lang.Exception

getValue

public float getValue(Node which_node)

Overrides:

getValue in class Affector

getNCValue

public float getNCValue(Node which_node)

Overrides:

getNCValue in class Affector