bio.singa.simulation.model.modules.concentration.imlementations

Class ComplexBuildingReaction

java.lang.Object

bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule<UpdatableDeltaFunction>

bio.singa.simulation.model.modules.concentration.imlementations.ComplexBuildingReaction

All Implemented Interfaces:

UpdateModule

public class ComplexBuildingReaction
extends ConcentrationBasedModule<UpdatableDeltaFunction>

Complex building or breaking reactions are a special kind of ReversibleReaction. In this kind of reaction association or dissociation of chemical entities results in a change of section. For example when a ligand is bound to a receptor the resulting complex is associated to the membrane section the receptor is located in.
Speaking in terms of this module a bindee in the bindee topology is bound to a binder in the binder topology, resulting in a complex in the binder topology.
The speed of the reaction is guided by any ForwardsRateConstant that determines the speed of the association reaction and a BackwardsRateConstant the determines the speed of the dissociation of the complex. Complex building reactions are UpdatableSpecific and supply IndependentUpdates.

  // From: Lauffenburger, Douglas A., and Jennifer J. Linderman.
  //       Receptors: models for binding, trafficking, and signaling. Oxford University Press, 1996.
  //       Table on Page 30
  // prazosin
  ChemicalEntity ligand = new SmallMolecule.Builder("ligand")
      .name("prazosin")
      .additionalIdentifier(new ChEBIIdentifier("CHEBI:8364"))
      .build();
  // alpha-1 adrenergic receptor
  Receptor receptor = new Receptor.Builder("receptor")
      .name("alpha-1 adrenergic receptor")
      .additionalIdentifier(new UniProtIdentifier("P35348"))
      .build();
  // the forwards rate constants
  RateConstant forwardsRate = RateConstant.create(2.4e8)
      .forward().secondOrder()
      .concentrationUnit(MOLE_PER_LITRE)
      .timeUnit(MINUTE)
      .build();
  // the backwards rate constants
  RateConstant backwardsRate = RateConstant.create(0.018)
      .backward().firstOrder()
      .timeUnit(MINUTE)
      .build();
  // create and add module
  ComplexBuildingReaction reaction = ComplexBuildingReaction.inSimulation(simulation)
      .identifier("binding reaction")
      .of(ligand, forwardsRate)
      .in(OUTER)
      .by(receptor, backwardsRate)
      .to(MEMBRANE)
      .build(); 

Author:

cl

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	ComplexBuildingReaction.BindeeSectionSelection
static interface	ComplexBuildingReaction.BindeeSelection
static interface	ComplexBuildingReaction.BinderSectionSelection
static interface	ComplexBuildingReaction.BinderSelection
static interface	ComplexBuildingReaction.BuilderStep
static class	ComplexBuildingReaction.ComplexBuildingReactionBuilder

Field Summary

Fields inherited from class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

supplier

Constructor Summary

Constructors

Constructor and Description
ComplexBuildingReaction()

Method Summary

Modifier and Type	Method and Description
void	checkFeatures()
ChemicalEntity	getBindee()
CellTopology	getBindeeTopology()
ChemicalEntity	getBinder()
CellTopology	getBinderTopology()
static ModuleBuilder	getBuilder(Simulation simulation)
ComplexedChemicalEntity	getComplex()
String	getReactionString()
void	initialize()
static ComplexBuildingReaction.BindeeSelection	inSimulation(Simulation simulation)
void	setBindee(ChemicalEntity bindee)
void	setBindeeTopology(CellTopology bindeeTopology)
void	setBinder(ChemicalEntity binder)
void	setBinderTopology(CellTopology binderTopology)
void	setComplex(ComplexedChemicalEntity complex)
String	toString()

Methods inherited from class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

addDeltaFunction, addModuleToSimulation, addReferencedEntities, addReferencedEntity, calculateUpdates, deltaIsValid, determineLargestLocalError, getApplicationCondition, getDeltaCutoff, getErrorCutoff, getFeature, getFeatures, getIdentifier, getReferencedEntities, getRequiredFeatures, getScaledFeature, getScaledFeature, getScope, getSimulation, getSpecificity, getState, getSupplier, handleDelta, onCompletion, onReset, optimizeTimeStep, resetState, scaleScalableFeatures, setApplicationCondition, setDeltaCutoff, setErrorCutoff, setFeature, setIdentifier, setSimulation

Methods inherited from class java.lang.Object

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

Constructor Detail

ComplexBuildingReaction

public ComplexBuildingReaction()

Method Detail

inSimulation

public static ComplexBuildingReaction.BindeeSelection inSimulation(Simulation simulation)

initialize

public void initialize()

getComplex

public ComplexedChemicalEntity getComplex()

setComplex

public void setComplex(ComplexedChemicalEntity complex)

getBinder

public ChemicalEntity getBinder()

setBinder

public void setBinder(ChemicalEntity binder)

getBinderTopology

public CellTopology getBinderTopology()

setBinderTopology

public void setBinderTopology(CellTopology binderTopology)

getBindee

public ChemicalEntity getBindee()

setBindee

public void setBindee(ChemicalEntity bindee)

getBindeeTopology

public CellTopology getBindeeTopology()

setBindeeTopology

public void setBindeeTopology(CellTopology bindeeTopology)

getReactionString

public String getReactionString()

checkFeatures

public void checkFeatures()

Specified by:

checkFeatures in interface UpdateModule

Overrides:

checkFeatures in class ConcentrationBasedModule<UpdatableDeltaFunction>

getBuilder

public static ModuleBuilder getBuilder(Simulation simulation)

toString

public String toString()

Overrides:

toString in class ConcentrationBasedModule<UpdatableDeltaFunction>