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

Class ReactionBuilder.StaticBuilder

java.lang.Object

bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticBuilder

All Implemented Interfaces:

ReactionBuilder.ComplexBuildingReactionStep, ReactionBuilder.FinalStep, ReactionBuilder.IrreversibleReactionStep, ReactionBuilder.MichaelisMentenReactionStep, ReactionBuilder.ParameterStep, ReactionBuilder.ReversibleReactionStep, ReactionBuilder.StaticReactantStep, ModuleBuilder

Enclosing class:

ReactionBuilder

public static class ReactionBuilder.StaticBuilder
extends ReactionBuilder.GeneralReactionBuilder
implements ReactionBuilder.StaticReactantStep

Field Summary

Fields inherited from class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

reaction, simulation

Constructor Summary

Constructors

Constructor and Description
StaticBuilder(Simulation simulation)

Method Summary

Modifier and Type	Method and Description
ReactionBuilder.StaticReactantStep	addCatalyst(ChemicalEntity chemicalEntity)
ReactionBuilder.StaticReactantStep	addCatalyst(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	addProduct(ChemicalEntity chemicalEntity)
ReactionBuilder.StaticReactantStep	addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	addProduct(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	addProduct(ChemicalEntity chemicalEntity, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	addSubstrate(ChemicalEntity chemicalEntity)
ReactionBuilder.StaticReactantStep	addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	addSubstrate(ChemicalEntity chemicalEntity, double stoichiometricNumber)
ReactionBuilder.ComplexBuildingReactionStep	complexBuilding() Complex building reactions classically require two substrates that react to build one complex.

Methods inherited from class bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.GeneralReactionBuilder

associationRate, backwardReactionRate, build, createModule, dissociationRate, forwardReactionRate, getModule, identifier, irreversible, kineticLaw, michaelisConstant, michaelisMenten, rate, referenceParameter, referenceParameter, referenceParameter, referenceParameter, referenceParameter, referenceParameter, referenceParameter, reversible, turnover

Methods inherited from class java.lang.Object

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

Methods inherited from interface bio.singa.simulation.model.modules.concentration.imlementations.reactions.ReactionBuilder.StaticReactantStep

irreversible, kineticLaw, michaelisMenten, reversible

Constructor Detail

StaticBuilder

public StaticBuilder(Simulation simulation)

Method Detail

complexBuilding

public ReactionBuilder.ComplexBuildingReactionStep complexBuilding()

Description copied from interface: ReactionBuilder.StaticReactantStep

Complex building reactions classically require two substrates that react to build one complex. The reaction rate is described by a association rate (k1 or forwards rate) and a dissociation rate (k-1 or backwards rate).

Specified by:

complexBuilding in interface ReactionBuilder.StaticReactantStep

Returns:

complex building reaction step

addSubstrate

public ReactionBuilder.StaticReactantStep addSubstrate(ChemicalEntity chemicalEntity)

Specified by:

addSubstrate in interface ReactionBuilder.StaticReactantStep

addSubstrate

public ReactionBuilder.StaticReactantStep addSubstrate(ChemicalEntity chemicalEntity,
                                                       CellTopology topology)

Specified by:

addSubstrate in interface ReactionBuilder.StaticReactantStep

addSubstrate

public ReactionBuilder.StaticReactantStep addSubstrate(ChemicalEntity chemicalEntity,
                                                       double stoichiometricNumber)

Specified by:

addSubstrate in interface ReactionBuilder.StaticReactantStep

addSubstrate

public ReactionBuilder.StaticReactantStep addSubstrate(ChemicalEntity chemicalEntity,
                                                       CellTopology topology,
                                                       double stoichiometricNumber)

Specified by:

addSubstrate in interface ReactionBuilder.StaticReactantStep

addProduct

public ReactionBuilder.StaticReactantStep addProduct(ChemicalEntity chemicalEntity)

Specified by:

addProduct in interface ReactionBuilder.StaticReactantStep

addProduct

public ReactionBuilder.StaticReactantStep addProduct(ChemicalEntity chemicalEntity,
                                                     CellTopology topology)

Specified by:

addProduct in interface ReactionBuilder.StaticReactantStep

addProduct

public ReactionBuilder.StaticReactantStep addProduct(ChemicalEntity chemicalEntity,
                                                     double stoichiometricNumber)

Specified by:

addProduct in interface ReactionBuilder.StaticReactantStep

addProduct

public ReactionBuilder.StaticReactantStep addProduct(ChemicalEntity chemicalEntity,
                                                     CellTopology topology,
                                                     double stoichiometricNumber)

Specified by:

addProduct in interface ReactionBuilder.StaticReactantStep

addCatalyst

public ReactionBuilder.StaticReactantStep addCatalyst(ChemicalEntity chemicalEntity)

Specified by:

addCatalyst in interface ReactionBuilder.StaticReactantStep

addCatalyst

public ReactionBuilder.StaticReactantStep addCatalyst(ChemicalEntity chemicalEntity,
                                                      CellTopology topology)

Specified by:

addCatalyst in interface ReactionBuilder.StaticReactantStep