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

Class ReactionBuilder.DynamicBuilder

java.lang.Object

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

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

All Implemented Interfaces:

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

Enclosing class:

ReactionBuilder

public static class ReactionBuilder.DynamicBuilder
extends ReactionBuilder.GeneralReactionBuilder
implements ReactionBuilder.DynamicReactantStep

Field Summary

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

reaction, simulation

Constructor Summary

Constructors

Constructor and Description
DynamicBuilder(Simulation simulation)

Method Summary

Modifier and Type	Method and Description
ReactionBuilder.DynamicReactantStep	addCatalyst(ChemicalEntity chemicalEntity)
ReactionBuilder.DynamicReactantStep	addCatalyst(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.DynamicReactantStep	addProduct(ChemicalEntity chemicalEntity)
ReactionBuilder.DynamicReactantStep	addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.DynamicReactantStep	addProduct(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.DynamicReactantStep	addProduct(ChemicalEntity chemicalEntity, double stoichiometricNumber)
ReactionBuilder.DynamicReactantStep	addProduct(DynamicChemicalEntity dynamicChemicalEntity, ComplexModification modification)
ReactionBuilder.DynamicReactantStep	addSubstrate(ChemicalEntity chemicalEntity)
ReactionBuilder.DynamicReactantStep	addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.DynamicReactantStep	addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.DynamicReactantStep	addSubstrate(ChemicalEntity chemicalEntity, double stoichiometricNumber)
ReactionBuilder.DynamicReactantStep	addSubstrate(DynamicChemicalEntity dynamicChemicalEntity)
ReactionBuilder.ComplexBuildingReactionStep	complexBuilding()
ReactionBuilder.DynamicReactantStep	targetProductToTopology(ChemicalEntity affectedEntity, CellTopology targetTopology)

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.DynamicReactantStep

irreversible, kineticLaw, michaelisMenten, reversible

Constructor Detail

DynamicBuilder

public DynamicBuilder(Simulation simulation)

Method Detail

complexBuilding

public ReactionBuilder.ComplexBuildingReactionStep complexBuilding()

Specified by:

complexBuilding in interface ReactionBuilder.DynamicReactantStep

addSubstrate

public ReactionBuilder.DynamicReactantStep addSubstrate(DynamicChemicalEntity dynamicChemicalEntity)

Specified by:

addSubstrate in interface ReactionBuilder.DynamicReactantStep

addSubstrate

public ReactionBuilder.DynamicReactantStep addSubstrate(ChemicalEntity chemicalEntity)

Specified by:

addSubstrate in interface ReactionBuilder.DynamicReactantStep

addSubstrate

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

Specified by:

addSubstrate in interface ReactionBuilder.DynamicReactantStep

addSubstrate

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

Specified by:

addSubstrate in interface ReactionBuilder.DynamicReactantStep

addSubstrate

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

Specified by:

addSubstrate in interface ReactionBuilder.DynamicReactantStep

addProduct

public ReactionBuilder.DynamicReactantStep addProduct(DynamicChemicalEntity dynamicChemicalEntity,
                                                      ComplexModification modification)

Specified by:

addProduct in interface ReactionBuilder.DynamicReactantStep

targetProductToTopology

public ReactionBuilder.DynamicReactantStep targetProductToTopology(ChemicalEntity affectedEntity,
                                                                   CellTopology targetTopology)

Specified by:

targetProductToTopology in interface ReactionBuilder.DynamicReactantStep

addProduct

public ReactionBuilder.DynamicReactantStep addProduct(ChemicalEntity chemicalEntity)

Specified by:

addProduct in interface ReactionBuilder.DynamicReactantStep

addProduct

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

Specified by:

addProduct in interface ReactionBuilder.DynamicReactantStep

addProduct

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

Specified by:

addProduct in interface ReactionBuilder.DynamicReactantStep

addProduct

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

Specified by:

addProduct in interface ReactionBuilder.DynamicReactantStep

addCatalyst

public ReactionBuilder.DynamicReactantStep addCatalyst(ChemicalEntity chemicalEntity)

Specified by:

addCatalyst in interface ReactionBuilder.DynamicReactantStep

addCatalyst

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

Specified by:

addCatalyst in interface ReactionBuilder.DynamicReactantStep