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

Interface ReactionBuilder.StaticReactantStep

All Known Implementing Classes:

ReactionBuilder.StaticBuilder

Enclosing class:

ReactionBuilder

public static interface ReactionBuilder.StaticReactantStep

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.
ReactionBuilder.IrreversibleReactionStep	irreversible()
ReactionBuilder.ParameterStep	kineticLaw(String expression)
ReactionBuilder.MichaelisMentenReactionStep	michaelisMenten()
ReactionBuilder.ReversibleReactionStep	reversible() Reversible reactions where the substrates form products, and products can also from substrates.

Method Detail

addSubstrate

ReactionBuilder.StaticReactantStep addSubstrate(ChemicalEntity chemicalEntity)

addSubstrate

ReactionBuilder.StaticReactantStep addSubstrate(ChemicalEntity chemicalEntity,
                                                CellTopology topology)

addSubstrate

ReactionBuilder.StaticReactantStep addSubstrate(ChemicalEntity chemicalEntity,
                                                double stoichiometricNumber)

addSubstrate

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

addProduct

ReactionBuilder.StaticReactantStep addProduct(ChemicalEntity chemicalEntity)

addProduct

ReactionBuilder.StaticReactantStep addProduct(ChemicalEntity chemicalEntity,
                                              CellTopology topology)

addProduct

ReactionBuilder.StaticReactantStep addProduct(ChemicalEntity chemicalEntity,
                                              double stoichiometricNumber)

addProduct

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

addCatalyst

ReactionBuilder.StaticReactantStep addCatalyst(ChemicalEntity chemicalEntity)

addCatalyst

ReactionBuilder.StaticReactantStep addCatalyst(ChemicalEntity chemicalEntity,
                                               CellTopology topology)

reversible

ReactionBuilder.ReversibleReactionStep reversible()

Reversible reactions where the substrates form products, and products can also from substrates.

  A <-> B

The corresponding rate law is as follows:

  v = kfwd * cA - kbwd * cB

where v is the velocity of the reaction, kfwd is any ForwardsRateConstant, kbwd is any BackwardsRateConstant, cA is the concentration of the substrate, and cB is the concentration of the product.

Returns:

reversible reaction step

irreversible

ReactionBuilder.IrreversibleReactionStep irreversible()

complexBuilding

ReactionBuilder.ComplexBuildingReactionStep complexBuilding()

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).

Returns:

complex building reaction step

michaelisMenten

ReactionBuilder.MichaelisMentenReactionStep michaelisMenten()

kineticLaw

ReactionBuilder.ParameterStep kineticLaw(String expression)