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

Class Reactant

java.lang.Object

bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants.Reactant

public class Reactant
extends Object

A Reactant encapsulates a ChemicalEntity for the use in Reactions. ReactantRole.CATALYTIC reactants influence the velocity (reaction rate), but are not consumed or produced. ReactantRole.SUBSTRATEs or ReactantRole.PRODUCT are consumed or produced during the reaction. A stoichiometric Reactant can be rate determining and has an associated stoichiometric number and/or reaction order. In Reactions that are not elementary reactions, the reaction order is used to determine the velocity of a reaction. In elementary reactions the stoichiometric number is used to this end.

Constructor Summary

Constructors

Constructor and Description
Reactant(ChemicalEntity entity, ReactantRole role) Creates a new reactant.
Reactant(ChemicalEntity entity, ReactantRole role, CellTopology preferredTopology)
Reactant(ChemicalEntity chemicalEntity, ReactantRole role, CellTopology topology, double stoichiometricNumber)
Reactant(ChemicalEntity entity, ReactantRole role, CellTopology preferredTopology, double stoichiometricNumber, double reactionOrder)
Reactant(ChemicalEntity entity, ReactantRole role, CellTopology preferredTopology, javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> preferredConcentrationUnit)
Reactant(ChemicalEntity entity, ReactantRole role, double stoichiometricNumber)
Reactant(ChemicalEntity entity, ReactantRole role, double stoichiometricNumber, double reactionOrder)
Reactant(ChemicalEntity entity, ReactantRole role, javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> preferredConcentrationUnit)

Method Summary

Modifier and Type	Method and Description
ChemicalEntity	getEntity() Gets the entity representing this reactant.
javax.measure.Unit<bio.singa.features.quantities.MolarConcentration>	getPreferredConcentrationUnit()
CellTopology	getPreferredTopology()
double	getReactionOrder() Returns the reaction order.
ReactantRole	getRole() Gets the role of this reactant.
double	getStoichiometricNumber() Returns the stoichiometric number (the number of molecules required for one reaction.).
boolean	isCatalyst()
boolean	isProduct() Returns true if this reactant is a product.
boolean	isSubstrate() Returns true if this reactant is a substrate.
void	setEntity(ChemicalEntity entity) Sets the entity representing this reactant.
void	setPreferredConcentrationUnit(javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> preferredConcentrationUnit)
void	setPreferredTopology(CellTopology preferredTopology)
void	setRole(ReactantRole role) Gets the role of this reactant.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Reactant

public Reactant(ChemicalEntity entity,
                ReactantRole role)

Creates a new reactant.

Parameters:

entity - The referenced entity.

role - The reactants role.

Reactant

public Reactant(ChemicalEntity entity,
                ReactantRole role,
                CellTopology preferredTopology)

Reactant

public Reactant(ChemicalEntity entity,
                ReactantRole role,
                CellTopology preferredTopology,
                javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> preferredConcentrationUnit)

Reactant

public Reactant(ChemicalEntity entity,
                ReactantRole role,
                double stoichiometricNumber)

Reactant

public Reactant(ChemicalEntity entity,
                ReactantRole role,
                javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> preferredConcentrationUnit)

Reactant

public Reactant(ChemicalEntity chemicalEntity,
                ReactantRole role,
                CellTopology topology,
                double stoichiometricNumber)

Reactant

public Reactant(ChemicalEntity entity,
                ReactantRole role,
                CellTopology preferredTopology,
                double stoichiometricNumber,
                double reactionOrder)

Reactant

public Reactant(ChemicalEntity entity,
                ReactantRole role,
                double stoichiometricNumber,
                double reactionOrder)

Method Detail

getEntity

public ChemicalEntity getEntity()

Gets the entity representing this reactant.

Returns:

The entity representing this reactant.

setEntity

public void setEntity(ChemicalEntity entity)

Sets the entity representing this reactant.

Parameters:

entity - The entity representing this reactant.

getRole

public ReactantRole getRole()

Gets the role of this reactant.

Returns:

The role of this reactant.

setRole

public void setRole(ReactantRole role)

Gets the role of this reactant.

Parameters:

role - The role of this reactant.

getPreferredTopology

public CellTopology getPreferredTopology()

setPreferredTopology

public void setPreferredTopology(CellTopology preferredTopology)

getPreferredConcentrationUnit

public javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> getPreferredConcentrationUnit()

setPreferredConcentrationUnit

public void setPreferredConcentrationUnit(javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> preferredConcentrationUnit)

getStoichiometricNumber

public double getStoichiometricNumber()

Returns the stoichiometric number (the number of molecules required for one reaction.).

Returns:

the stoichiometric number.

getReactionOrder

public double getReactionOrder()

Returns the reaction order.

Returns:

The reaction order.

isSubstrate

public boolean isSubstrate()

Returns true if this reactant is a substrate.

Returns:

true if this reactant is a substrate.

isProduct

public boolean isProduct()

Returns true if this reactant is a product.

Returns:

true if this reactant is a product.

isCatalyst

public boolean isCatalyst()

toString

public String toString()

Overrides:

toString in class Object