org.sigpath.datamodel
Class KineticCustom

java.lang.Object
  org.sigpath.datamodel.lset.CollectableImpl
      org.sigpath.datamodel.SigPathEntityImpl
          org.sigpath.datamodel.Kinetic
              org.sigpath.datamodel.KineticCustom

All Implemented Interfaces:

InstanceCallbacks, Collectable, SigPathEntity

public class KineticCustom
extends Kinetic

A class to define custom kinetics. Custom kinetics require rate law expressions and list of symbols used in the rate laws. Each symbol is defined with a BindingDeclaration, that specifies the name of the symbol and the unit the symbol must be provided in, for the expression to be correct. The kinetic is defined by a String formulas describing the forward and backward reaction velocities (for instance: S * VMax /(Km + S) for the forward rate, 0.0 for the backward rate), a speciesDeclaration BindingSet with species involved in the kinetic definition ( here a single species binding involved : name = "S", description= "substrate", unitType = mol/l, and two ConstantBindings : describing Vmax and Km.

See Also:

for other ways to define kinetics., for other ways to define kinetics.

Field Summary

Fields inherited from class org.sigpath.datamodel.SigPathEntityImpl

forwardReferences

Constructor Summary

KineticCustom()
Creates a new KineticCustom object.

KineticCustom(SigPathFactory spf)
Constructor used by NavigatorFactoryImpl to create a new Kinetic such as KineticCustom.

KineticCustom(SigPathFactory spf, SPDBManager dbm)

KineticCustom(SigPathFactory spf, SPDBManager dbm, String spid)

KineticCustom(SigPathFactory spf, String spid)
Constructor used by NavigatorFactoryImpl to create a new Kinetic such as KineticCustom.

Method Summary

BindingSet	generateDefaultChemicalBindings(KineticInteraction kInt) No default bindings definition for custom kinetic.
Formula	getBackwardVelocity(KineticInteraction kInt) Get the product formation rate for a specific interaction.
BindingSet	getChemicalBindingsDeclaration() Returns the chemical declarations.
BindingSet	getConstantBindingsDeclaration() Returns the constant declaration.
BindingSet	getConstantsDeclaration()
String	getFormulaBackward()
String	getFormulaForward()
Set	getForwardReferences() Returns the set of direct forward references of this entity.
Formula	getForwardVelocity(KineticInteraction kInt) Get the product destruction rate for a specific interaction.
Unit	getRefUnit() This is the unit used to express forward and backward velocities.
BindingSet	getSpeciesDeclaration()
boolean	isFullyQuantified(BindingSet bindings) Needed to enable autovalidation by the instance.
static boolean	isFullyQuantified(KineticCustom kinetic, BindingSet bindings) Returns the binding needed for a kinetic interaction using a custom kinetic to be included in a model.
void	jdoPreDelete()
void	setConstantAndSpecies(KineticInteraction kInt, BindingSet bindings)
void	setConstantsDeclaration(BindingSet constantsDeclaration)
void	setFormulaBackward(String formulaBackward)
void	setFormulaForward(String formulaForward)
void	setKineticInteraction(KineticInteraction interaction) Ignored by this implementation.
void	setRefUnit(Unit refUnit)
void	setSpeciesDeclaration(BindingSet speciesDeclaration)

Methods inherited from class org.sigpath.datamodel.Kinetic

getMissingBindings

Methods inherited from class org.sigpath.datamodel.SigPathEntityImpl

addAlias, addAliases, addAliases, addReview, addUserComment, changeAlias, getAliases, getAliasesCollection, getAliasesIterator, getChangeLog, getCombinedStringLength, getComments, getDescription, getExternalReferences, getLiteratureReferences, getName, getReviews, getSpid, getUserComments, isExportable, isIndexed, jdoPostLoad, jdoPreClear, jdoPreStore, removeAlias, removeAliases, removeReviews, setAliases, setAliasesCollection, setChangeLog, setComments, setDescription, setExportable, setForwardReferences, setIndexed, setName, setSpid

Methods inherited from class org.sigpath.datamodel.lset.CollectableImpl

createCollectionsSet, getCollections

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.sigpath.datamodel.lset.Collectable

getCollections

Constructor Detail

KineticCustom

public KineticCustom()

Creates a new KineticCustom object.

KineticCustom

public KineticCustom(SigPathFactory spf,
                     SPDBManager dbm,
                     String spid)

KineticCustom

public KineticCustom(SigPathFactory spf,
                     SPDBManager dbm)

KineticCustom

public KineticCustom(SigPathFactory spf)

Constructor used by NavigatorFactoryImpl to create a new Kinetic such as KineticCustom.

Parameters:

spf -

KineticCustom

public KineticCustom(SigPathFactory spf,
                     String spid)

Constructor used by NavigatorFactoryImpl to create a new Kinetic such as KineticCustom.

Parameters:

spf -

spid -

Method Detail

setKineticInteraction

public void setKineticInteraction(KineticInteraction interaction)

Ignored by this implementation.

Specified by:

setKineticInteraction in class Kinetic

Parameters:

interaction -

jdoPreDelete

public void jdoPreDelete()

Specified by:

jdoPreDelete in interface InstanceCallbacks

Overrides:

jdoPreDelete in class SigPathEntityImpl

getBackwardVelocity

public Formula getBackwardVelocity(KineticInteraction kInt)
                            throws SigPathKineticException

Description copied from class: Kinetic

Get the product formation rate for a specific interaction. In some parts of the documentation, this rate is also called "creation rate law". This creation rate law is a function that describes the rate at which reactants are turned into products. For instance, consider the reaction A + B <--kb, kf--> C. for MassActionKinetic, getBackwardVelocity() returns the Formula value kf[A][B]. Depending on the process, the unit and the formulation of the rate law may change. This will be specified by specific implementations of the Kinetic interface. In SigPath, the rate law formula may be expressed in substance.time-1 or in concentration.time-1.

Specified by:

getBackwardVelocity in class Kinetic

Parameters:

kInt - a specific interaction.

Returns:

a Formula to calculate the rate as a function of parameters, species and constants.

Throws:

SigPathKineticException

getForwardVelocity

public Formula getForwardVelocity(KineticInteraction kInt)
                           throws SigPathKineticException

Description copied from class: Kinetic

Get the product destruction rate for a specific interaction. This destruction rate is a function that describes the rate at which products are turned back into substrates of this interaction. For instance, consider the reaction A + B <--kb, kf--> C for MassActionKinetic, getForwardVelocity() returns a formula value kb[C]. Depending on the process, the unit and the formulation of the rate law may change. This will be specified by specific implementations of the Kinetic interface.

Specified by:

getForwardVelocity in class Kinetic

Parameters:

kInt - a specific interaction.

Returns:

a Formula to calculate the rate as a function of parameters, species and constants.

Throws:

SigPathKineticException

getConstantBindingsDeclaration

public BindingSet getConstantBindingsDeclaration()

Returns the constant declaration. Note that they cannnot be deduced from the formula only because in formulae constantsDeclarations and SpeciesDeclarations have the same status.

Specified by:

getConstantBindingsDeclaration in class Kinetic

Returns:

BindingSet

getChemicalBindingsDeclaration

public BindingSet getChemicalBindingsDeclaration()
                                          throws SigPathKineticException

Returns the chemical declarations. Note that they cannnot be deduced from the formula only because in formulae constantsDeclarations and SpeciesDeclarations have the same status.

Specified by:

getChemicalBindingsDeclaration in class Kinetic

Returns:

Throws:

SigPathKineticException

getFormulaForward

public String getFormulaForward()

setFormulaForward

public void setFormulaForward(String formulaForward)

getFormulaBackward

public String getFormulaBackward()

setFormulaBackward

public void setFormulaBackward(String formulaBackward)

getSpeciesDeclaration

public BindingSet getSpeciesDeclaration()

setSpeciesDeclaration

public void setSpeciesDeclaration(BindingSet speciesDeclaration)

getConstantsDeclaration

public BindingSet getConstantsDeclaration()

setConstantsDeclaration

public void setConstantsDeclaration(BindingSet constantsDeclaration)

getRefUnit

public Unit getRefUnit()

Description copied from class: Kinetic

This is the unit used to express forward and backward velocities. A IS unit is expected here.

Specified by:

getRefUnit in class Kinetic

Returns:

generateDefaultChemicalBindings

public BindingSet generateDefaultChemicalBindings(KineticInteraction kInt)

No default bindings definition for custom kinetic. These have to be explicitely defined in the kineticInteraction using this custom kinetic

Specified by:

generateDefaultChemicalBindings in class Kinetic

Parameters:

kInt -

Returns:

BindingSet

isFullyQuantified

public static boolean isFullyQuantified(KineticCustom kinetic,
                                        BindingSet bindings)
                                 throws SigPathKineticException

Returns the binding needed for a kinetic interaction using a custom kinetic to be included in a model.

Parameters:

bindings -

Returns:

Throws:

SigPathKineticException

isFullyQuantified

public boolean isFullyQuantified(BindingSet bindings)
                          throws SigPathKineticException

Needed to enable autovalidation by the instance.

Specified by:

isFullyQuantified in class Kinetic

Parameters:

bindings -

Returns:

Throws:

SigPathKineticException

setConstantAndSpecies

public void setConstantAndSpecies(KineticInteraction kInt,
                                  BindingSet bindings)

setRefUnit

public void setRefUnit(Unit refUnit)

getForwardReferences

public Set getForwardReferences()

Description copied from interface: SigPathEntity

Returns the set of direct forward references of this entity. Forward references are defined as the set of entities that this entity refer to directly. For instance, if this entity is a reaction that involves chemicals, the set of forward references will contain the chemicals involved in the reaction. If the entity is a model, the forward references will contain all the reactions, chemical, concentrations, etc. that the model refer to directly.

Returns:

forward references of this entity (a Set of SigPathEntity)