org.biopax.paxtools.impl.level3
Class BiochemicalReactionImpl

java.lang.Object
  org.biopax.paxtools.impl.BioPAXElementImpl
      org.biopax.paxtools.impl.level3.L3ElementImpl
          org.biopax.paxtools.impl.level3.XReferrableImpl
              org.biopax.paxtools.impl.level3.NamedImpl
                  org.biopax.paxtools.impl.level3.EntityImpl
                      org.biopax.paxtools.impl.level3.ProcessImpl
                          org.biopax.paxtools.impl.level3.InteractionImpl
                              org.biopax.paxtools.impl.level3.ConversionImpl
                                  org.biopax.paxtools.impl.level3.BiochemicalReactionImpl

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, BioPAXElement, BiochemicalReaction, Conversion, Entity, Interaction, Level3Element, Named, Observable, Process, XReferrable

Direct Known Subclasses:

TransportWithBiochemicalReactionImpl

@Entity
@Indexed
public class BiochemicalReactionImpl
extends ConversionImpl
implements BiochemicalReaction

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

Fields inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

SEARCH_FIELD_AVAILABILITY, SEARCH_FIELD_COMMENT, SEARCH_FIELD_EC_NUMBER, SEARCH_FIELD_KEYWORD, SEARCH_FIELD_NAME, SEARCH_FIELD_SEQUENCE, SEARCH_FIELD_TERM, SEARCH_FIELD_XREF_DB, SEARCH_FIELD_XREF_ID, SEARCH_INDEX_NAME

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

BiochemicalReactionImpl()

Method Summary

void	addDeltaG(DeltaG deltaG) Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o.
void	addDeltaH(float deltaH) For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'o.
void	addDeltaS(float deltaS) For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'o.
void	addECNumber(java.lang.String eCNumber) The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.
void	addKEQ(KPrime kEQ) This quantity is dimensionless and is usually a single number.
java.util.Set<DeltaG>	getDeltaG() Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o.
java.util.Set<java.lang.Float>	getDeltaH() For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'o.
java.util.Set<java.lang.Float>	getDeltaS() For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'o.
java.util.Set<java.lang.String>	getECNumber() The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.
java.util.Set<KPrime>	getKEQ() This quantity is dimensionless and is usually a single number.
java.lang.Class<? extends BiochemicalReaction>	getModelInterface() This method returns the actual model interface that a class implements.
void	removeDeltaG(DeltaG deltaG) Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o.
void	removeDeltaH(float deltaH) For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'o.
void	removeDeltaS(float deltaS) For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'o.
void	removeECNumber(java.lang.String eCNumber) The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.
void	removeKEQ(KPrime kEQ) This quantity is dimensionless and is usually a single number.
protected void	setDeltaG(java.util.Set<DeltaG> deltaG)
protected void	setDeltaH(java.util.Set<java.lang.Float> deltaH)
protected void	setDeltaS(java.util.Set<java.lang.Float> deltaS)
protected void	setECNumber(java.util.Set<java.lang.String> eCNumber)
protected void	setKEQ(java.util.Set<KPrime> kEQ)

Methods inherited from class org.biopax.paxtools.impl.level3.ConversionImpl

addLeft, addParticipantStoichiometry, addRight, equivalenceCode, getConversionDirection, getLeft, getParticipantStoichiometry, getRight, getSpontaneous, removeLeft, removeParticipantStoichiometry, removeRight, semanticallyEquivalent, setConversionDirection, setLeft, setParticipantStoichiometry, setRight, setSpontaneous

Methods inherited from class org.biopax.paxtools.impl.level3.InteractionImpl

addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant, setInteractionType, setParticipant

Methods inherited from class org.biopax.paxtools.impl.level3.ProcessImpl

getControlledOf, getPathwayComponentOf, getStepProcessOf, setControlledOf, setPathwayComponentOf, setStepProcessOf

Methods inherited from class org.biopax.paxtools.impl.level3.EntityImpl

addAvailability, addDataSource, addEvidence, getAvailability, getDataSource, getEvidence, getParticipantOf, removeAvailability, removeDataSource, removeEvidence, setAvailability, setDataSource, setEvidence, setParticipantOf

Methods inherited from class org.biopax.paxtools.impl.level3.NamedImpl

addName, getDisplayName, getDisplayNameX, getName, getNameX, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setNameX, setStandardName, setStandardNameX

Methods inherited from class org.biopax.paxtools.impl.level3.XReferrableImpl

addXref, getXref, hasCommonUnificationXref, removeXref, setXref

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

getAnnotations, getProxyId, getRDFId, getVersion, isEquivalent, setProxyId, setRDFId, setVersion, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biopax.paxtools.model.level3.Conversion

addLeft, addParticipantStoichiometry, addRight, getConversionDirection, getLeft, getParticipantStoichiometry, getRight, getSpontaneous, removeLeft, removeParticipantStoichiometry, removeRight, setConversionDirection, setSpontaneous

Methods inherited from interface org.biopax.paxtools.model.level3.Interaction

addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant

Methods inherited from interface org.biopax.paxtools.model.level3.Process

getControlledOf, getPathwayComponentOf, getStepProcessOf

Methods inherited from interface org.biopax.paxtools.model.level3.Entity

addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getRDFId, isEquivalent

Constructor Detail

BiochemicalReactionImpl

public BiochemicalReactionImpl()

Method Detail

getModelInterface

public java.lang.Class<? extends BiochemicalReaction> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Overrides:

getModelInterface in class ConversionImpl

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getDeltaG

public java.util.Set<DeltaG> getDeltaG()

Description copied from interface: BiochemicalReaction

Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.

Since Delta-G can change based on multiple factors including ionic strength and temperature a reaction can have multiple DeltaG values.

Specified by:

getDeltaG in interface BiochemicalReaction

Returns:

a set of DeltaG's for this reaction.

setDeltaG

protected void setDeltaG(java.util.Set<DeltaG> deltaG)

addDeltaG

public void addDeltaG(DeltaG deltaG)

Description copied from interface: BiochemicalReaction

Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.

Since Delta-G can change based on multiple factors including ionic strength and temperature a reaction can have multiple DeltaG values.

Specified by:

addDeltaG in interface BiochemicalReaction

Parameters:

deltaG - to be added.

removeDeltaG

public void removeDeltaG(DeltaG deltaG)

Description copied from interface: BiochemicalReaction

Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'^o.

Since Delta-G can change based on multiple factors including ionic strength and temperature a reaction can have multiple DeltaG values.

Specified by:

removeDeltaG in interface BiochemicalReaction

Parameters:

deltaG - to be removed.

getDeltaH

public java.util.Set<java.lang.Float> getDeltaH()

Description copied from interface: BiochemicalReaction

For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o.

delta-G'^o = delta-H'^o - T delta-S'^o

Units: kJ/mole

Specified by:

getDeltaH in interface BiochemicalReaction

Returns:

standard transformed enthalpy change

setDeltaH

protected void setDeltaH(java.util.Set<java.lang.Float> deltaH)

addDeltaH

public void addDeltaH(float deltaH)

Description copied from interface: BiochemicalReaction

For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o.

delta-G'^o = delta-H'^o - T delta-S'^o

Units: kJ/mole

Specified by:

addDeltaH in interface BiochemicalReaction

Parameters:

deltaH - standard transformed enthalpy change

removeDeltaH

public void removeDeltaH(float deltaH)

Description copied from interface: BiochemicalReaction

For biochemical reactions this property refers to the standard transformed enthalpy change for a reaction written in terms of biochemical reactants (sums of species), delta-H'^o.

delta-G'^o = delta-H'^o - T delta-S'^o

Units: kJ/mole

Specified by:

removeDeltaH in interface BiochemicalReaction

Parameters:

deltaH - standard transformed enthalpy change

getDeltaS

public java.util.Set<java.lang.Float> getDeltaS()

Description copied from interface: BiochemicalReaction

For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o.

delta-G'^o = delta-H'^o - T delta-S'^o

Specified by:

getDeltaS in interface BiochemicalReaction

Returns:

standard transformed entropy change

setDeltaS

protected void setDeltaS(java.util.Set<java.lang.Float> deltaS)

addDeltaS

public void addDeltaS(float deltaS)

Description copied from interface: BiochemicalReaction

For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o.

delta-G'^o = delta-H'^o - T delta-S'^o

Specified by:

addDeltaS in interface BiochemicalReaction

removeDeltaS

public void removeDeltaS(float deltaS)

Description copied from interface: BiochemicalReaction

For biochemical reactions, this property refers to the standard transformed entropy change for a reaction written in terms of biochemical reactants (sums of species), delta-S'^o.

delta-G'^o = delta-H'^o - T delta-S'^o

Specified by:

removeDeltaS in interface BiochemicalReaction

getECNumber

@Field(name="ecnumber",
       index=TOKENIZED)
@FieldBridge(impl=SetStringBridge.class)
public java.util.Set<java.lang.String> getECNumber()

Description copied from interface: BiochemicalReaction

The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.

Specified by:

getECNumber in interface BiochemicalReaction

Returns:

The unique number assigned to a reaction by the Enzyme Commission

setECNumber

protected void setECNumber(java.util.Set<java.lang.String> eCNumber)

addECNumber

public void addECNumber(java.lang.String eCNumber)

Description copied from interface: BiochemicalReaction

The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.

Specified by:

addECNumber in interface BiochemicalReaction

Parameters:

eCNumber - The unique number assigned to a reaction by the Enzyme Commission

removeECNumber

public void removeECNumber(java.lang.String eCNumber)

Description copied from interface: BiochemicalReaction

The unique number assigned to a reaction by the Enzyme Commission of the International Union of Biochemistry and Molecular Biology.

Specified by:

removeECNumber in interface BiochemicalReaction

Parameters:

eCNumber - The unique number assigned to a reaction by the Enzyme Commission

getKEQ

public java.util.Set<KPrime> getKEQ()

Description copied from interface: BiochemicalReaction

This quantity is dimensionless and is usually a single number. The measured equilibrium constant for a biochemical reaction, encoded by the slot KEQ, is actually the apparent equilibrium constant, K'. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate:

K' = [ADP][P_i]/[ATP],

The concentration of ATP refers to the total concentration of all of the following species:

[ATP] = [ATP^4-] + [HATP^3-] + [H₂ATP^2-] + [MgATP^2-] + [MgHATP^-] + [Mg₂ATP].

The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm³) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log₁₀[Mg²⁺]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K' T I pH pMg). This property may have multiple values, representing different measurements for K' obtained under the different experimental conditions listed in the 5-tuple.

Specified by:

getKEQ in interface BiochemicalReaction

Returns:

measured equilibrium constant for a biochemical reaction

setKEQ

protected void setKEQ(java.util.Set<KPrime> kEQ)

addKEQ

public void addKEQ(KPrime kEQ)

Description copied from interface: BiochemicalReaction

This quantity is dimensionless and is usually a single number. The measured equilibrium constant for a biochemical reaction, encoded by the slot KEQ, is actually the apparent equilibrium constant, K'. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate:

K' = [ADP][P_i]/[ATP],

The concentration of ATP refers to the total concentration of all of the following species:

[ATP] = [ATP^4-] + [HATP^3-] + [H₂ATP^2-] + [MgATP^2-] + [MgHATP^-] + [Mg₂ATP].

The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm³) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log₁₀[Mg²⁺]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K' T I pH pMg). This property may have multiple values, representing different measurements for K' obtained under the different experimental conditions listed in the 5-tuple.

Specified by:

addKEQ in interface BiochemicalReaction

Parameters:

kEQ - measured equilibrium constant for a biochemical reaction

removeKEQ

public void removeKEQ(KPrime kEQ)

Description copied from interface: BiochemicalReaction

This quantity is dimensionless and is usually a single number. The measured equilibrium constant for a biochemical reaction, encoded by the slot KEQ, is actually the apparent equilibrium constant, K'. Concentrations in the equilibrium constant equation refer to the total concentrations of all forms of particular biochemical reactants. For example, in the equilibrium constant equation for the biochemical reaction in which ATP is hydrolyzed to ADP and inorganic phosphate:

K' = [ADP][P_i]/[ATP],

The concentration of ATP refers to the total concentration of all of the following species:

[ATP] = [ATP^4-] + [HATP^3-] + [H₂ATP^2-] + [MgATP^2-] + [MgHATP^-] + [Mg₂ATP].

The apparent equilibrium constant is formally dimensionless, and can be kept so by inclusion of as many of the terms (1 mol/dm³) in the numerator or denominator as necessary. It is a function of temperature (T), ionic strength (I), pH, and pMg (pMg = -log₁₀[Mg²⁺]). Therefore, these quantities must be specified to be precise, and values for KEQ for biochemical reactions may be represented as 5-tuples of the form (K' T I pH pMg). This property may have multiple values, representing different measurements for K' obtained under the different experimental conditions listed in the 5-tuple.

Specified by:

removeKEQ in interface BiochemicalReaction

Parameters:

kEQ - measured equilibrium constant for a biochemical reaction