org.biopax.paxtools.model.level3
Interface BiochemicalReaction

All Superinterfaces:

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

All Known Subinterfaces:

TransportWithBiochemicalReaction

All Known Implementing Classes:

BiochemicalReactionImpl, TransportWithBiochemicalReactionImpl

public interface BiochemicalReaction
extends Conversion

Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products). The substrates of biochemical reactions are defined in terms of sums of species. This is convention in biochemistry, and, in principle, all of the EC reactions should be biochemical reactions. Examples: ATP + H2O = ADP + Pi Comment: In the example reaction above, ATP is considered to be an equilibrium mixture of several species, namely ATP4-, HATP3-, H2ATP2-, MgATP2-, MgHATP-, and Mg2ATP. Additional species may also need to be considered if other ions (e.g. Ca2+) that bind ATP are present. Similar considerations apply to ADP and to inorganic phosphate (Pi). When writing biochemical reactions, it is not necessary to attach charges to the biochemical reactants or to include ions such as H+ and Mg2+ in the equation. The reaction is written in the direction specified by the EC nomenclature system, if applicable, regardless of the physiological direction(s) in which the reaction proceeds. Polymerization reactions involving large polymers whose structure is not explicitly captured should generally be represented as unbalanced reactions in which the monomer is consumed but the polymer remains unchanged, e.g. glycogen + glucose = glycogen.

Nested Class Summary

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

BioPAXElement.Key

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

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 delta_h) 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 delta_s) 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 ec_number) 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.
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 delta_h) 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 delta_s) 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 ec_number) 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.

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, getModelInterface, getRDFId, isEquivalent

Method Detail

getDeltaG

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.

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

Returns:

a set of DeltaG's for this reaction.

addDeltaG

void addDeltaG(DeltaG deltaG)

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.

Parameters:

deltaG - to be added.

removeDeltaG

void removeDeltaG(DeltaG deltaG)

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.

Parameters:

deltaG - to be removed.

getDeltaH

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.

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

Units: kJ/mole

Returns:

standard transformed enthalpy change

addDeltaH

void addDeltaH(float delta_h)

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

Parameters:

delta_h - standard transformed enthalpy change

removeDeltaH

void removeDeltaH(float delta_h)

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

Parameters:

delta_h - standard transformed enthalpy change

getDeltaS

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.

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

Returns:

standard transformed entropy change

addDeltaS

void addDeltaS(float delta_s)

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

removeDeltaS

void removeDeltaS(float delta_s)

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

getECNumber

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.

Returns:

The unique number assigned to a reaction by the Enzyme Commission

addECNumber

void addECNumber(java.lang.String ec_number)

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

Parameters:

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

removeECNumber

void removeECNumber(java.lang.String ec_number)

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

Parameters:

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

getKEQ

java.util.Set<KPrime> getKEQ()

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.

Returns:

measured equilibrium constant for a biochemical reaction

addKEQ

void addKEQ(KPrime keq)

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.

Parameters:

keq - measured equilibrium constant for a biochemical reaction

removeKEQ

void removeKEQ(KPrime keq)

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.

Parameters:

keq - measured equilibrium constant for a biochemical reaction