org.biopax.paxtools.model.level2
Interface biochemicalReaction

All Superinterfaces:

BioPAXElement, java.lang.Cloneable, conversion, entity, interaction, InteractionParticipant, Level2Element, pathwayComponent, physicalInteraction, process, java.io.Serializable, XReferrable

All Known Subinterfaces:

transportWithBiochemicalReaction

public interface biochemicalReaction
extends conversion

A conversion interaction in which one or more entities (substrates) undergo ovalent 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	addDELTA_G(deltaGprimeO DELTA_G)
void	addDELTA_H(double DELTA_H)
void	addDELTA_S(double DELTA_S)
void	addEC_NUMBER(java.lang.String EC_NUMBER)
void	addKEQ(kPrime KEQ)
java.util.Set<deltaGprimeO>	getDELTA_G()
java.util.Set<java.lang.Double>	getDELTA_H()
java.util.Set<java.lang.Double>	getDELTA_S()
java.util.Set<java.lang.String>	getEC_NUMBER()
java.util.Set<kPrime>	getKEQ()
void	removeDELTA_G(deltaGprimeO DELTA_G)
void	removeDELTA_H(double DELTA_H)
void	removeDELTA_S(double DELTA_S)
void	removeEC_NUMBER(java.lang.String EC_NUMBER)
void	removeKEQ(kPrime KEQ)
void	setDELTA_G(java.util.Set<deltaGprimeO> DELTA_G)
void	setDELTA_H(java.util.Set<java.lang.Double> DELTA_H)
void	setDELTA_S(java.util.Set<java.lang.Double> DELTA_S)
void	setEC_NUMBER(java.util.Set<java.lang.String> EC_NUMBER)
void	setKEQ(java.util.Set<kPrime> KEQ)

Methods inherited from interface org.biopax.paxtools.model.level2.conversion

addLEFT, addRIGHT, getLEFT, getRIGHT, getSPONTANEOUS, removeLEFT, removeRIGHT, setLEFT, setRIGHT, setSPONTANEOUS

Methods inherited from interface org.biopax.paxtools.model.level2.physicalInteraction

addINTERACTION_TYPE, getINTERACTION_TYPE, removeINTERACTION_TYPE, setINTERACTION_TYPE

Methods inherited from interface org.biopax.paxtools.model.level2.interaction

addPARTICIPANTS, getPARTICIPANTS, removePARTICIPANTS, setPARTICIPANTS

Methods inherited from interface org.biopax.paxtools.model.level2.process

addEVIDENCE, getEVIDENCE, isCONTROLLEDOf, isPATHWAY_COMPONENTSof, isSTEP_INTERACTIONSOf, removeEVIDENCE, setEVIDENCE

Methods inherited from interface org.biopax.paxtools.model.level2.entity

addAVAILABILITY, addDATA_SOURCE, addSYNONYMS, getAVAILABILITY, getDATA_SOURCE, getNAME, getSHORT_NAME, getSYNONYMS, removeAVAILABILITY, removeDATA_SOURCE, removeSYNONYMS, setAVAILABILITY, setDATA_SOURCE, setNAME, setSHORT_NAME, setSYNONYMS

Methods inherited from interface org.biopax.paxtools.model.level2.XReferrable

addXREF, findCommonPublications, findCommonRelationships, findCommonUnifications, getXREF, removeXREF, setXREF

Methods inherited from interface org.biopax.paxtools.model.level2.InteractionParticipant

isPARTICIPANTSof

Methods inherited from interface org.biopax.paxtools.model.level2.Level2Element

addCOMMENT, getCOMMENT, removeCOMMENT, setCOMMENT

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

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Method Detail

getDELTA_G

java.util.Set<deltaGprimeO> getDELTA_G()

setDELTA_G

void setDELTA_G(java.util.Set<deltaGprimeO> DELTA_G)

addDELTA_G

void addDELTA_G(deltaGprimeO DELTA_G)

removeDELTA_G

void removeDELTA_G(deltaGprimeO DELTA_G)

getDELTA_H

java.util.Set<java.lang.Double> getDELTA_H()

setDELTA_H

void setDELTA_H(java.util.Set<java.lang.Double> DELTA_H)

addDELTA_H

void addDELTA_H(double DELTA_H)

removeDELTA_H

void removeDELTA_H(double DELTA_H)

getDELTA_S

java.util.Set<java.lang.Double> getDELTA_S()

setDELTA_S

void setDELTA_S(java.util.Set<java.lang.Double> DELTA_S)

addDELTA_S

void addDELTA_S(double DELTA_S)

removeDELTA_S

void removeDELTA_S(double DELTA_S)

getEC_NUMBER

java.util.Set<java.lang.String> getEC_NUMBER()

setEC_NUMBER

void setEC_NUMBER(java.util.Set<java.lang.String> EC_NUMBER)

addEC_NUMBER

void addEC_NUMBER(java.lang.String EC_NUMBER)

removeEC_NUMBER

void removeEC_NUMBER(java.lang.String EC_NUMBER)

getKEQ

java.util.Set<kPrime> getKEQ()

setKEQ

void setKEQ(java.util.Set<kPrime> KEQ)

addKEQ

void addKEQ(kPrime KEQ)

removeKEQ

void removeKEQ(kPrime KEQ)