Package org.biopax.paxtools.model.level2

Interface biochemicalReaction

All Superinterfaces:
BioPAXElement, Cloneable, conversion, entity, interaction, InteractionParticipant, Level2Element, pathwayComponent, physicalInteraction, process, 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.

  • Method Details

    • getDELTA_G

      Set<deltaGprimeO> getDELTA_G()

    • setDELTA_G

      void setDELTA_G(Set<deltaGprimeO> DELTA_G)

    • addDELTA_G

      void addDELTA_G(deltaGprimeO DELTA_G)

    • removeDELTA_G

      void removeDELTA_G(deltaGprimeO DELTA_G)

    • getDELTA_H

      Set<Double> getDELTA_H()

    • setDELTA_H

      void setDELTA_H(Set<Double> DELTA_H)

    • addDELTA_H

      void addDELTA_H(double DELTA_H)

    • removeDELTA_H

      void removeDELTA_H(double DELTA_H)

    • getDELTA_S

      Set<Double> getDELTA_S()

    • setDELTA_S

      void setDELTA_S(Set<Double> DELTA_S)

    • addDELTA_S

      void addDELTA_S(double DELTA_S)

    • removeDELTA_S

      void removeDELTA_S(double DELTA_S)

    • getEC_NUMBER

      Set<String> getEC_NUMBER()

    • setEC_NUMBER

      void setEC_NUMBER(Set<String> EC_NUMBER)

    • addEC_NUMBER

      void addEC_NUMBER(String EC_NUMBER)

    • removeEC_NUMBER

      void removeEC_NUMBER(String EC_NUMBER)

    • getKEQ

      Set<kPrime> getKEQ()

    • setKEQ

      void setKEQ(Set<kPrime> KEQ)

    • addKEQ

      void addKEQ(kPrime KEQ)

    • removeKEQ

      void removeKEQ(kPrime KEQ)