Package org.biopax.paxtools.model.level3

Interface BiochemicalReaction

All Superinterfaces:
BioPAXElement, Cloneable, Conversion, Entity, Interaction, Level3Element, Named, Observable, Process, 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.

  • Method Details

    • getDeltaG

      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

      Set<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

      Set<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 standard transformed entropy change
      Parameters:
      delta_s - value

    • 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 standard transformed entropy change
      Parameters:
      delta_s - value

    • getECNumber

      Set<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(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(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

      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][Pi]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP4-] + [HATP3-] + [H2ATP2-] + [MgATP2-] + [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][Pi]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP4-] + [HATP3-] + [H2ATP2-] + [MgATP2-] + [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][Pi]/[ATP], The concentration of ATP refers to the total concentration of all of the following species: [ATP] = [ATP4-] + [HATP3-] + [H2ATP2-] + [MgATP2-] + [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