Package 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:
Serializable, Cloneable, BioPAXElement, BiochemicalReaction, Conversion, Entity, Interaction, Level3Element, Named, Observable, Process, XReferrable
Direct Known Subclasses:
TransportWithBiochemicalReactionImpl
public class BiochemicalReactionImpl extends ConversionImpl implements BiochemicalReaction
See Also:

  • Constructor Details

    • BiochemicalReactionImpl

      public BiochemicalReactionImpl()

  • Method Details

    • getModelInterface

      public 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 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(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 Set<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

    • 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 Set<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

    • 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 standard transformed entropy change
      Specified by:
      addDeltaS in interface BiochemicalReaction
      Parameters:
      deltaS - value

    • 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 standard transformed entropy change
      Specified by:
      removeDeltaS in interface BiochemicalReaction
      Parameters:
      deltaS - value

    • getECNumber

      public Set<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

    • addECNumber

      public void addECNumber(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(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 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][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.
      Specified by:
      getKEQ in interface BiochemicalReaction
      Returns:
      measured equilibrium constant for a biochemical reaction

    • 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][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.
      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][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.
      Specified by:
      removeKEQ in interface BiochemicalReaction
      Parameters:
      kEQ - measured equilibrium constant for a biochemical reaction