Package org.biopax.paxtools.impl.level3

Class CatalysisImpl

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.ControlImpl
org.biopax.paxtools.impl.level3.CatalysisImpl
All Implemented Interfaces:
Serializable, Cloneable, BioPAXElement, Catalysis, Control, Entity, Interaction, Level3Element, Named, Observable, Process, XReferrable
public class CatalysisImpl extends ControlImpl implements Catalysis
See Also:

  • Constructor Details

    • CatalysisImpl

      public CatalysisImpl()

  • Method Details

    • getModelInterface

      public Class<? extends Catalysis> 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 ControlImpl
      Returns:
      an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

    • getCatalysisDirection

      public CatalysisDirectionType getCatalysisDirection()
      Description copied from interface: Catalysis
      This property represents the direction of this catalysis under all physiological conditions if there is one. Note that chemically a catalyst will increase the rate of the reaction in both directions. In biology, however, there are cases where the enzyme is expressed only when the controlled bidirectional conversion is on one side of the chemical equilibrium. olled bidirectional conversion is on one side of the chemical equilibrium. For example E.Coli's lac operon ensures that lacZ gene is only synthesized when there is enough lactose in the medium. If that is the case and the controller, under biological conditions, is always catalyzing the conversion in one direction then this fact can be captured using this property. If the enzyme is active for both directions, or the conversion is not bidirectional, this property should be left empty.
      Specified by:
      getCatalysisDirection in interface Catalysis
      Returns:
      direction of this catalysis under all physiological conditions if there is one

    • setCatalysisDirection

      public void setCatalysisDirection(CatalysisDirectionType catalysisDirection)
      Description copied from interface: Catalysis
      This property represents the direction of this catalysis under all physiological conditions if there is one. Note that chemically a catalyst will increase the rate of the reaction in both directions. In biology, however, there are cases where the enzyme is expressed only when the controlled bidirectional conversion is on one side of the chemical equilibrium. olled bidirectional conversion is on one side of the chemical equilibrium. For example E.Coli's lac operon ensures that lacZ gene is only synthesized when there is enough lactose in the medium. If that is the case and the controller, under biological conditions, is always catalyzing the conversion in one direction then this fact can be captured using this property. If the enzyme is active for both directions, or the conversion is not bidirectional, this property should be left empty.
      Specified by:
      setCatalysisDirection in interface Catalysis
      Parameters:
      catalysisDirection - direction of this catalysis under all physiological conditions if there is one

    • getCofactor

      public Set<PhysicalEntity> getCofactor()
      Description copied from interface: Catalysis
      Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. This is a suproperty of participants.
      Specified by:
      getCofactor in interface Catalysis
      Returns:
      cofactor(s) or coenzyme(s) required for catalysis of the conversion

    • addCofactor

      public void addCofactor(PhysicalEntity cofactor)
      Description copied from interface: Catalysis
      Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. This is a suproperty of participants.
      Specified by:
      addCofactor in interface Catalysis
      Parameters:
      cofactor - cofactor(s) or coenzyme(s) required for catalysis of the conversion

    • removeCofactor

      public void removeCofactor(PhysicalEntity cofactor)
      Description copied from interface: Catalysis
      Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. This is a suproperty of participants.
      Specified by:
      removeCofactor in interface Catalysis
      Parameters:
      cofactor - cofactor(s) or coenzyme(s) required for catalysis of the conversion

    • addController

      public void addController(Controller controller)
      Description copied from interface: Control
      The controlling entity, e.g., in a biochemical reaction, an enzyme is the controlling entity of the reaction. Controller is a sub-property of participants.
      Specified by:
      addController in interface Control
      Overrides:
      addController in class ControlImpl
      Parameters:
      controller - The controlling entity

    • checkControlled

      protected boolean checkControlled(Process controlled)
      Overrides:
      checkControlled in class ControlImpl