Package org.biopax.paxtools.model.level3

Interface Conversion

All Superinterfaces:
BioPAXElement, Cloneable, Entity, Interaction, Level3Element, Named, Observable, Process, Serializable, XReferrable
All Known Subinterfaces:
BiochemicalReaction, ComplexAssembly, Degradation, Transport, TransportWithBiochemicalReaction
All Known Implementing Classes:
BiochemicalReactionImpl, ComplexAssemblyImpl, ConversionImpl, DegradationImpl, TransportImpl, TransportWithBiochemicalReactionImpl
public interface Conversion extends Interaction
Definition: An interaction in which molecules of one or more PhysicalEntity pools are physically transformed and become a member of one or more other PhysicalEntity pools. Rationale: Conversion and pools of entities are two central abstractions of chemistry. They can be quantized with rate and concentration respectively. A conversion in BioPAX, similar to chemistry, is stoichiometric and closed world, i.e. it is assumed that all of the participants are listed. These properties are due to the law of mass conservation. This differs from Control for example where multiple entities might be controlling the controlled and everything that is not listed is assumed to be unknown. Conversions in BioPAX can be reversible -- the property names Left and Right were preferred specifically because they are direction neutral as opposed to substrate and product or input and output. Usage: Subclasses of conversion represent different types of transformation reflected by the properties of different physicalEntity. BiochemicalReactions will change the ModificationFeatures on a PhysicalEntity, Transport will change the Cellular Location and ComplexAssembly will change BindingFeatures. Generic Conversion class should only be used when the modification does not fit into a any of these classes. Example: Opening of a voltage gated channel.

  • Method Details

    • getLeft

      Set<PhysicalEntity> getLeft()
      The participants on the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.
      Returns:
      The participants on the left side of the conversion interaction.

    • addLeft

      void addLeft(PhysicalEntity left)
      Adds a participant to the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.
      Parameters:
      left - participants to be added to the left side of the conversion interaction.

    • removeLeft

      void removeLeft(PhysicalEntity left)
      Removes a participant from the left side of the conversion interaction. Since conversion interactions may proceed in either the left-to-right or right-to-left direction, occupants of the left property may be either reactants or products. left is a sub-property of participants.
      Parameters:
      left - participants to be removed from the left side of the conversion interaction.

    • getParticipantStoichiometry

      Set<Stoichiometry> getParticipantStoichiometry()
      Stoichiometry of the left (getLeft()) and right(getRight()) participants. Note: This is a "bridge" workaround for the n-ary relationship problem. There is no default stoichiometry ( e.g. 1). Leaving this out will create reactions with unknown stoichiometry. It is a best practice to define the stoichiometry of each participant. It is invalid to define more than one stoichiometry per participant. It is invalid to reuse stoichiometry instances across conversions.
      Returns:
      Stoichiometry of the left (getLeft()) and right(getRight()) participants.

    • addParticipantStoichiometry

      void addParticipantStoichiometry(Stoichiometry stoichiometry)
      This method adds a stoichiometry for one of the participants of this conversion.
      Parameters:
      stoichiometry - to be added

    • removeParticipantStoichiometry

      void removeParticipantStoichiometry(Stoichiometry stoichiometry)
      This method removes a stoichiometry for one of the participants of this conversion.
      Parameters:
      stoichiometry - to be removed

    • getRight

      Set<PhysicalEntity> getRight()
      The participants on the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.
      Returns:
      The participants on the right side of the conversion interaction.

    • addRight

      void addRight(PhysicalEntity right)
      Adds a participant to the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.
      Parameters:
      right - participants to be added to the right side of the conversion interaction.

    • removeRight

      void removeRight(PhysicalEntity right)
      Removes a participant from the right side of the conversion interaction. Since conversion interactions may proceed in either the right-to-right or right-to-right direction, occupants of the right property may be either reactants or products. right is a sub-property of participants.
      Parameters:
      right - participants to be removed from the right side of the conversion interaction.

    • getSpontaneous

      Boolean getSpontaneous()
      Specifies whether a conversion occurs spontaneously or not. If the spontaneity is not known,this property should not be specified.
      Returns:
      whether if this conversion is spontaneous.

    • setSpontaneous

      void setSpontaneous(Boolean spontaneous)
      Specifies whether a conversion occurs spontaneously or not. If the spontaneity is not known,this property should not be specified.
      Parameters:
      spontaneous - Whether if this conversion is spontaneous.

    • getConversionDirection

      ConversionDirectionType getConversionDirection()
      This property represents the direction of the reaction. If a reaction will run in a single direction under all biological contexts then it is considered irreversible and has a direction. Otherwise it is reversible.
      Returns:
      One of REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT

    • setConversionDirection

      void setConversionDirection(ConversionDirectionType conversionDirection)
      This property represents the direction of the reaction. If a reaction will run in a single direction under all biological contexts then it is considered irreversible and has a direction. Otherwise it is reversible.
      Parameters:
      conversionDirection - One of REVERSIBLE, LEFT-TO-RIGHT or RIGHT-TO-LEFT -- null for unknown.