Package org.biopax.paxtools.model.level3

Interface BiochemicalPathwayStep

All Superinterfaces:
BioPAXElement, Cloneable, Level3Element, Observable, PathwayStep, Serializable, UtilityClass
All Known Implementing Classes:
BiochemicalPathwayStepImpl
public interface BiochemicalPathwayStep extends PathwayStep
Definition: Imposes ordering on a step in a biochemical pathway. Retionale: A biochemical reaction can be reversible by itself, but can be physiologically directed in the context of a pathway, for instance due to flux of reactants and products. Usage: Only one conversion interaction can be ordered at a time, but multiple catalysis or modulation instances can be part of one step.

  • Method Details

    • getStepConversion

      Conversion getStepConversion()
      This method returns the central conversion of this BiochemicalPathwayStep. The returned conversion is also stepProcess of this PathwayStep. The step direction defines the direction of this conversion. The conversion must be reversible.
      Returns:
      The central conversion that take place at this step of the biochemical pathway.

    • setStepConversion

      void setStepConversion(Conversion stepConversion)
      This method sets the conversion of this BiochemicalPathwayStep to the new Step_Conversion. Old step conversion is also removed from the stepProcess list.
      Parameters:
      stepConversion - the Conversion interaction of this biological pathway step

    • getStepDirection

      StepDirection getStepDirection()
      This property can be used for annotating direction of enzymatic activity. Even if an enzyme catalyzes a reaction reversibly, the flow of matter through the pathway will force the equilibrium in a given direction for that particular pathway.
      Returns:
      Direction of the conversion in this particular pathway context.

    • setStepDirection

      void setStepDirection(StepDirection stepDirection)
      This property can be used for annotating direction of enzymatic activity. Even if an enzyme catalyzes a reaction reversibly, the flow of matter through the pathway will force the equilibrium in a given direction for that particular pathway.
      Parameters:
      stepDirection - Direction of the conversion in this particular pathway context.