Package org.biopax.paxtools.model.level3

Interface Stoichiometry

All Superinterfaces:
BioPAXElement, Cloneable, Level3Element, Serializable, UtilityClass
All Known Implementing Classes:
StoichiometryImpl
public interface Stoichiometry extends UtilityClass
Stoichiometric coefficient of a physical entity in the context of a conversion or complex. For each participating element there must be 0 or 1 stoichiometry element. A non-existing stoichiometric element is treated as unknown. This is an n-ary bridge for left, right and component properties.

  • Method Details

    • getPhysicalEntity

      PhysicalEntity getPhysicalEntity()
      Returns:
      the physical entity to be annotated with stoichiometry.

    • setPhysicalEntity

      void setPhysicalEntity(PhysicalEntity physicalEntity)
      Parameters:
      physicalEntity - entity to be annotated with stoichiometry.

    • getStoichiometricCoefficient

      float getStoichiometricCoefficient()
      Stoichiometric coefficient of the physicalEntity specified by getPhysicalEntity() in the context of the owner interaction or complex. This value can be any rational number. Generic values such as "n" or "n+1" should not be used - polymers are currently not covered.
      Returns:
      Stoichiometric coefficient for one of the entities in an interaction or complex

    • setStoichiometricCoefficient

      void setStoichiometricCoefficient(float newStoichiometricCoefficient)
      Sets the stoichiometric coefficient of the physicalEntity specified by getPhysicalEntity() in the context of the owner interaction or complex. { can be any rational number. Generic values such as "n" or "n+1" should not be used - polymers are currently not covered.
      Parameters:
      newStoichiometricCoefficient - of the physical entity