001package org.biopax.paxtools.model.level3; 002 003/** 004 * Definition: Imposes ordering on a step in a biochemical pathway. 005 * 006 * Retionale: A biochemical reaction can be reversible by itself, but can be physiologically directed in the context 007 * of a pathway, for instance due to flux of reactants and products. 008 * 009 * Usage: Only one conversion interaction can be ordered at a time, but multiple catalysis or modulation instances 010 * can be part of one step. 011 */ 012public interface BiochemicalPathwayStep extends PathwayStep 013{ 014 015 016 /** 017 * This method returns the central conversion of this BiochemicalPathwayStep. The 018 * returned conversion is also stepProcess of this PathwayStep. The step direction defines the direction 019 * of this conversion. The conversion must be reversible. 020 * 021 * @return The central conversion that take place at this step of the biochemical pathway. 022 */ 023 Conversion getStepConversion(); 024 025 /** 026 * This method sets the conversion of this BiochemicalPathwayStep to the 027 * new Step_Conversion. Old step conversion is also removed from the 028 * stepProcess list. 029 * 030 * @param stepConversion the Conversion interaction of this biological pathway step 031 */ 032 void setStepConversion(Conversion stepConversion); 033 034 /** 035 * This property can be used for annotating direction of enzymatic activity. Even if an enzyme catalyzes a 036 * reaction reversibly, the flow of matter through the pathway will force the equilibrium in a given direction 037 * for that particular pathway. 038 * 039 * @return Direction of the conversion in this particular pathway context. 040 */ 041 StepDirection getStepDirection(); 042 043 /** 044 * This property can be used for annotating direction of enzymatic activity. Even if an enzyme catalyzes a 045 * reaction reversibly, the flow of matter through the pathway will force the equilibrium in a given direction 046 * for that particular pathway. 047 * 048 * @param stepDirection Direction of the conversion in this particular pathway context. 049 */ 050 void setStepDirection(StepDirection stepDirection); 051}