001package org.biopax.paxtools.model.level2; 002 003import java.util.Set; 004 005/** 006 * A conversion interaction in which one or more entities (substrates) undergo 007 * ovalent changes to become one or more other entities (products). The substrates 008 * of biochemical reactions are defined in terms of sums of species. 009 * This is convention in biochemistry, and, in principle, all of the EC 010 * reactions should be biochemical reactions. 011 * 012 * <b>Examples:</b> ATP + H2O = ADP + Pi 013 * 014 * <b>Comment:</b> In the example reaction above, ATP is considered to be an 015 * equilibrium mixture of several species, namely ATP4-, HATP3-, H2ATP2-, 016 * MgATP2-, MgHATP-, and Mg2ATP. Additional species may also need to be 017 * considered if other ions (e.g. Ca2+) that bind ATP are present. 018 * Similar considerations apply to ADP and to inorganic phosphate (Pi). 019 * When writing biochemical reactions, it is not necessary to attach charges to 020 * the biochemical reactants or to include ions such as H+ and Mg2+ in the 021 * equation. The reaction is written in the direction specified by the EC 022 * nomenclature system, if applicable, regardless of the physiological 023 * direction(s) in which the reaction proceeds. Polymerization reactions 024 * involving large polymers whose structure is not explicitly captured should 025 * generally be represented as unbalanced reactions in which the monomer is 026 * consumed but the polymer remains unchanged, e.g. glycogen + glucose = 027 * glycogen. 028 */ 029public interface biochemicalReaction extends conversion 030{ 031// -------------------------- OTHER METHODS -------------------------- 032 033 Set<deltaGprimeO> getDELTA_G(); 034 035 void setDELTA_G(Set<deltaGprimeO> DELTA_G); 036 037 void addDELTA_G(deltaGprimeO DELTA_G); 038 039 void removeDELTA_G(deltaGprimeO DELTA_G); 040 041 042 Set<Double> getDELTA_H(); 043 044 void setDELTA_H(Set<Double> DELTA_H); 045 046 void addDELTA_H(double DELTA_H); 047 048 void removeDELTA_H(double DELTA_H); 049 050 051 Set<Double> getDELTA_S(); 052 053 void setDELTA_S(Set<Double> DELTA_S); 054 055 void addDELTA_S(double DELTA_S); 056 057 void removeDELTA_S(double DELTA_S); 058 059 060 Set<String> getEC_NUMBER(); 061 062 void setEC_NUMBER(Set<String> EC_NUMBER); 063 064 void addEC_NUMBER(String EC_NUMBER); 065 066 void removeEC_NUMBER(String EC_NUMBER); 067 068 069 Set<kPrime> getKEQ(); 070 071 void setKEQ(Set<kPrime> KEQ); 072 073 void addKEQ(kPrime KEQ); 074 075 void removeKEQ(kPrime KEQ); 076 077}