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}