Class BioChemicalReaction

java.lang.Object

org.episteme.natural.chemistry.ChemicalReaction

org.episteme.natural.biology.BioChemicalReaction

All Implemented Interfaces:

Serializable, Commented, ComprehensiveIdentification, Identified<Identification>, Named

public class BioChemicalReaction
extends ChemicalReaction

Represents a biochemical reaction converting reactants to products.

This class extends the core ChemicalReaction with support for catalysts (enzymes) and detailed Molecule linking.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	BioChemicalReaction.BioProduct
static class	BioChemicalReaction.BioReactant

Constructor Summary

Constructors

Constructor	Description
BioChemicalReaction(String name)

Method Summary

Modifier and Type	Method	Description
void	addCatalyst(Molecule enzyme)
void	addProduct(Molecule molecule, double stoichiometry)
void	addReactant(Molecule molecule, double stoichiometry)
List<BioChemicalReaction.BioProduct>	getBioProducts()
List<BioChemicalReaction.BioReactant>	getBioReactants()
List<Molecule>	getCatalysts()
boolean	isReversible()
void	setReversible(boolean reversible)
String	toString()

Methods inherited from class ChemicalReaction

calculateRateConstant, countProductAtoms, countReactantAtoms, getEnthalpy, getEquation, getGibbsFreeEnergy, getId, getProducts, getReactants, getTraits, isBalanced, massToMass, parse, setEnthalpy, setGibbsFreeEnergy, setKinetics, stoichiometry

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface Commented

getComments, getTrait, setComments

Methods inherited from interface ComprehensiveIdentification

getName, getTrait, setName, setTrait

Constructor Details

BioChemicalReaction

public BioChemicalReaction(String name)

Method Details

addReactant

public void addReactant(Molecule molecule,
 double stoichiometry)

addProduct

public void addProduct(Molecule molecule,
 double stoichiometry)

addCatalyst

public void addCatalyst(Molecule enzyme)

getBioReactants

public List<BioChemicalReaction.BioReactant> getBioReactants()

getBioProducts

public List<BioChemicalReaction.BioProduct> getBioProducts()

getCatalysts

public List<Molecule> getCatalysts()

isReversible

public boolean isReversible()

setReversible

public void setReversible(boolean reversible)

toString

public String toString()

Overrides:

toString in class ChemicalReaction