Uses of Class
org.episteme.natural.chemistry.Molecule

Packages that use Molecule

Package	Description
org.episteme.natural.biology
org.episteme.natural.biology.loaders.biopax	BioPAX loader for biological pathways and networks.
org.episteme.natural.biology.loaders.sbml	Systems Biology Markup Language (SBML) loader for Episteme.
org.episteme.natural.chemistry
org.episteme.natural.chemistry.biochemistry
org.episteme.natural.chemistry.computational
org.episteme.natural.chemistry.computational.quantum
org.episteme.natural.chemistry.loaders
org.episteme.natural.chemistry.loaders.cml	Provides the org.episteme.natural.chemistry.loaders.cml module.
org.episteme.natural.chemistry.polymer
org.episteme.natural.chemistry.thermodynamics
org.episteme.natural.physics.loaders.thermoml	ThermoML loader for IUPAC/NIST thermodynamic property data.

Uses of Molecule in org.episteme.natural.biology

Subclasses of Molecule in org.episteme.natural.biology

Modifier and Type	Class	Description
class	Protein	Represents a protein structure composed of polypeptide chains.

Methods in org.episteme.natural.biology that return Molecule

Modifier and Type	Method	Description
Molecule	BioChemicalReaction.BioProduct.getMolecule()
Molecule	BioChemicalReaction.BioReactant.getMolecule()

Methods in org.episteme.natural.biology that return types with arguments of type Molecule

Modifier and Type	Method	Description
List<Molecule>	BioChemicalReaction.getCatalysts()

Methods in org.episteme.natural.biology with parameters of type Molecule

Modifier and Type	Method	Description
void	BioChemicalReaction.addCatalyst(Molecule enzyme)
void	BioChemicalReaction.addProduct(Molecule molecule, double stoichiometry)
void	BioChemicalReaction.addReactant(Molecule molecule, double stoichiometry)

Constructors in org.episteme.natural.biology with parameters of type Molecule

Modifier	Constructor	Description
	BioProduct(Molecule molecule, double stoichiometry)
	BioReactant(Molecule molecule, double stoichiometry)

Uses of Molecule in org.episteme.natural.biology.loaders.biopax

Methods in org.episteme.natural.biology.loaders.biopax that return Molecule

Modifier and Type	Method	Description
Molecule	BioPAXBridge.convertSmallMolecule(BioPAXPhysicalEntity entity)	Converts BioPAX small molecule to Episteme Molecule.

Uses of Molecule in org.episteme.natural.biology.loaders.sbml

Methods in org.episteme.natural.biology.loaders.sbml that return Molecule

Modifier and Type	Method	Description
Molecule	SBMLBridge.convertToMolecule(SBMLSpecies sbmlSpecies)	Converts a single SBML species to a Episteme Molecule.

Methods in org.episteme.natural.biology.loaders.sbml that return types with arguments of type Molecule

Modifier and Type	Method	Description
Map<String, List<Molecule>>	SBMLBridge.getCompartmentMoleculeMap(SBMLModel model)	Creates a compartment-to-species mapping for spatial modeling.
List<Molecule>	SBMLBridge.toMolecules(SBMLModel model)	Converts SBML species (metabolites) to Episteme Molecule objects.

Method parameters in org.episteme.natural.biology.loaders.sbml with type arguments of type Molecule

Modifier and Type	Method	Description
BioChemicalReaction	SBMLBridge.convertToReaction(SBMLReaction sbmlReaction, Map<String,Molecule> moleculeMap)	Converts a single SBML reaction to a Episteme BioChemicalReaction.

Uses of Molecule in org.episteme.natural.chemistry

Methods in org.episteme.natural.chemistry with parameters of type Molecule

Modifier and Type	Method	Description
static void	MolecularDynamics.step(Molecule molecule, double dt)	Legacy step method for double.
static void	MolecularDynamics.step(Molecule molecule, Real dt)	Performs a single simulation step.

Uses of Molecule in org.episteme.natural.chemistry.biochemistry

Subclasses of Molecule in org.episteme.natural.chemistry.biochemistry

Modifier and Type	Class	Description
class	AminoAcid	Standard amino acid data.

Uses of Molecule in org.episteme.natural.chemistry.computational

Methods in org.episteme.natural.chemistry.computational with parameters of type Molecule

Modifier and Type	Method	Description
static Real	ForceField.calculatePotentialEnergy(Molecule molecule)	Calculates total potential energy of a molecule.
static double	EnergyMinimizer.conjugateGradient(Molecule molecule, int maxIterations)	Conjugate Gradient minimization.
static double	EnergyMinimizer.steepestDescent(Molecule molecule, int maxIterations, double learningRate, double tolerance)	Steepest Descent minimization.

Uses of Molecule in org.episteme.natural.chemistry.computational.quantum

Fields in org.episteme.natural.chemistry.computational.quantum declared as Molecule

Modifier and Type	Field	Description
protected Molecule	SCFMethod.molecule

Constructors in org.episteme.natural.chemistry.computational.quantum with parameters of type Molecule

Modifier	Constructor	Description
	HartreeFockSCFMethod(Molecule molecule)
	SCFMethod(Molecule molecule)

Uses of Molecule in org.episteme.natural.chemistry.loaders

Methods in org.episteme.natural.chemistry.loaders that return Molecule

Modifier and Type	Method	Description
static Molecule	ChemistryDataReader.getMolecule(String name)	Gets a new instance (deep clone) of a loaded molecule.

Uses of Molecule in org.episteme.natural.chemistry.loaders.cml

Methods in org.episteme.natural.chemistry.loaders.cml that return Molecule

Modifier and Type	Method	Description
Molecule	CMLBridge.toMolecule(CMLMolecule cmlMolecule)	Converts a CML molecule representation to a Episteme Molecule.

Methods in org.episteme.natural.chemistry.loaders.cml that return types with arguments of type Molecule

Modifier and Type	Method	Description
List<Molecule>	CMLBridge.toMolecules(List<CMLMolecule> cmlMolecules)	Converts multiple CML molecules to Episteme Molecules.

Uses of Molecule in org.episteme.natural.chemistry.polymer

Methods in org.episteme.natural.chemistry.polymer that return Molecule

Modifier and Type	Method	Description
Molecule	Polymer.generateMolecule(int dp)	Generates a representative single-chain Molecule with the specified Degree of Polymerization.

Uses of Molecule in org.episteme.natural.chemistry.thermodynamics

Methods in org.episteme.natural.chemistry.thermodynamics that return Molecule

Modifier and Type	Method	Description
Molecule	ThermodynamicProperty.getCompound()

Methods in org.episteme.natural.chemistry.thermodynamics that return types with arguments of type Molecule

Modifier and Type	Method	Description
List<Molecule>	ThermodynamicDataset.getCompounds()
List<Molecule>	ThermodynamicProperty.getMixtureComponents()

Methods in org.episteme.natural.chemistry.thermodynamics with parameters of type Molecule

Modifier and Type	Method	Description
void	ThermodynamicDataset.addCompound(Molecule m)
void	ThermodynamicProperty.setCompound(Molecule compound)

Method parameters in org.episteme.natural.chemistry.thermodynamics with type arguments of type Molecule

Modifier and Type	Method	Description
void	ThermodynamicProperty.setMixtureComponents(List<Molecule> mixtureComponents)

Uses of Molecule in org.episteme.natural.physics.loaders.thermoml

Methods in org.episteme.natural.physics.loaders.thermoml that return Molecule

Modifier and Type	Method	Description
Molecule	ThermoMLBridge.convertCompound(ThermoMLCompound compound)	Converts ThermoML compound to Episteme Molecule.

Method parameters in org.episteme.natural.physics.loaders.thermoml with type arguments of type Molecule

Modifier and Type	Method	Description
ThermodynamicProperty	ThermoMLBridge.convertMixtureProperty(ThermoMLMixtureProperty prop, Map<String,Molecule> compoundMap)	Converts ThermoML mixture property.
ThermodynamicProperty	ThermoMLBridge.convertPureProperty(ThermoMLPureCompoundProperty prop, Map<String,Molecule> compoundMap)	Converts ThermoML pure compound property.