de.bioforscher.singa.simulation.model.concentrations

Class MembraneContainer

java.lang.Object

de.bioforscher.singa.simulation.model.concentrations.MembraneContainer

All Implemented Interfaces:

ConcentrationContainer

public class MembraneContainer
extends Object
implements ConcentrationContainer

In this representation of a membrane is divided into four parts. An outer aqueous phase, an inner aqueous phase, the layer of the membrane oriented to the outer phase, and the layer of the membrane oriented to the inner phase. This class is modelled after the representation in: Dickson 2016 - Structure-kinetic relationships of passive membrane permeation from multiscale modeling.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
MembraneContainer(CellSection outerPhaseSection, CellSection innerPhaseSection, Membrane membrane)
MembraneContainer(MembraneContainer container)

Method Summary

Modifier and Type	Method and Description
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	getAllConcentrations() Returns the representative concentrations of all referenced chemical entities.
Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>>	getAllConcentrationsForSection(CellSection cellSection) Returns all concentrations for a particular CellSection.
Set<ChemicalEntity<?>>	getAllReferencedEntities() Returns all ChemicalEntities that are referenced in this container.
Set<CellSection>	getAllReferencedSections() Returns all Compartments that are referenced in this container.
javax.measure.Quantity<MolarConcentration>	getAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity) Returns the concentration of the specified ChemicalEntity available in the CellSection.
javax.measure.Quantity<MolarConcentration>	getConcentration(ChemicalEntity chemicalEntity) Returns the representative concentration of a chemical entity.
MembraneContainer	getCopy() Returns a copy of this concentration container.
CellSection	getInnerLayerSection()
javax.measure.Quantity<MolarConcentration>	getInnerMembraneLayerConcentration(ChemicalEntity chemicalEntity)
javax.measure.Quantity<MolarConcentration>	getInnerPhaseConcentration(ChemicalEntity chemicalEntity)
CellSection	getInnerPhaseSection()
Membrane	getMembrane()
CellSection	getOuterLayerSection()
javax.measure.Quantity<MolarConcentration>	getOuterMembraneLayerConcentration(ChemicalEntity chemicalEntity)
javax.measure.Quantity<MolarConcentration>	getOuterPhaseConcentration(ChemicalEntity chemicalEntity)
CellSection	getOuterPhaseSection()
void	setAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration) Sets the available concentration based on the given compartment.
void	setConcentration(ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration) Sets the representative concentration of a chemical entity.

Methods inherited from class java.lang.Object

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

Constructor Detail

MembraneContainer

public MembraneContainer(CellSection outerPhaseSection,
                         CellSection innerPhaseSection,
                         Membrane membrane)

MembraneContainer

public MembraneContainer(MembraneContainer container)

Method Detail

getConcentration

public javax.measure.Quantity<MolarConcentration> getConcentration(ChemicalEntity chemicalEntity)

Description copied from interface: ConcentrationContainer

Returns the representative concentration of a chemical entity. If the concentration is available differently for multiple compartments the average concentration is returned.

Specified by:

getConcentration in interface ConcentrationContainer

Parameters:

chemicalEntity - The ChemicalEntity.

Returns:

The concentration.

getOuterPhaseConcentration

public javax.measure.Quantity<MolarConcentration> getOuterPhaseConcentration(ChemicalEntity chemicalEntity)

getInnerPhaseConcentration

public javax.measure.Quantity<MolarConcentration> getInnerPhaseConcentration(ChemicalEntity chemicalEntity)

getOuterMembraneLayerConcentration

public javax.measure.Quantity<MolarConcentration> getOuterMembraneLayerConcentration(ChemicalEntity chemicalEntity)

getInnerMembraneLayerConcentration

public javax.measure.Quantity<MolarConcentration> getInnerMembraneLayerConcentration(ChemicalEntity chemicalEntity)

getAllConcentrationsForSection

public Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>> getAllConcentrationsForSection(CellSection cellSection)

Description copied from interface: ConcentrationContainer

Returns all concentrations for a particular CellSection.

Specified by:

getAllConcentrationsForSection in interface ConcentrationContainer

Parameters:

cellSection - The CellSection

Returns:

All concentrations in this CellSection.

getAvailableConcentration

public javax.measure.Quantity<MolarConcentration> getAvailableConcentration(CellSection cellSection,
                                                                            ChemicalEntity chemicalEntity)

Description copied from interface: ConcentrationContainer

Returns the concentration of the specified ChemicalEntity available in the CellSection.

Specified by:

getAvailableConcentration in interface ConcentrationContainer

Parameters:

cellSection - The CellSection

chemicalEntity - The ChemicalEntity.

Returns:

The concentration of the ChemicalEntity in the CellSection.

setConcentration

public void setConcentration(ChemicalEntity chemicalEntity,
                             javax.measure.Quantity<MolarConcentration> concentration)

Description copied from interface: ConcentrationContainer

Sets the representative concentration of a chemical entity. This resets the available concentrations for all registered compartments.

Specified by:

setConcentration in interface ConcentrationContainer

Parameters:

chemicalEntity - The ChemicalEntity.

concentration - The concentration.

setAvailableConcentration

public void setAvailableConcentration(CellSection cellSection,
                                      ChemicalEntity chemicalEntity,
                                      javax.measure.Quantity<MolarConcentration> concentration)

Description copied from interface: ConcentrationContainer

Sets the available concentration based on the given compartment.

Specified by:

setAvailableConcentration in interface ConcentrationContainer

Parameters:

cellSection - The identifier of the compartment.

chemicalEntity - The ChemicalEntity.

concentration - The concentration.

getAllReferencedEntities

public Set<ChemicalEntity<?>> getAllReferencedEntities()

Description copied from interface: ConcentrationContainer

Returns all ChemicalEntities that are referenced in this container.

Specified by:

getAllReferencedEntities in interface ConcentrationContainer

Returns:

All ChemicalEntities that are referenced in this container.

getAllReferencedSections

public Set<CellSection> getAllReferencedSections()

Description copied from interface: ConcentrationContainer

Returns all Compartments that are referenced in this container.

Specified by:

getAllReferencedSections in interface ConcentrationContainer

Returns:

All Compartments that are referenced in this container.

getMembrane

public Membrane getMembrane()

getOuterPhaseSection

public CellSection getOuterPhaseSection()

getOuterLayerSection

public CellSection getOuterLayerSection()

getInnerLayerSection

public CellSection getInnerLayerSection()

getInnerPhaseSection

public CellSection getInnerPhaseSection()

getAllConcentrations

public Map<ChemicalEntity<?>,javax.measure.Quantity<MolarConcentration>> getAllConcentrations()

Description copied from interface: ConcentrationContainer

Returns the representative concentrations of all referenced chemical entities.

Specified by:

getAllConcentrations in interface ConcentrationContainer

Returns:

The representative concentrations of all referenced chemical entities.

getCopy

public MembraneContainer getCopy()

Description copied from interface: ConcentrationContainer

Returns a copy of this concentration container.

Specified by:

getCopy in interface ConcentrationContainer

Returns:

A copy of this concentration container.