All Classes

Class	Description
AbstractComplexEntityModification
AbstractConcentrationCondition
AbstractDeltaFunction<FunctionReturnType>	Delta Functions are used to calculate updates for Updatables during simulation.
AbstractGraphComplexReactor
AbstractKineticLaw
AbstractUpdateModule
ActinBoostVelocity
ActinBoostVelocity.Builder
AdditionExpressionNode	An ExpressionNode that handles additions and subtractions.
AddModification
AffectedRegion
AffectedRegion.Builder
AffectedSection
AffectedSection.Builder
AppliedVesicleState
AppliedVesicleState.Builder
AreaCondition
AssignmentRule
AssignmentRules
AttachedFilament
AttachedFilament.Builder
AttachedMotor
AttachedMotor.Builder
AttachmentDistance
AttachmentDistance.Builder
AutomatonEdge
AutomatonGraph	The Automaton graph class is the underlying graph of cellular graph automaton Simulations.
AutomatonGraphs
AutomatonNode	A node of the AutomatonGraph.
AutomatonNode.AreaMapping
BindingSite
BindModification
BlackListVesicleStates
BlackListVesicleStates.Builder
BoostMediatingEntity
BoostMediatingEntity.Builder
CandidateCondition
CandidateConditionBuilder
Cargo
Cargo.Builder
CargoAdditionRate
CargoAdditionRate.Builder
Cargoes
Cargoes.Builder
CellRegion
CellRegions
CellSubsection	A cell subsection organizes the contents of a Updatable.
CellSubsections
CellTopology	The cell topology defines how the subsections are spatially organized.
ChemicalEntities
ChemicalEntity	Chemical Entity is an abstract class that provides the common features of all chemical substances on a descriptive level.
ClathrinMediatedEndocytosis
ComplexEntity
ComplexEntityBuilder
ComplexEntityBuilder.CombineStep
ComplexEntityBuilder.ComplexEntityCombiner
ComplexEntityModification
ComplexEntityModificationBuilder
ComplexReactor
ConcentrationApplier
ConcentrationBasedModule<DeltaFunctionType extends AbstractDeltaFunction>	Concentration based modules handle updates that are applied to the concentrations in Updatables during a simulation.
ConcentrationBuilder
ConcentrationBuilder.AdditionalConditionsStep
ConcentrationBuilder.BuildStep
ConcentrationBuilder.ConcentrationBuilderImpl
ConcentrationBuilder.ConcentrationStep
ConcentrationBuilder.ConcentrationUnitStep
ConcentrationBuilder.EntityStep
ConcentrationBuilder.PoolStep
ConcentrationBuilder.TimedUnitStep
ConcentrationCondition
ConcentrationContainer	The concentration container manages the concentrations of one updatable.
ConcentrationDelta	The delta object manages the change that will be applied to the concentration of a specific ChemicalEntity in a CellSubsection.
ConcentrationDeltaIdentifier	Used to identify changes to concentrations (ConcentrationDeltas) (mostly in maps).
ConcentrationDeltaManager	The ConcentrationDeltaManager handles current concentrations of an updatable and the updates to those concentrations that should be applied during simulation.
ConcentrationPool	The concentration pool manages the MolarConcentration of ChemicalEntitys in CellSubsections.
ConcentrationStateChange
ConstantExpressionNode	An ExpressionNode that stores a constant value
ContainmentRegion
ContainmentRegion.Builder
DebugRecorder
DeltaBehavior
DependentUpdate	Dependent Updatable ConcentrationBasedModules require an integer state of basically all updatables in a simulation.
Diffusion	Diffusion is the fundamental force governing the random movement of molecules in cells.
Diffusion.BuildStep
Diffusion.DiffusionBuilder
Diffusion.EntityLimitationStep
Diffusion.SectionLimitationStep
DiffusivityScaling
DisplacementBasedModule
DisplacementDelta
DisplacementDeltaManager	The DisplacementDeltaManager handles the current position an updatable amd the updates to this position during simulation.
DisplacementDeviation
DynamicKineticLaw
EndocytosisActinBoost
EndocytosisCheckpointConcentration
EndocytosisCheckpointConcentration.Builder
EndocytosisCheckpointTime
EndocytosisCheckpointTime.Builder
EndocytoticPit
EndocytoticPitAbsorption
EndocytoticPitAbsorption.AccelerationStep
EndocytoticPitAbsorption.BuildStep
EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder
EndocytoticPitAbsorption.EntityStep
EndocytoticPitAbsorption.InhibitionStep
EndocytoticPitAbsorption.RateStep
EntityDeltaFunction	Entity delta functions are AbstractDeltaFunctions which return only one concentration delta.
EntityFeature
EntityRegistry
EntitySpecific	Entity specific ConcentrationBasedModules calculate their AbstractDeltaFunction for every chemical entity and every subsection of an updatable.
ErrorManager
ErrorManager.CalculationStage
ErrorManager.Reason
EvaluationException	A simple subclass of RuntimeException that indicates errors when trying to evaluate an expression.
ExponentiationExpressionNode	An ExpressionNode that handles exponentiation.
ExpressionNode	An interface for expression nodes.
ExpressionNodeVisitor	An interface for the visitor design pattern.
ExpressionParser	A parser for mathematical expressions.
FeatureManager
FeatureRandomizer
FeatureTable
FeatureTableRow
FieldSupplier	The field supplier manages all files required for different behaviours of a module.
FlatUpdateRecorder	This class can be used to write the concentration of chemical entities of a node and the changes applied to the node to a file.
FlatUpdateRecorder.BuildStep
FlatUpdateRecorder.ConcentrationUnitStep
FlatUpdateRecorder.DirectoryStep
FlatUpdateRecorder.EpochUpdateWriterBuilder
FlatUpdateRecorder.SimulationStep
FlatUpdateRecorder.TimeUnitStep
FlatUpdateRecorder.WorkspaceStep
FormatFeature
FormatModule
FormatReactionEquation
FormatReactionKinetics
FunctionExpressionNode	An ExpressionNode that handles mathematical functions.
FusionTime
FusionTime.Builder
GeneralModuleRow
GlobalDisplacementDeviationManager
GlobalNumericalErrorManager
GraphComplexEdge
GraphComplexNode
GraphEventEmitter	The implementation of an UpdateEventEmitter emitting updates of the graph to all listeners.
GraphUpdatedEvent	The Event that is emitted from the GraphEventEmitter, encapsulating a graph.
GridImageReader
GridMembraneBuilder
HasAnyNumberOfEntities
HasNoMoreThanNumberOfPartners
HasNumberOfEntities
HasOccupiedBindingSite
HasUnoccupiedBindingSite
IndependentUpdate	Independent Updatable ConcentrationBasedModules require the integer state of the currently calculated Updatable.
InitialConcentration
InitialConcentrations
InitialConcentrations.Builder
IrreversibleKineticLaw
IsOnlyBoundAt
KineticLaw
LateralMembraneDiffusion
LateralMembraneDiffusion.BuildStep
LateralMembraneDiffusion.EntityLimitationStep
LateralMembraneDiffusion.LateralMembraneDiffusionBuilder
LateralMembraneDiffusion.SectionLimitationStep
LineLikeAgent
LineLikeAgent.GrowthBehaviour
LineLikeAgentAttachment
LineLikeAgentLayer
LineLikeAgentTemplate
MatchingQSnares
MatchingQSnares.Builder
MatchingRSnares
MatchingRSnares.Builder
MaturationTime
MaturationTime.Builder
Membrane
MembraneDiffusion	The membrane diffusion module describes the movement of chemical entities across Membranes driven by the MembranePermeability of the cargo.
MembraneDiffusion.BuildStep
MembraneDiffusion.CargoStep
MembraneDiffusion.MembraneDiffusionBuilder
MembraneLayer
MembraneRestrictedBehavior
MembraneSegment
MembraneTickness
MembraneTickness.Builder
MembraneTracer	Deprecated.
MichaelisMentenKineticLaw
MicrotubuleOrganizingCentre
ModuleBuilder<ModuleType extends ConcentrationBasedModule>
ModuleCalculationException
ModuleFactory	Handles module creation with certain UpdateScope and UpdateSpecificity.
ModuleFactory.Scope	The type of UpdateScope.
ModuleFactory.Specificity	The type of UpdateSpecificity.
ModuleState	The state of the module is used to schedule the processing of modules in the UpdateScheduler.
ModuleSummaryTable
ModuleTable
ModuleTableConverter
ModuleTableRow
MotorMovementVelocity
MotorMovementVelocity.Builder
MotorPullDirection
MotorPullDirection.Builder
MultiEntityFeature
MultiplicationExpressionNode	An ExpressionNode that handles multiplications and divisions.
MultiStringFeature
NeighborhoodMappingManager
NestedUpdateRecorder
NodeBehavior
NodeEventEmitter	The implementation of an UpdateEventEmitter emitting updates of specific nodes to all listeners.
NodeIdentifierCondition
NodeTypeCondition
NumericalError	The LocalError object stores the error as an result of the currently applied time step.
NumericalInstabilityException
OneToOneReactor	This is for add and remove modifications.
OneToTwoReactor	This is for release modifications.
OrganelleImageParser
OrganelleTemplate
OrganelleTypes
Parameter<QuantityType extends javax.measure.Quantity<QuantityType>>
ParameterStorage
ParserException	A simple subclass of RuntimeException that indicates errors when trying to parse the input to Parser.
PitFormationRate
PitFormationRate.Builder
PorousDiffusion	Calculates diffusion through large pores (pore significantly larger than the cargo) in the membrane.
PorousDiffusion.BuildStep
PorousDiffusion.FeatureStep
PorousDiffusion.PorousDiffusionBuilder
PrimaryCargoes
PrimaryCargoes.Builder
QualitativeModule
Ratio
Ratio.Builder
Reactant	A Reactant encapsulates a ChemicalEntity for the use in Reactions.
ReactantBehavior
ReactantConcentration
ReactantDelta
ReactantRole	The role of the reactant: Increasing, for products and accelerating reactants and decreasing for substrates and inhibiting reactants.
ReactantSet
Reaction
ReactionBuilder
ReactionBuilder.ComplexBuildingReactionStep
ReactionBuilder.FinalStep
ReactionBuilder.GeneralReactionBuilder
ReactionBuilder.IrreversibleReactionStep
ReactionBuilder.KineticStep
ReactionBuilder.MichaelisMentenReactionStep
ReactionBuilder.ParameterStep
ReactionBuilder.ReversibleReactionStep
ReactionBuilder.RuleBasedBuilder
ReactionBuilder.RuleBasedStep
ReactionBuilder.StaticBuilder
ReactionBuilder.StaticReactantStep
ReactionChain
ReactionChainBuilder
ReactionChainBuilder.AbstractReactorBuilder
ReactionChainBuilder.AddReactionChainBuilder
ReactionChainBuilder.AddReactorPrimaryConditionStep
ReactionChainBuilder.AddReactorSecondarySubstrateStep
ReactionChainBuilder.BindReactionChainBuilder
ReactionChainBuilder.BindReactorPrimaryConditionStep
ReactionChainBuilder.BindReactorSecondaryConditionStep
ReactionChainBuilder.BindReactorSecondarySubstrateStep
ReactionChainBuilder.ConnectorStep
ReactionChainBuilder.ReactorChoiceStep
ReactionChainBuilder.ReleaseReactionChainBuilder
ReactionChainBuilder.ReleaseReactorPrimaryConditionStep
ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep
ReactionChainBuilder.RemoveReactionChainBuilder
ReactionChainBuilder.RemoveReactorPrimaryConditionStep
ReactionChainBuilder.RemoveReactorSecondarySubstrateStep
ReactionElement
ReactionEvent
ReactionGraph
ReactionGraphConverter
ReactionGraphEdge
ReactionGraphNode
ReactionNetworkGenerator
ReactionTableRow
ReactionTrack
Recorders
RegionCondition
RegionFeature
ReleaseModification
RemoveModification
RequiredVesicleState
RequiredVesicleState.Builder
ReversibleKineticLaw
RuleBasedReactantBehavior
ScalingEntities
ScalingEntities.Builder
SectionCondition
SectionDeltaFunction	Section delta functions are AbstractDeltaFunctions which return a list of concentration deltas.
SectionSpecific	Section specific ConcentrationBasedModules calculate their AbstractDeltaFunction for every subsection of an updatable.
SemiDependentUpdate	Semidependent Updatable ConcentrationBasedModules require the integer state of a subset of updatables.
SequenceExpressionNode	A base class for AdditionExpressionNode and MultiplicationExpressionNode.
SetVariable	A visitor that sets a variable with a specific name to a given value
SimpleEntity
SimpleEntity.SimpleEntityBuilder
Simulation
SimulationManager	Changes in simulations can be observed by tagging AutomatonNodes of the AutomatonGraph.
SimulationStatus
SingleFileChannelMembraneTransport	The single file channel transport describes the movement of cargo molecules through Transporter proteins, so called membrane channels.
SingleFileChannelMembraneTransport.BuildStep
SingleFileChannelMembraneTransport.CargoStep
SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder
SingleFileChannelMembraneTransport.SolutesStep
SingleFileChannelMembraneTransport.TransporterStep
SNAREFusionPairs	Snare pairs required for fusion event to trigger
SNAREFusionPairs.Builder
Solutes
Solutes.Builder
SpawnRate
StaticReactantBehavior
TeXFormat
TimedCondition
TimedCondition.Relation
TimeStepManager
Token	A token that is produced by Tokenizer and fed into Parser.parse A token consists of a token identifier, a string that the token was created from and the position in the input string that the token was found.
Tokenizer	A class for reading an input string and separating it into tokens that can be fed into Parser.
TopologyCondition
Trajectories
TrajectoryData
TrajectoryDataPoint
TrajectoryDataPoint.SubsectionDataPoint
Transporter
Transporter.Builder
TwoToOneReactor
Updatable
UpdatableDeltaFunction	Updatable delta functions are AbstractDeltaFunctions which return a map with ConcentrationDeltaIdentifiers mapping to to concentration deltas.
UpdatableSpecific	Updatable specific ConcentrationBasedModules calculate their AbstractDeltaFunction for every updatable.
UpdatableUpdatedEvent	The Event that is emitted from the NodeEventEmitter, encapsulating a updatable.
UpdateModule
UpdateScheduler
UpdateScope	The Update Scope determines the modules dependence on the rest of the simulation.
UpdateSpecificity<DeltaFunctionType extends AbstractDeltaFunction>	Determines how fine-grained the updates need to be calculated.
VariableExpressionNode	An ExpressionNode that stores a named variable
VariationTable
Vesicle
VesicleConfinedDiffusion
VesicleCytoplasmDiffusion
VesicleFusion
VesicleLayer
VesicleRadius
VesicleRadius.Builder
VesicleStateRegistry
VesicleTransport
VolumeLayer
VolumeLikeAgent
VolumeLikeAgentContainment	For vesicles state changes upon entering certain regions represented by volume like agents
VolumeLikeAgentFactory
WhiteListVesicleStates
WhiteListVesicleStates.Builder