alchemist-incarnation-biochemistry/it.unibo.alchemist.model.biochemistry.actions

Package-level declarations

Types

abstract class AbstractNeighborAction<T>(reaction: NodeReaction<T>, environment: Environment<T, *>, randomGenerator: RandomGenerator) : AbstractRandomizableAction<T>

A local action applied to a neighbor of the node.

AbstractRandomizableAction

abstract class AbstractRandomizableAction<T>(reaction: NodeReaction<T>, randomGenerator: RandomGenerator) : AbstractLocalAction<T>

A local action relying on a randomGenerator.

AddJunctionInCell

class AddJunctionInCell(environment: Environment<Double, *>, reaction: NodeReaction<Double>, junction: Junction, randomGenerator: RandomGenerator) : AbstractNeighborAction<Double>

Adds junction between the node and a neighbor, inside the node only: the neighbor is unaware of it. AddJunctionInNeighbor performs the other part of the junction creation.

AddJunctionInNeighbor

class AddJunctionInNeighbor<P : Position<out P>>(environment: Environment<Double, P>, reaction: NodeReaction<Double>, junction: Junction, randomGenerator: RandomGenerator) : AbstractNeighborAction<Double>

Adds junction between a neighbor and the node, inside the neighbor only: the node is unaware of it. AddJunctionInCell performs the other part of the junction creation.

CellMove

class CellMove(environment: Environment<Double, Euclidean2DPosition>, reaction: NodeReaction<Double>, inPercent: Boolean, requestedDelta: Double) : AbstractMoveNode<Double, Euclidean2DPosition>

Moves a cell, namely a node with a CellProperty, along its polarization versor, then resets the versor.

CellTensionPolarization

class CellTensionPolarization(environment: EnvironmentSupportingDeformableCells<Euclidean2DPosition>, reaction: NodeReaction<Double>) : AbstractLocalAction<Double>

Models the tension polarization of a cell with a CircularDeformableCellProperty in an EnvironmentSupportingDeformableCells: the cell is pushed away from the overlapping cells.

ChangeBiomolConcentrationInCell

class ChangeBiomolConcentrationInCell(reaction: NodeReaction<Double>, molecule: Biomolecule, deltaConcentration: Double) : AbstractActionOnSingleMolecule<Double>

Changes the concentration of molecule in the cell by deltaConcentration, which must not be zero.

ChangeBiomolConcentrationInEnv

class ChangeBiomolConcentrationInEnv(environment: Environment<Double, *>, reaction: NodeReaction<Double>, biomolecule: Biomolecule, deltaConcentration: Double, randomGenerator: RandomGenerator) : AbstractRandomizableAction<Double>

Changes the concentration of biomolecule in the environment nodes around the node by deltaConcentration. The node must be an EnvironmentNode or have a CellProperty.

ChangeBiomolConcentrationInNeighbor

class ChangeBiomolConcentrationInNeighbor(randomGenerator: RandomGenerator, environment: Environment<Double, *>, reaction: NodeReaction<Double>, val molecule: Biomolecule, val deltaConcentration: Double) : AbstractNeighborAction<Double>

Changes the concentration of a Biomolecule (molecule) in a randomly-selected compatible neighbor cell by deltaConcentration.

ChemotacticPolarization

class ChemotacticPolarization(environment: Environment<Double, Euclidean2DPosition>, reaction: NodeReaction<Double>, biomolecule: Biomolecule, ascendGrad: String) : AbstractLocalAction<Double>

Models the chemotactic polarization of a cell: the polarization versor of the cell is directed towards the highest concentration of biomolecule in the neighboring environment nodes if ascendGrad is up, or in the opposite direction if it is down.

RandomPolarization

class RandomPolarization(environment: Environment<Double, Euclidean2DPosition>, reaction: NodeReaction<Double>, randomGenerator: RandomGenerator) : AbstractRandomizableAction<Double>

Polarizes a cell with a CellProperty in a random direction.

RemoveJunctionInCell

class RemoveJunctionInCell(environment: Environment<Double, *>, reaction: NodeReaction<Double>, junction: Junction, randomGenerator: RandomGenerator) : AbstractNeighborAction<Double>

Removes junction between the node and a neighbor, inside the node only: the neighbor is unaware of it. RemoveJunctionInNeighbor performs the other part of the junction removal.

RemoveJunctionInNeighbor

class RemoveJunctionInNeighbor(environment: Environment<Double, *>, reaction: NodeReaction<Double>, junction: Junction, randomGenerator: RandomGenerator) : AbstractNeighborAction<Double>

Removes junction between a neighbor and the node, inside the neighbor only: the node is unaware of it. RemoveJunctionInCell performs the other part of the junction removal.