alchemist/it.unibo.alchemist.model.biochemistry/BiochemistryIncarnation

BiochemistryIncarnation

class BiochemistryIncarnation : Incarnation<Double, Euclidean2DPosition>

Factory for the biochemistry incarnation entities.

Constructors

BiochemistryIncarnation

constructor()

Functions

open fun createAction(randomGenerator: RandomGenerator, environment: Environment<Double, Euclidean2DPosition>, node: Node<Double>, reaction: Reaction<Double>, @Nullable additionalParameters: Any): Action<Double>

Creates an Action hosted by reaction, and by node (if any), in environment, using randomGenerator and parsing additionalParameters.

createConcentration

open fun createConcentration(@Nullable descriptor: Any): Double

Creates a new concentration of a specific concrete type, parsing descriptor.

createCondition

open fun createCondition(randomGenerator: RandomGenerator, environment: Environment<Double, Euclidean2DPosition>, node: Node<Double>, reaction: Reaction<Double>, @Nullable additionalParameters: Any): Condition<Double>

Creates a Condition hosted by reaction, and by node (if any), in environment, using randomGenerator and parsing additionalParameters.

open fun createMolecule(s: String): Biomolecule

Parses s into a Molecule.

open fun createNode(randomGenerator: RandomGenerator, environment: Environment<Double, Euclidean2DPosition>, @Nullable parameter: Any): Node<Double>

Creates a Node for environment, using randomGenerator and parsing parameter.

createNodeReaction

open fun createNodeReaction(randomGenerator: RandomGenerator, environment: Environment<Double, Euclidean2DPosition>, node: Node<Double>, timeDistribution: TimeDistribution<Double>, @Nullable parameter: Any): NodeReaction<Double>

Creates a NodeReaction hosted by node in environment, scheduled by timeDistribution, using randomGenerator and parsing parameter.

open fun createReaction(randomGenerator: RandomGenerator, environment: Environment<Double, Euclidean2DPosition>, @Nullable parameter: Any): Reaction<Double>

Creates an environment-level Reaction in environment, using randomGenerator and parsing parameter.

createTimeDistribution

open fun createTimeDistribution(randomGenerator: RandomGenerator, environment: Environment<Double, Euclidean2DPosition>, node: Node<Double>, @Nullable parameter: Any): TimeDistribution<Double>

Creates a TimeDistribution for a reaction hosted by node (if any) in environment, using randomGenerator and parsing parameter.

readConcentration

open fun readConcentration(node: Node<Double>, molecule: Molecule, property: String): Double

Extracts a numeric value from node, given a molecule and a property.

open fun toString(): String