alchemist/it.unibo.alchemist.model.biochemistry.conditions/BiomolPresentInNeighbor

BiomolPresentInNeighbor

class BiomolPresentInNeighbor : AbstractNeighborCondition<T>

This condition is valid if a selected biomolecule is present in the neighborhood of the node.

Constructors

constructor(environment: Environment<Double, out Any>, node: Node<Double>, molecule: Biomolecule, concentration: Double)

Properties

node

val node: Node<T>

Functions

cloneCondition

abstract fun cloneCondition(node: Node<T>, reaction: Reaction<T>): Condition<T>

open fun cloneCondition(node: Node<Double>, reaction: Reaction<Double>): BiomolPresentInNeighbor

open fun cloneCondition(newNode: Node<T>, newReaction: Reaction<T>): Condition<T>

This method allows cloning this action on a new node.

getContext

fun getContext(): Context

getInboundDependencies

fun getInboundDependencies(): ListSet<? extends Dependency>

How to override: if you intend your condition to be potentially changed by any change in the context, return null.

getPropensityContribution

open fun getPropensityContribution(): Double

Override if the desired behavior differs.

getValidNeighbors

fun getValidNeighbors(): Map<Node<T>, Double>

Searches in the given neighborhood which nodes satisfy the condition and returns a list of valid neighbors.

isValid

open fun isValid(): Boolean

reactionReady

open fun reactionReady()

This method is called by the Simulation once the Reaction whose this Condition belongs to is the next one to be executed, and all its conditions passed (namely, the next operation will be the reaction execution).

toString

open fun toString(): String