37.1.1

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

BiomolPresentInEnv

class BiomolPresentInEnv<P : Position<out P>?> : GenericMoleculePresent<T>

Parameters

<P>

Position type

Constructors

BiomolPresentInEnv

constructor(environment: Environment<Double, P>, node: Node<Double>, biomolecule: Biomolecule, concentration: Double)

Initialize condition for extracellular environment, implemented as a set of EnvironmentNode.

Properties

val molecule: Molecule

val node: Node<T>

Functions

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

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

This method allows to clone this action on a new node.

open fun cloneCondition(node: Node<Double>, r: Reaction<Double>): BiomolPresentInEnv<P>

How to override: create a new action of your concrete subtype.

open 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

Propensity influence is computed through the binomial coefficient.

open fun getQuantity(): T

Allows to access the threshold.

open fun isValid(): Boolean

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).

open fun toString(): String