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

Package-level declarations

Types

abstract class AbstractNeighborCondition<T>(environment: Environment<T, *>, reaction: NodeReaction<T>) : AbstractLocalCondition<T>

A condition satisfied when at least one neighbor has a positive reaction-specific selection weight.

BiomolPresentInCell

class BiomolPresentInCell(reaction: NodeReaction<Double>, molecule: Molecule, requiredQuantity: Double) : GenericMoleculePresent<Double>

A condition requiring at least requiredQuantity units of molecule in the cell.

BiomolPresentInEnv

class BiomolPresentInEnv<P : Position<out P>>(environment: Environment<Double, P>, reaction: NodeReaction<Double>, biomolecule: Biomolecule, requiredQuantity: Double) : GenericMoleculePresent<Double>

A condition requiring requiredQuantity units of biomolecule in the surrounding environment.

BiomolPresentInNeighbor

class BiomolPresentInNeighbor(environment: Environment<Double, *>, reaction: NodeReaction<Double>, molecule: Biomolecule, concentration: Double) : AbstractNeighborCondition<Double>

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

EnvPresent

class EnvPresent(environment: Environment<Double, *>, reaction: NodeReaction<Double>) : AbstractLocalCondition<Double>

A condition valid when at least one EnvironmentNode is in the neighborhood of the node.

GenericMoleculePresent

open class GenericMoleculePresent<T : Number>(reaction: NodeReaction<T>, molecule: Molecule, val requiredQuantity: T) : AbstractLocalCondition<T>

A condition requiring at least requiredQuantity units of molecule in its node.

GenericMoleculeUnderLevel

class GenericMoleculeUnderLevel<T : Number>(reaction: NodeReaction<T>, molecule: Molecule, requiredQuantity: T) : GenericMoleculePresent<T>

A condition valid when the concentration of molecule in the node is lower than requiredQuantity; the reaction-specific rate law may use the distance from the threshold.

JunctionPresentInCell

class JunctionPresentInCell(environment: Environment<Double, *>, reaction: NodeReaction<Double>, junction: Junction) : AbstractNeighborCondition<Double>

A condition valid when junction is present in the cell.

NeighborhoodPresent

class NeighborhoodPresent<T>(environment: Environment<T, *>, reaction: NodeReaction<T>) : AbstractNeighborCondition<T>

A condition valid when the node has at least one neighboring cell, namely a neighbor with a CellProperty.

TensionPresent

class TensionPresent(environment: EnvironmentSupportingDeformableCells<*>, reaction: NodeReaction<Double>) : AbstractLocalCondition<Double>

A condition requiring mechanical tension from at least one nearby circular cell.