pyLM.RDME.RDMERegion Class Reference

A class that represents a type region of an RDME simulation. More...

Public Member Functions
def	__init__
	Creates a new RDMERegion. More...
def	addReaction
	Adds a 0th, 1st or 2nd order reaction that can occur in the region. More...
def	setDefaultDiffusionRate
	Specifies the default diffusion rate of all particles in the region. More...
def	setDiffusionRate
	Specify the diffusion rate for a particular particle type. More...
def	getReactionCount
	Return the number of reactions defined in this region. More...

Public Attributes
	name
	reactions
	defaultDiffusionRate
	diffusionRate

Detailed Description

A class that represents a type region of an RDME simulation.

Reactions may be specified that live within a region. In addition a specie's diffusion constant is region dependent and diffusion between regions must be specified. For example: cytosol, membrane, extracellular, nucleoid, etc.

Constructor & Destructor Documentation

def pyLM.RDME.RDMERegion.__init__	(		self,
			name
	)

Creates a new RDMERegion.

Parameters

self
name	The name of the region (e.g. cytosol)

Member Function Documentation

def pyLM.RDME.RDMERegion.addReaction	(		self,
			reactant,
			product,
			rate
	)

Adds a 0th, 1st or 2nd order reaction that can occur in the region.

Parameters

self
reactant	A set of reactants either as a singleton or a list
product	A set of products either as a singeton or a list

Returns

self

def pyLM.RDME.RDMERegion.getReactionCount

(

self

)

Return the number of reactions defined in this region.

Parameters

self

Returns

Get the number of reactions in the region

def pyLM.RDME.RDMERegion.setDefaultDiffusionRate	(		self,
			rate
	)

Specifies the default diffusion rate of all particles in the region.

Parameters

self
rate	The rate of diffusion in um^2/s or um/s for 3D or 2D diffusion

Returns

self

def pyLM.RDME.RDMERegion.setDiffusionRate	(		self,
			species,
			rate
	)

Specify the diffusion rate for a particular particle type.

Parameters

self
species	The particle type
rate	The rate of diffusion in um^2/s or um/s for 3D or 2D diffusion

Returns

self

Member Data Documentation

pyLM.RDME.RDMERegion.defaultDiffusionRate

pyLM.RDME.RDMERegion.diffusionRate

pyLM.RDME.RDMERegion.name

pyLM.RDME.RDMERegion.reactions

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The documentation for this class was generated from the following file:

• RDME.py