pyLM.RDME.RDMERegion Class Reference

Public Member Functions
	__init__ (self, name)
	addReaction (self, reactant, product, rate)
	setDefaultDiffusionRate (self, rate)
	setDiffusionRate (self, species, rate)
	getReactionCount (self)

Public Attributes
	name = name
list	reactions = []
float	defaultDiffusionRate = 0.0
dict	diffusionRate = {}

Protected Member Functions
	_repr_html_ (self)
	Create a representation that is loadable in iPython.

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.

Args:
    name:
        The name of the region (e.g. cytosol)

Constructor & Destructor Documentation

__init__()

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

Member Function Documentation

_repr_html_()

pyLM.RDME.RDMERegion._repr_html_ ( self )

protected

Create a representation that is loadable in iPython.

Returns

A string containing an HTML object that can be displayed in the Jupyter notebook

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addReaction()

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

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

Reaction rates are specified as *stochastic* rates: i.e. in units of
:math:`1/\mathrm{s}`.

Args:
    reactant:
        A set of reactants either as a singleton or a list
    product:
        A set of products either as a singeton or a list
    rate:
        The *stochastic* rate of the reaction.

Returns:
    RDMERegion

getReactionCount()

pyLM.RDME.RDMERegion.getReactionCount

(

self

)

Return the number of reactions defined in this region

Returns:
    Get the number of reactions in the region

setDefaultDiffusionRate()

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

Specifies the default diffusion rate of all particles in the region 

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

Returns:
    RDMERegion

setDiffusionRate()

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

Specify the diffusion rate for a particular particle type

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

Returns:
    RDMERegion

Member Data Documentation

defaultDiffusionRate

float pyLM.RDME.RDMERegion.defaultDiffusionRate = 0.0

diffusionRate

dict pyLM.RDME.RDMERegion.diffusionRate = {}

name

pyLM.RDME.RDMERegion.name = name

reactions

pyLM.RDME.RDMERegion.reactions = []

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

• /data2/LM_zls_github/Lattice-Microbes/src/pylm/pyLM/RDME.py