pyLM.RDME.RDMESimulation Class Reference

A class that contains all regions, reactions, diffusions and rules for a RDME simulation. More...

Public Member Functions
def	__init__
	Specify a cuboid region that represents the extents to the reaction region as well as the lattice spacing. More...
def	addRegion
	Add a region to the simulation. More...
def	addCuboidRegion
	Add a cuboid to the builder. More...
def	addShape
def	modifyRegion
	Return a pointer to a region so that it may be modified. More...
def	defineSpecies
	Define a specie/s of particles that exist in the simulation. More...
def	siteVolume
	Get the actual volume of a specific site in L. More...
def	buildCapsidCell
	Build a capsule based shell in this RDMESimulation centered within the simulation domain that includes a membrane and cytoplasm. More...
def	buildSphericalCell
	Build a spherical based shell in this RDMESimulation centered within the simulation domain that includes a membrane and cytoplasm. More...
def	addParticles
	Add a specified number of particles of the specified type to the specified region. More...
def	packRegion
	Add nonmoving obstacles to a particular region. More...
def	setTransitionRate
	Specify the diffusion rate between species; this is a one directional rate e.g. More...
def	setTwoWayTransitionRate
	Specify the diffusion rate between species; this is a two directional rate. More...
def	buildDiffusionModel
	Return the Lattice Microbes DiffusionModel object for fine-tuning. More...
def	buildReactionModel
	Return the Lattice Microbes ReactionModel object for fine-tuning. More...
def	buildSpatialModel
	Return the Lattice Microbes SpatialModel object for fine-tuning. More...
def	setWriteInterval
def	setLatticeWriteInterval
def	setSimulationTime
def	setTimestep
def	setRandomSeed
def	getLattice
	Get a discretized version of the simulation domain. More...
def	setLatticeSite
	Set a particular lattice site type. More...
def	getLatticeSite
	Get a particular lattice site. More...
def	addParticleAt
	Add a particle/ to a particular site. More...
def	addParticleAtIdx
	Create an HDF5 version of the simulation amenable for later running or stand-alone running. More...
def	save
	Create an HDF5 version of the simulation amenable for later running or stand-alone running. More...
def	run
def	runMPI
	Run the simulation using a call to mpirun with the given options. More...
def	runSolver
def	buildVector
def	buildPoint
def	buildSphere
def	buildEllipse
def	buildDifference

Public Attributes
	siteTypes
	particleMap
	customAddedParticleList
	species_id
	regions
	transitionRates
	initial_counts
	parameters
	continousDimensions
	latticeSpacing
	lm_builder
	lattice
	hasBeenDiscretized
	name
	replicates
	filename

Detailed Description

A class that contains all regions, reactions, diffusions and rules for a RDME simulation.

Constructor & Destructor Documentation

def pyLM.RDME.RDMESimulation.__init__	(		self,
			dimensions,
			spacing,
			name = "unnamed",
			defaultRegion = "default"
	)

Specify a cuboid region that represents the extents to the reaction region as well as the lattice spacing.

Parameters

self
dimensions	A list of [x,y,z]
spacing	Lattice spacing
name	The name of the RDME simulation; default: "unnamed"
defaultRegion	The name of the region that is associated with the lattice sites before any other regions are added; default:"default"

Returns

self

Member Function Documentation

def pyLM.RDME.RDMESimulation.addCuboidRegion	(		self,
			name,
			a,
			b
	)

Add a cuboid to the builder.

Parameters

self
name	Name of the site type for this region
a	tuple for the first corner in continous space
b	tuple for the second corner in continous space

def pyLM.RDME.RDMESimulation.addParticleAt	(		self,
			index,
			particleType
	)

Add a particle/ to a particular site.

Parameters

index	(x,y,z) a list of spatial location
specie	The specie type to add

def pyLM.RDME.RDMESimulation.addParticleAtIdx	(		self,
			index,
			particleType
	)

Create an HDF5 version of the simulation amenable for later running or stand-alone running.

Parameters

self
filename	A file to write the simulation to Add a particle/ to a particular site
index	(x,y,z) a list of lattice site indices
specie	The specie type to add

def pyLM.RDME.RDMESimulation.addParticles	(		self,
			species = 'unknown',
			region = 'default',
			count = 1
	)

Add a specified number of particles of the specified type to the specified region.

Parameters

self
species	The species to add to the region
region	The region to add particles to
count	Number of particles to add (default: 1)

Returns

The simulation object

def pyLM.RDME.RDMESimulation.addRegion	(		self,
			region
	)

Add a region to the simulation.

Parameters

self
region	The region to add to the simulation

Returns

The region just added

def pyLM.RDME.RDMESimulation.addShape	(		self,
			shape
	)

def pyLM.RDME.RDMESimulation.buildCapsidCell	(		self,
			length,
			diameter,
			membraneThickness,
			points = False
	)

Build a capsule based shell in this RDMESimulation centered within the simulation domain that includes a membrane and cytoplasm.

Parameters

self
length	The length of the capsule from one sphere origin to the other
diameter	The diameter of the cell
membraneThickness	The thickness of the membrane
points	OPTIONAL: List of lists containing the coordinates of the centers of the sphereoids that cap the capsid cell, e.g. [[x1, y1, z1], [x2, y2, z2]]. If not given, cell is centered in the volume and aligned in the z-direction

Returns

The simulation object

def pyLM.RDME.RDMESimulation.buildDifference	(		self,
			arg1,
			arg2,
			arg3
	)

def pyLM.RDME.RDMESimulation.buildDiffusionModel

(

self

)

Return the Lattice Microbes DiffusionModel object for fine-tuning.

Parameters

self	The diffusion modle for the simulation

def pyLM.RDME.RDMESimulation.buildEllipse	(		self,
			arg1,
			arg2,
			arg3,
			arg4,
			arg5,
			arg6,
			arg7
	)

def pyLM.RDME.RDMESimulation.buildPoint	(		self,
			arg1,
			arg2,
			arg3
	)

def pyLM.RDME.RDMESimulation.buildReactionModel

(

self

)

Return the Lattice Microbes ReactionModel object for fine-tuning.

Parameters

self

Returns

The reaction model for this simulation

def pyLM.RDME.RDMESimulation.buildSpatialModel

(

self

)

Return the Lattice Microbes SpatialModel object for fine-tuning.

Parameters

self

Returns

The spatial model (i.e. obstacles, sites, etc.) for this simulation

def pyLM.RDME.RDMESimulation.buildSphere	(		self,
			arg1,
			arg2,
			arg3
	)

def pyLM.RDME.RDMESimulation.buildSphericalCell	(		self,
			diameter,
			membraneThickness,
			point = False
	)

Build a spherical based shell in this RDMESimulation centered within the simulation domain that includes a membrane and cytoplasm.

Parameters

self
diameter	The diameter of the cell
membraneThickness	The thickness of the membrane
point	The center of the spherical cell

Returns

The simulation object

def pyLM.RDME.RDMESimulation.buildVector	(		self,
			arg1,
			arg2,
			arg3
	)

def pyLM.RDME.RDMESimulation.defineSpecies	(		self,
			species
	)

Define a specie/s of particles that exist in the simulation.

Parameters

self
species	A list of species to add to the simulation

Returns

The simulation object

def pyLM.RDME.RDMESimulation.getLattice

(

self

)

Get a discretized version of the simulation domain.

Call this after building all spherical and capsule cells

Parameters

self

Returns

A lattice object. This function should only be called once.

def pyLM.RDME.RDMESimulation.getLatticeSite	(		self,
			index
	)

Get a particular lattice site.

Parameters

index

(x,y,z) a list of coordinates

Returns

The type of the lattice site (string)

def pyLM.RDME.RDMESimulation.modifyRegion	(		self,
			region
	)

Return a pointer to a region so that it may be modified.

Parameters

self
region	Get a region that is attached to the simulation for modification

Returns

The region to modify

def pyLM.RDME.RDMESimulation.packRegion	(		self,
			region,
			radius,
			percentage,
			obstacleID
	)

Add nonmoving obstacles to a particular region.

Parameters

self
region	The name of the region in which to add particles to
radius	The radius of the particles
percentage	The percentage of the total region volume that should be packed
obstacleID	an identifier for the obstacle

Returns

The simulation object

def pyLM.RDME.RDMESimulation.run	(		self,
			filename,
			method,
			replicates = 1,
			seed = None
	)

def pyLM.RDME.RDMESimulation.runMPI	(		self,
			filename,
			method,
			replicates = 1,
			driver = "mpirun",
			ppe = 1,
			seed = None
	)

Run the simulation using a call to mpirun with the given options.

Parameters

self
filename	The HDF file to write to
method	The class name for the solver to use (e.g., lm::cme::GillespieDSolver")
replicates	The number of replicates to serially run
driver	The program to execute the parallel run, e.g. "mpirun", "aprun", "ibrun", etc.
ppe	The number of processing elements to use
seed	A seed for the random number generator to use when running the simulation; None indicates default

def pyLM.RDME.RDMESimulation.runSolver	(		self,
			filename,
			solver,
			replicates = 1
	)

def pyLM.RDME.RDMESimulation.save	(		self,
			filename
	)

Create an HDF5 version of the simulation amenable for later running or stand-alone running.

Parameters

self
filename	A file to write the simulation to

def pyLM.RDME.RDMESimulation.setLatticeSite	(		self,
			index,
			siteType
	)

Set a particular lattice site type.

Parameters

index	(x,y,z) a list of coordinates
siteType	The type to set the lattice point to. This would be the name of a region that has previously been performed"

def pyLM.RDME.RDMESimulation.setLatticeWriteInterval	(		self,
			time
	)

def pyLM.RDME.RDMESimulation.setRandomSeed	(		self,
			seed
	)

def pyLM.RDME.RDMESimulation.setSimulationTime	(		self,
			time
	)

def pyLM.RDME.RDMESimulation.setTimestep	(		self,
			time
	)

def pyLM.RDME.RDMESimulation.setTransitionRate	(		self,
			species,
			via,
			to,
			rate
	)

Specify the diffusion rate between species; this is a one directional rate e.g.

membrane->cytosol or extracellular->membrane

Parameters

self
species	The specie that can transition between regions
via	From this region
to	To this region
rate	Diffusion rate between regions

Returns

The simulation object

def pyLM.RDME.RDMESimulation.setTwoWayTransitionRate	(		self,
			species,
			one,
			two,
			rate
	)

Specify the diffusion rate between species; this is a two directional rate.

Parameters

self
species	The specie that can transition between regions
one	A region
two	The other region
rate	Diffusion rate between regions

Returns

The simulation object

def pyLM.RDME.RDMESimulation.setWriteInterval	(		self,
			time
	)

def pyLM.RDME.RDMESimulation.siteVolume

(

self

)

Get the actual volume of a specific site in L.

Returns

the volume of the site in L

Member Data Documentation

pyLM.RDME.RDMESimulation.continousDimensions

pyLM.RDME.RDMESimulation.customAddedParticleList

pyLM.RDME.RDMESimulation.filename

pyLM.RDME.RDMESimulation.hasBeenDiscretized

pyLM.RDME.RDMESimulation.initial_counts

pyLM.RDME.RDMESimulation.lattice

pyLM.RDME.RDMESimulation.latticeSpacing

pyLM.RDME.RDMESimulation.lm_builder

pyLM.RDME.RDMESimulation.name

pyLM.RDME.RDMESimulation.parameters

pyLM.RDME.RDMESimulation.particleMap

pyLM.RDME.RDMESimulation.regions

pyLM.RDME.RDMESimulation.replicates

pyLM.RDME.RDMESimulation.siteTypes

pyLM.RDME.RDMESimulation.species_id

pyLM.RDME.RDMESimulation.transitionRates

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

• RDME.py