pyLM.RDME#

Functions

getReactionString(rct, prd, rate)

setLMLogConsole([level])

Set the logger to write to the console as the code is working

setLMLogFile(filename[, level])

Set up file handler to print log to file

setLMLoggerLevel(level)

Set the level of the logger for the application

visualizeRDMEInitialConditions(sim)

Visualize the RDME simulation volume inside Jupyter.

writeTable(columnNames, rows)

Classes

IntRDMESimulation(dimensions, spacing[, ...])

RDMERegion(name)

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

RDMESimulation(dimensions, spacing[, name, ...])

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

tqdm(*_, **__)

Decorate an iterable object, returning an iterator which acts exactly like the original iterable, but prints a dynamically updating progressbar every time a value is requested.
class pyLM.RDME.IntRDMESimulation(dimensions, spacing, name='unnamed', defaultRegion='default')[source]#

Bases: RDMESimulation

addCuboidRegion(name, a, b)#

Add a cuboid to the builder

Parameters:

  • 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

addParticleAt(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

addParticleAtIdx(index, particleType)#

Add a particle/ to a particular site

Parameters:

  • index (x,y,z) – a list of lattice site indices

  • specie – The specie type to add

addParticles(species='unknown', region='default', count=1)#

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

Parameters:

  • 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

addRegion(region)#

Add a region to the simulation

Parameters:

region – The region to add to the simulation

Returns:

region just added

addShape(shape)#

Add a Shape to the builder

Parameters:

shape – The Shape to add to the builder

allocateLattice()[source]#
buildCapsidCell(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:

  • 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

buildDifference(arg1, arg2, arg3)#
buildDiffusionModel()#

Return the Lattice Microbes DiffusionModel object for fine-tuning

Returns:

Simulation diffusion model

buildEllipse(arg1, arg2, arg3, arg4, arg5, arg6, arg7)#
buildPoint(arg1, arg2, arg3)#
buildReactionModel()#

Return the Lattice Microbes ReactionModel object for fine-tuning

Returns:

The reaction model for this simulation

buildSpatialModel()#

Return the Lattice Microbes SpatialModel object for fine-tuning

Returns:

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

buildSphere(arg1, arg2, arg3)#
buildSphericalCell(diameter, membraneThickness, point=False)#

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

Parameters:

  • diameter – The diameter of the cell

  • membraneThickness – The thickness of the membrane

  • point – The center of the spherical cell

Returns:

The simulation object

buildVector(arg1, arg2, arg3)#
defineSpecies(species)#

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

Parameters:

species – A list of species to add to the simulation

Returns:

The simulation object

getLattice(force=False)#

Get a discretized version of the simulation domain. Call this after building all spherical and capsule cells

Parameters:

force – Force a rediscretization of the lattice. This will throw away any additional changes made after the first call.

Returns:

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

getLatticeSite(index)#

Get a particular lattice site

Parameters:

index (x,y,z) – a list of coordinates

Returns:

The type of the lattice site (string)

modifyRegion(region)#

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

Parameters:

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

Returns:

The region to modify

packRegion(region, radius, percentage, obstacleID)#

Add nonmoving obstacles to a particular region

Parameters:

  • 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

run(filename, method, replicates=1, seed=None, cudaDevices=None, checkpointInterval=0)#

Run the simulation using the specified solver (e.g. NextSubvolume, MultiParticleDiffusion, etc.) for the specified amount of time

Parameters:

  • filename – The HDF file to write to

  • method – The class name for the solver to use (e.g., lm::rdme::MpdRdmeSolver”)

  • replicates – The number of replicates to serially run

  • seed – A seed for the random number generator to use when running the simulation; None indicates default

runMPI(filename, method, replicates=1, driver='mpirun', ppe=1, seed=None)#

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

Parameters:

  • 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 (e.g. number of nodes)

  • seed – A seed for the random number generator to use when running the simulation; None indicates default

runSolver(filename, solver, replicates=1, cudaDevices=None, checkpointInterval=0)#

Run a simulation with a given solver

Parameters:

  • filename – The HDF file to write to

  • solver – An MESolver object

  • replicates – The number of replicates to serially run

save(filename)#

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

Parameters:

filename – A file to write the simulation to

setHookInterval(time)#

Set the hook interval

Parameters:

time – The interval to call hookSimulation

setLatticeSite(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

setLatticeWriteInterval(time)#

Set the time interval to write latticedata at during simulation

Parameters:

time – The length of time between lattice data writes

setOverflowHandler(mode)#
setRandomSeed(seed)#

Set a known random seed

Parameters:

seed – The seed value

setSimulationTime(time)#

Set the simulation time length

Parameters:

time – The length of simulation time

setTimestep(time)#

Set the simulation time step

Parameters:

time – The length of simulation timestep for RDME

setTransitionRate(species, via, to, rate)#

Specify the diffusion rate between species; this is a one directional rate e.g. membrane->cytosol or extracellular->membrane

Parameters:

  • 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

setTwoWayTransitionRate(species, one, two, rate)#

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

Parameters:

  • species – The specie that can transition between regions

  • one – A region

  • two – The other region

  • rate – Diffusion rate between regions

Returns:

The simulation object

setWriteInterval(time)#

Set the time interval to write data at during simulation

Parameters:

time – The length of time between data writes

siteVolume()#

Get the actual volume of a specific site in L

Returns:

The volume of the site in L

class pyLM.RDME.RDMERegion(name)[source]#

Bases: object

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.

Parameters:

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

addReaction(reactant, product, rate)[source]#

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 \(1/\mathrm{s}\).

Parameters:

  • 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()[source]#

Return the number of reactions defined in this region

Returns:

Get the number of reactions in the region

setDefaultDiffusionRate(rate)[source]#

Specifies the default diffusion rate of all particles in the region

Parameters:

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

Returns:

RDMERegion

setDiffusionRate(species, rate)[source]#

Specify the diffusion rate for a particular particle type

Parameters:

  • species – The particle type

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

Returns:

RDMERegion

class pyLM.RDME.RDMESimulation(dimensions, spacing, name='unnamed', defaultRegion='default')[source]#

Bases: object

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

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

Parameters:

  • 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”

addCuboidRegion(name, a, b)[source]#

Add a cuboid to the builder

Parameters:

  • 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

addParticleAt(index, particleType)[source]#

Add a particle/ to a particular site

Parameters:

  • index (x,y,z) – a list of spatial location

  • specie – The specie type to add

addParticleAtIdx(index, particleType)[source]#

Add a particle/ to a particular site

Parameters:

  • index (x,y,z) – a list of lattice site indices

  • specie – The specie type to add

addParticles(species='unknown', region='default', count=1)[source]#

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

Parameters:

  • 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

addRegion(region)[source]#

Add a region to the simulation

Parameters:

region – The region to add to the simulation

Returns:

region just added

addShape(shape)[source]#

Add a Shape to the builder

Parameters:

shape – The Shape to add to the builder

allocateLattice()[source]#
buildCapsidCell(length, diameter, membraneThickness, points=False)[source]#

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

Parameters:

  • 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

buildDifference(arg1, arg2, arg3)[source]#
buildDiffusionModel()[source]#

Return the Lattice Microbes DiffusionModel object for fine-tuning

Returns:

Simulation diffusion model

buildEllipse(arg1, arg2, arg3, arg4, arg5, arg6, arg7)[source]#
buildPoint(arg1, arg2, arg3)[source]#
buildReactionModel()[source]#

Return the Lattice Microbes ReactionModel object for fine-tuning

Returns:

The reaction model for this simulation

buildSpatialModel()[source]#

Return the Lattice Microbes SpatialModel object for fine-tuning

Returns:

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

buildSphere(arg1, arg2, arg3)[source]#
buildSphericalCell(diameter, membraneThickness, point=False)[source]#

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

Parameters:

  • diameter – The diameter of the cell

  • membraneThickness – The thickness of the membrane

  • point – The center of the spherical cell

Returns:

The simulation object

buildVector(arg1, arg2, arg3)[source]#
defineSpecies(species)[source]#

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

Parameters:

species – A list of species to add to the simulation

Returns:

The simulation object

getLattice(force=False)[source]#

Get a discretized version of the simulation domain. Call this after building all spherical and capsule cells

Parameters:

force – Force a rediscretization of the lattice. This will throw away any additional changes made after the first call.

Returns:

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

getLatticeSite(index)[source]#

Get a particular lattice site

Parameters:

index (x,y,z) – a list of coordinates

Returns:

The type of the lattice site (string)

modifyRegion(region)[source]#

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

Parameters:

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

Returns:

The region to modify

packRegion(region, radius, percentage, obstacleID)[source]#

Add nonmoving obstacles to a particular region

Parameters:

  • 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

run(filename, method, replicates=1, seed=None, cudaDevices=None, checkpointInterval=0)[source]#

Run the simulation using the specified solver (e.g. NextSubvolume, MultiParticleDiffusion, etc.) for the specified amount of time

Parameters:

  • filename – The HDF file to write to

  • method – The class name for the solver to use (e.g., lm::rdme::MpdRdmeSolver”)

  • replicates – The number of replicates to serially run

  • seed – A seed for the random number generator to use when running the simulation; None indicates default

runMPI(filename, method, replicates=1, driver='mpirun', ppe=1, seed=None)[source]#

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

Parameters:

  • 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 (e.g. number of nodes)

  • seed – A seed for the random number generator to use when running the simulation; None indicates default

runSolver(filename, solver, replicates=1, cudaDevices=None, checkpointInterval=0)[source]#

Run a simulation with a given solver

Parameters:

  • filename – The HDF file to write to

  • solver – An MESolver object

  • replicates – The number of replicates to serially run

save(filename)[source]#

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

Parameters:

filename – A file to write the simulation to

setHookInterval(time)[source]#

Set the hook interval

Parameters:

time – The interval to call hookSimulation

setLatticeSite(index, siteType)[source]#

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

setLatticeWriteInterval(time)[source]#

Set the time interval to write latticedata at during simulation

Parameters:

time – The length of time between lattice data writes

setOverflowHandler(mode)[source]#
setRandomSeed(seed)[source]#

Set a known random seed

Parameters:

seed – The seed value

setSimulationTime(time)[source]#

Set the simulation time length

Parameters:

time – The length of simulation time

setTimestep(time)[source]#

Set the simulation time step

Parameters:

time – The length of simulation timestep for RDME

setTransitionRate(species, via, to, rate)[source]#

Specify the diffusion rate between species; this is a one directional rate e.g. membrane->cytosol or extracellular->membrane

Parameters:

  • 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

setTwoWayTransitionRate(species, one, two, rate)[source]#

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

Parameters:

  • species – The specie that can transition between regions

  • one – A region

  • two – The other region

  • rate – Diffusion rate between regions

Returns:

The simulation object

setWriteInterval(time)[source]#

Set the time interval to write data at during simulation

Parameters:

time – The length of time between data writes

siteVolume()[source]#

Get the actual volume of a specific site in L

Returns:

The volume of the site in L

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