jLM.Types

Simulation objects. Species, Reaction, etc.

Classes

BuilderReaction(sim, idx, *args, **kwargs)	Chemical reaction, in the context of simulation construction
BuilderRegion(sim, idx, *args, **kwargs)	Compartment, in the context of simulation construction
BuilderSpecies(sim, idx, *args, **kwargs)	Chemical species, in the context of simulation construction
DiffusionConst(sim, idx, *args, **kwargs)	Diffusion constant
RateConst(sim, idx, *args, **kwargs)	Reaction rate constant
Reaction(sim, idx, *args, **kwargs)	Chemical reaction
Region(sim, idx, *args, **kwargs)	Simulation compartment
Species(sim, idx, *args, **kwargs)	Chemical species
TrajRegion(sim, idx, *args, **kwargs)	Compartment, in the context of trajectory analysis
TrajSpecies(sim, idx, *args, **kwargs)	Chemical species, in the context of trajectory analysis

class jLM.Types.BuilderReaction(sim, idx, *args, **kwargs)

Bases: Reaction

Chemical reaction, in the context of simulation construction

assignToRegion(region)

Assign to a region

Parameters:

region (Region) – Target region

class jLM.Types.BuilderRegion(sim, idx, *args, **kwargs)

Bases: Region

Compartment, in the context of simulation construction

addReaction(*args, **kwargs)

Add a reaction to this region

Parameters:

• *args – Either a Reaction instance or the parameters needed to create a reaction

• *kwargs – kwargs necessary to create new reaction

diffusionRate(rate, value=None)

Set diffusion rate for all particles

Parameters:

• rate (DiffusionConst) – Diffusion rate

• value (float) – If str given for rate and the DiffusionConst does not exist, create it with this value

placeSpeciesConcentration(sps, conc)

Distribute a concentration of species

Parameters:

• sps (Species) – Species type

• conc (float) – Concentration

placeSpeciesNumber(sps, count)

Distribute a number of species

Parameters:

• sps (Species) – Species type

• count (int) – Number

transitionRateIn(rate, value=None)

Set diffusion rate for all particles entering this region

Parameters:

• rate (DiffusionConst) – Diffusion rate

• value (float) – If str given for rate and the DiffusionConst does not exist, create it with this value

transitionRateOut(rate, value=None)

Set diffusion rate for all particles leaving this region

Parameters:

• rate (DiffusionConst) – Diffusion rate

• value (float) – If str given for rate and the DiffusionConst does not exist, create it with this value

property NAV

property volume

class jLM.Types.BuilderSpecies(sim, idx, *args, **kwargs)

Bases: Species

Chemical species, in the context of simulation construction

diffusionRate(region, rate, value=None)

Set the diffusion rate

Parameters:

• region (Region) – Region

• rate (DiffusionConst) – Diffusion rate

• value (float) – If str given for rate and the DiffusionConst does not exist, create it with this value

placeConcentrationInto(region, conc)

Distribute a concentration within a region

Parameters:

• region (Region) – Target region

• conc (float) – Concentration in mol/L

placeNumberInto(region, count)

Distribute a number within a region

Parameters:

• region (Region) – Target region

• count (int) – number

placeParticle(x, y, z, count)

Place in a subvolume.

Parameters:

• x (int) – x-coordinate

• y (int) – y-coordinate

• z (int) – z-coordinate

• count (int) – Number of particles

show()

transitionRate(regionFrom, regionTo, rate, value=None)

Set the diffusion rate

Parameters:

• regionFrom (Region) – Source region

• regionTo (Region) – Destination region

• rate (DiffusionConst) – Diffusion rate

• value (float) – If str given for rate and the DiffusionConst does not exist, create it with this value

class jLM.Types.DiffusionConst(sim, idx, *args, **kwargs)

Bases: SimObj

Diffusion constant

class jLM.Types.RateConst(sim, idx, *args, **kwargs)

Bases: SimObj

Reaction rate constant

property stochasticRate

Return the stochastic rate constant \(k_{det}*N_A*V_sv^{1-o}\)

class jLM.Types.Reaction(sim, idx, *args, **kwargs)

Bases: SimObj

Chemical reaction

class jLM.Types.Region(sim, idx, *args, **kwargs)

Bases: SimObj

Simulation compartment

property NAV

property volume

class jLM.Types.Species(sim, idx, *args, **kwargs)

Bases: SimObj

Chemical species

show()

class jLM.Types.TrajRegion(sim, idx, *args, **kwargs)

Bases: Region

Compartment, in the context of trajectory analysis

getNumberTrajectoryFromRegion(**kwargs)

Get number trajectory a species spec for this region

See getNumberTrajectoryFromRegion()

property NAV

property volume

class jLM.Types.TrajSpecies(sim, idx, *args, **kwargs)

Bases: Species

Chemical species, in the context of trajectory analysis

getLatticeHistogram(**kwargs)

Get lattice histogram for this species

See getLatticeHistogram()

getLatticeTrajectory(**kwargs)

Get lattice trajectory for this species

See getLatticeTrajectory()

getNumberTrajectory(**kwargs)

Get particle number trajectory for this species

See getNumberTrajectory()

getNumberTrajectoryFromRegion(**kwargs)

Get number trajectory for a region spec for this species

See getNumberTrajectoryFromRegion()

show()