Lattice Microbes 2.5
This is for whole cell modeling
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jLM.RDMEExtended.SpatialModelExtended Member List

This is the complete list of members for jLM.RDMEExtended.SpatialModelExtended, including all inherited members.

__init__(self, name, filename, dimensions, latticeSpacing, latticeType=None, enable_size_checking=True)jLM.RDMEExtended.SpatialModelExtended
_copy_lattice_data(self, source, dest)jLM.ParticleSizeSupport.ParticleSizeMixinprotected
_particle_sizesjLM.ParticleSizeSupport.ParticleSizeMixinprotected
_particleDistConcjLM.RDME.SpatialModelprotected
_particleDistCountjLM.RDME.SpatialModelprotected
_particlePlacementjLM.RDME.SpatialModelprotected
_perfPrintIntervaljLM.RDME.SpatialModelprotected
_reactionLocationsjLM.RDME.SpatialModelprotected
_size_validatorjLM.ParticleSizeSupport.ParticleSizeMixinprotected
_transitionRatesjLM.RDME.SpatialModelprotected
_upgrade_to_extended_lattice(self)jLM.ParticleSizeSupport.ParticleSizeMixinprotected
assignReaction(self, reaction, region)jLM.RDME.SpatialModel
diffRateListjLM.RDME.SpatialModel
diffusionConst(self, rate, value, **kwargs)jLM.RDME.SpatialModel
diffusionFast(self)jLM.RDME.SpatialModel
diffusionZero(self)jLM.RDME.SpatialModel
distribute_concentration_safe(self, species, region, float concentration)jLM.ParticleSizeSupport.ParticleSizeMixin
distribute_number_safe(self, species, region, int count)jLM.ParticleSizeSupport.ParticleSizeMixin
distributeConcentration(self, sp, reg, conc)jLM.RDME.SpatialModel
distributeNumber(self, sp, reg, count)jLM.RDME.SpatialModel
enable_particle_sizes(self, bool enable=True)jLM.ParticleSizeSupport.ParticleSizeMixin
filenamejLM.RDME.SpatialModel
get_all_particle_sizes(self)jLM.ParticleSizeSupport.ParticleSizeMixin
get_capacity_summary(self)jLM.ParticleSizeSupport.ParticleSizeMixin
get_particle_size(self, species)jLM.ParticleSizeSupport.ParticleSizeMixin
hookInterval(self)jLM.RDME.SpatialModel
hookInterval(self, val)jLM.RDME.SpatialModel
jLM::ParticleSizeSupport::ParticleSizeMixin.latticejLM.ParticleSizeSupport.ParticleSizeMixin
latticeSpacingjLM.RDME.SpatialModel
latticeTypejLM.RDME.SpatialModel
latticeWriteInterval(self)jLM.RDME.SpatialModel
latticeWriteInterval(self, val)jLM.RDME.SpatialModel
maxConcentrationjLM.RDME.SpatialModel
maxDiffusionRate(self, latticeSpacing=None, dt=None)jLM.RDME.SpatialModel
NAjLM.RDME.SpatialModel
namejLM.RDME.SpatialModel
jLM::ParticleSizeSupport::ParticleSizeMixin.particleLatticejLM.ParticleSizeSupport.ParticleSizeMixin
perfPrintInterval(self)jLM.RDME.SpatialModel
perfPrintInterval(self, val)jLM.RDME.SpatialModel
placeNumber(self, sp, x, y, z, n)jLM.RDME.SpatialModel
ppsjLM.RDME.SpatialModel
print_capacity_summary(self)jLM.ParticleSizeSupport.ParticleSizeMixin
rateConst(self, rate, value, order, **kwargs)jLM.RDME.SpatialModel
reaction(self, reactants, products, rate, value=None, regions=None, **kwargs)jLM.RDME.SpatialModel
region(self, name, **kwargs)jLM.RDME.SpatialModel
resizeLattice(self, dimensions, latticeSpacing, latticeType=None)jLM.RDME.SpatialModel
run(self, solver=None, replicate=1, seed=None, cudaDevices=None, checkpointInterval=0, sample_frame=False, max_frames=100)jLM.RDME.SpatialModel
set_particle_size(self, species, int size)jLM.ParticleSizeSupport.ParticleSizeMixin
setMaximumTimestep(self)jLM.RDME.SpatialModel
shapejLM.RDME.SpatialModel
simulationTime(self)jLM.RDME.SpatialModel
simulationTime(self, val)jLM.RDME.SpatialModel
jLM::ParticleSizeSupport::ParticleSizeMixin.siteLatticejLM.ParticleSizeSupport.ParticleSizeMixin
siteNAVjLM.RDME.SpatialModel
siteVjLM.RDME.SpatialModel
size_validator(self)jLM.ParticleSizeSupport.ParticleSizeMixin
species(self, name, **kwargs)jLM.RDME.SpatialModel
speciesListjLM.ParticleSizeSupport.ParticleSizeMixin
speciesWriteInterval(self)jLM.RDME.SpatialModel
speciesWriteInterval(self, val)jLM.RDME.SpatialModel
transitionRate(self, sp, rFrom, rTo, rate, value=None)jLM.RDME.SpatialModel
validate_all_species(self)jLM.ParticleSizeSupport.ParticleSizeMixin