| __init__(self, *, name, filename, dimensions, latticeSpacing, regionName, latticeType=None, dt=None, enable_size_checking=True) | jLM.RDMEExtended.SimExtended | |
| _configure_solver_particle_sizes(self, solver) | jLM.RDMEExtended.SimExtended | protected |
| _copy_lattice_data(self, source, dest) | jLM.ParticleSizeSupport.ParticleSizeMixin | protected |
| _particle_sizes | jLM.ParticleSizeSupport.ParticleSizeMixin | protected |
| _particleDistConc | jLM.RDME.SpatialModel | protected |
| _particleDistCount | jLM.RDME.SpatialModel | protected |
| _particlePlacement | jLM.RDME.SpatialModel | protected |
| _particlesPlaced | jLM.RDME.Sim | protected |
| _perfPrintInterval | jLM.RDME.SpatialModel | protected |
| _reactionLocations | jLM.RDME.SpatialModel | protected |
| _size_validator | jLM.ParticleSizeSupport.ParticleSizeMixin | protected |
| _transitionRates | jLM.RDME.SpatialModel | protected |
| _upgrade_to_extended_lattice(self) | jLM.ParticleSizeSupport.ParticleSizeMixin | protected |
| analyze_occupancy_distribution(self) | jLM.RDMEExtended.SimExtended | |
| assignReaction(self, reaction, region) | jLM.RDME.SpatialModel | |
| bytesPerParticle | jLM.RDME.Sim | |
| construct(self) | jLM.RDMEExtended.SimExtended | |
| dc | jLM.RDME.Sim | |
| diffRateList | jLM.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.RDMEExtended.SimExtended | |
| distributeNumber(self, sp, reg, count) | jLM.RDMEExtended.SimExtended | |
| enable_particle_sizes(self, bool enable=True) | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| filename | jLM.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 | |
| get_site_analysis(self, x, y, z) | jLM.RDMEExtended.SimExtended | |
| hookInterval(self) | jLM.RDME.SpatialModel | |
| hookInterval(self, val) | jLM.RDME.SpatialModel | |
| jLM::ParticleSizeSupport::ParticleSizeMixin.lattice | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| latticeSpacing | jLM.RDME.SpatialModel | |
| latticeType | jLM.RDME.SpatialModel | |
| latticeWriteInterval(self) | jLM.RDME.SpatialModel | |
| latticeWriteInterval(self, val) | jLM.RDME.SpatialModel | |
| maxConcentration | jLM.RDME.SpatialModel | |
| maxDiffusionRate(self, latticeSpacing=None, dt=None) | jLM.RDME.SpatialModel | |
| NA | jLM.RDME.SpatialModel | |
| name | jLM.RDME.SpatialModel | |
| particle_sizes_passed | jLM.RDMEExtended.SimExtended | |
| jLM::ParticleSizeSupport::ParticleSizeMixin.particleLattice | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| particleStatistics(self, particleLattice=None, siteLattice=None) | jLM.RDME.Sim | |
| perfPrintInterval(self) | jLM.RDME.SpatialModel | |
| perfPrintInterval(self, val) | jLM.RDME.SpatialModel | |
| placeNumber(self, sp, x, y, z, n) | jLM.RDME.SpatialModel | |
| pps | jLM.RDME.SpatialModel | |
| print_capacity_summary(self) | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| print_occupancy_stats(self) | jLM.RDMEExtended.SimExtended | |
| rateConst(self, rate, value, order, **kwargs) | jLM.RDME.SpatialModel | |
| rc | jLM.RDME.Sim | |
| reaction(self, reactants, products, rate, value=None, regions=None, **kwargs) | jLM.RDME.SpatialModel | |
| reactionList | jLM.RDME.Sim | |
| reg | jLM.RDME.Sim | |
| region(self, name, **kwargs) | jLM.RDME.SpatialModel | |
| regionList | jLM.RDME.Sim | |
| 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.RDMEExtended.SimExtended | |
| rxnRateList | jLM.RDME.Sim | |
| set_particle_size(self, species, int size) | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| set_verbosity(self, verbosity) | jLM.RDMEExtended.SimExtended | |
| setMaximumTimestep(self) | jLM.RDME.SpatialModel | |
| shape | jLM.RDME.SpatialModel | |
| simulationTime(self) | jLM.RDME.SpatialModel | |
| simulationTime(self, val) | jLM.RDME.SpatialModel | |
| jLM::ParticleSizeSupport::ParticleSizeMixin.siteLattice | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| siteNAV | jLM.RDME.SpatialModel | |
| siteV | jLM.RDME.SpatialModel | |
| size_validator(self) | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| sp | jLM.RDME.Sim | |
| species(self, name, particle_size=1, **kwargs) | jLM.RDMEExtended.SimExtended | |
| jLM::ParticleSizeSupport::ParticleSizeMixin.speciesList | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| speciesWriteInterval(self) | jLM.RDME.SpatialModel | |
| speciesWriteInterval(self, val) | jLM.RDME.SpatialModel | |
| timestep | jLM.RDME.Sim | |
| transitionRate(self, sp, rFrom, rTo, rate, value=None) | jLM.RDME.SpatialModel | |
| validate_all_species(self) | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| verbosity | jLM.RDMEExtended.SimExtended | |
1.14.0