| __init__(self, fname, replicate=1, latticeType=None, sample_frame=False, max_frames=100, enable_size_checking=False) | jLM.RDMEExtended.FileExtended | |
| _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 |
| _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_trajectory_occupancy(self, frame_indices=None) | jLM.RDMEExtended.FileExtended | |
| assignReaction(self, reaction, region) | jLM.RDME.SpatialModel | |
| close_hdf_file | jLM.RDME.File | |
| close_hdf_file(self) | jLM.RDME.File | |
| counts | jLM.RDME.File | |
| dc | jLM.RDME.File | |
| 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.RDME.SpatialModel | |
| distributeNumber(self, sp, reg, count) | jLM.RDME.SpatialModel | |
| 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 | |
| h5 | jLM.RDME.File | |
| hookInterval(self) | jLM.RDME.SpatialModel | |
| hookInterval(self, val) | jLM.RDME.SpatialModel | |
| init_worker(self, file_name) | jLM.RDME.File | |
| 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 | |
| load_particle_sizes_from_metadata(self) | jLM.RDMEExtended.FileExtended | |
| maxConcentration | jLM.RDME.SpatialModel | |
| maxDiffusionRate(self, latticeSpacing=None, dt=None) | jLM.RDME.SpatialModel | |
| NA | jLM.RDME.SpatialModel | |
| name | jLM.RDME.SpatialModel | |
| jLM::ParticleSizeSupport::ParticleSizeMixin.particleLattice | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| 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 | |
| process_frame(self, frame_index, siteTypesLattice, numberSpecies, numberSiteTypes) | jLM.RDME.File | |
| rateConst(self, rate, value, order, **kwargs) | jLM.RDME.SpatialModel | |
| rc | jLM.RDME.File | |
| reaction(self, reactants, products, rate, value=None, regions=None, **kwargs) | jLM.RDME.SpatialModel | |
| reactionList | jLM.RDME.File | |
| reduce_trajectory_file(self, file_name, max_frames) | jLM.RDME.File | |
| reg | jLM.RDME.File | |
| region(self, name, **kwargs) | jLM.RDME.SpatialModel | |
| regionList | jLM.RDME.File | |
| replicate | jLM.RDMEExtended.FileExtended | |
| 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 | |
| rxnRateList | jLM.RDME.File | |
| set_particle_size(self, species, int size) | jLM.ParticleSizeSupport.ParticleSizeMixin | |
| 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.File | |
| species(self, name, **kwargs) | jLM.RDME.SpatialModel | |
| jLM::ParticleSizeSupport::ParticleSizeMixin.speciesList | jLM.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 | |
| vmd_precomp(self, file_name) | jLM.RDME.File | |
| write_to_h5(self, file_name, maxParticleCounts, maxSiteCounts) | jLM.RDME.File | |
1.14.0