Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z A add_dependency_matrix() (lm.ReactionModel method) add_diffusion_matrix() (lm.DiffusionModel method) add_initial_species_count() (lm.ReactionModel method) add_rate_constant() (lm.ReactionModel_Reaction method) add_reaction() (lm.ReactionModel method) add_reaction_location_matrix() (lm.DiffusionModel method) add_stoichiometric_matrix() (lm.ReactionModel method) addConcentration() (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) addCuboidRegion() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) addLacTwoStateSystem() (in module pySTDLM.StandardReactionSystems) addMembraneTransporter() (in module pySTDLM.StandardReactions) addMichaelisMenten() (in module pySTDLM.StandardReactions) addMinDESystem() (in module pySTDLM.StandardReactionSystems) addParticle() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) addParticleAt() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) addParticleAtIdx() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) addParticles() (jLM.CME.CMESimulation method) (lm.LatticeBuilder method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) addParticlesToRegion() (pySTDLM.Distributions.ParticleGenerator method) addPassiveTransport() (in module pySTDLM.StandardReactions) addPTSPathway() (in module pySTDLM.StandardReactionSystems) addReaction() (jLM.CME.CMESimulation method) (jLM.Types.BuilderRegion method) (pyLM.CME.CMESimulation method) (pyLM.RDME.RDMERegion method) addRegion() (lm.LatticeBuilder method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) addReversibleMichaelisMenten() (in module pySTDLM.StandardReactions) addShape() (lm.UnionSet method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) addToSimulation() (pySTDLM.CellArranger.CellArranger method) (pySTDLM.CellArranger.LooseGridArranger method) (pySTDLM.CellArranger.RandomArranger method) (pySTDLM.CellArranger.RandomSphericalArranger method) (pySTDLM.CellArranger.TightGridArranger method) (pySTDLM.Cells.BoxCell method) (pySTDLM.Cells.CapsuleCell method) (pySTDLM.Cells.CapsuleShellCell method) (pySTDLM.Cells.CellShape method) (pySTDLM.Cells.SphereCell method) advance() (lm.SwigPyIterator method) allocateLattice() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) angstrom() (in module pyLM.units) append() (lm.stdVectorInt method) appendParticle() (in module jLM.Lattice) assign() (lm.stdVectorInt method) assignReaction() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) assignToRegion() (jLM.Types.BuilderReaction method) B back() (lm.stdVectorInt method) begin() (lm.stdVectorInt method) bounding_box (class in lm) boundingBox() (pySTDLM.Cells.BoxCell method) (pySTDLM.Cells.CapsuleCell method) (pySTDLM.Cells.CapsuleShellCell method) (pySTDLM.Cells.CellShape method) (pySTDLM.Cells.SphereCell method) boundingBoxesIntersect() (lm.Capsule method) (lm.CapsuleShell method) (lm.Cone method) (lm.Cuboid method) (lm.Cylinder method) (lm.Difference method) (lm.Ellipse method) (lm.Hemisphere method) (lm.Intersection method) (lm.Shape method) (lm.Sphere method) (lm.Torus method) (lm.Union method) (lm.UnionSet method) box() (jLM.RegionBuilder.RegionBuilder method) BoxCell (class in pySTDLM.Cells) buildCapsidCell() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) buildData (in module jLM) buildDifference() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) buildDiffusionModel() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) buildDividingEColiCell() (in module pySTDLM.StandardCells) buildEColiCell() (in module pySTDLM.StandardCells) buildEllipse() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) BuilderReaction (class in jLM.Types) BuilderRegion (class in jLM.Types) BuilderSpecies (class in jLM.Types) buildFilamentousEColiCell() (in module pySTDLM.StandardCells) buildPoint() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) buildReactionModel() (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) buildSpatialModel() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) buildSphere() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) buildSphericalCell() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) buildSphericalEColiCell() (in module pySTDLM.StandardCells) buildVector() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) ByteLattice (class in lm) bytes_per_particle() (lm.DiffusionModel method) C capacity() (lm.stdVectorInt method) Capsule (class in lm) capsule() (jLM.RegionBuilder.RegionBuilder method) CapsuleCell (class in pySTDLM.Cells) CapsuleShell (class in lm) CapsuleShellCell (class in pySTDLM.Cells) CellArranger (class in pySTDLM.CellArranger) cellFactory() (pySTDLM.CellArranger.CellArranger method) (pySTDLM.CellArranger.LooseGridArranger method) (pySTDLM.CellArranger.RandomArranger method) (pySTDLM.CellArranger.RandomSphericalArranger method) (pySTDLM.CellArranger.TightGridArranger method) CellShape (class in pySTDLM.Cells) checkParticle() (in module jLM.Lattice) checkSite() (in module jLM.Lattice) clear() (lm.stdVectorInt method) close() (lm.SimulationFile method) close_hdf_file() (jLM.RDME.File method) closeLMFile() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) closing() (jLM.RegionBuilder.RegionBuilder class method) cm() (in module pyLM.units) CMESimulation (class in jLM.CME) (class in pyLM.CME) CMESolver (class in lm) ColorGen (class in jLM.ColorGen) colorWheel() (in module jLM.DisplayUtils) compose() (jLM.RegionBuilder.RegionBuilder method) computeVolume() (pySTDLM.Cells.BoxCell method) (pySTDLM.Cells.CapsuleCell method) (pySTDLM.Cells.CapsuleShellCell method) (pySTDLM.Cells.SphereCell method) Cone (class in lm) ConstBoundaryConc (class in jLM.Solvers) construct() (jLM.JupyterDisplay.JupyterDisplayMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) contains() (lm.Capsule method) (lm.CapsuleShell method) (lm.Cone method) (lm.Cuboid method) (lm.Cylinder method) (lm.Difference method) (lm.Ellipse method) (lm.Hemisphere method) (lm.Intersection method) (lm.Shape method) (lm.Sphere method) (lm.Torus method) (lm.Union method) (lm.UnionSet method) convexHull() (jLM.RegionBuilder.RegionBuilder class method) copy() (lm.SwigPyIterator method) copyParticleLattice() (jLM.LmInteract.LmWriteMixin method) (jLM.RDME.Sim method) countParticlesInLattice() (in module jLM.Lattice) countSites() (in module jLM.Lattice) create() (lm.SimulationFile static method) createExpressionModel() (in module pySTDLM.StandardReactions) createModelCell() (pySTDLM.Cells.BoxCell method) (pySTDLM.Cells.CapsuleCell method) (pySTDLM.Cells.CapsuleShellCell method) (pySTDLM.Cells.CellShape method) (pySTDLM.Cells.SphereCell method) Cuboid (class in lm) CudaByteLattice (class in lm) CudaIntLattice (class in lm) Cylinder (class in lm) cylinder() (jLM.RegionBuilder.RegionBuilder method) D day() (in module pyLM.units) dc (jLM.RDME.Sim attribute) decr() (lm.SwigPyIterator method) defineSpecies() (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) Difference (class in lm) diffRateList (jLM.RDME.Sim attribute) diffusion_matrix() (lm.DiffusionModel method) DiffusionConst (class in jLM.Types) diffusionConst() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) diffusionFast (jLM.RDME.File property) (jLM.RDME.Sim property) (jLM.RDME.SpatialModel property) DiffusionModel (class in lm) diffusionRate() (jLM.Types.BuilderRegion method) (jLM.Types.BuilderSpecies method) diffusionZero (jLM.RDME.File property) (jLM.RDME.Sim property) (jLM.RDME.SpatialModel property) dilate() (jLM.RegionBuilder.RegionBuilder class method) discretizeTo() (lm.LatticeBuilder method) displayGeometry() (jLM.JupyterDisplay.JupyterDisplayMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) displayj2html() (in module jLM.Template) distance() (lm.point method) (lm.SwigPyIterator method) distanceSquared() (lm.point method) distributeConcentration() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) distributeNumber() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) doesIntersect() (pySTDLM.CellArranger.RandomArranger method) E Ellipse (class in lm) ellipsoid() (jLM.RegionBuilder.RegionBuilder method) empty() (lm.stdVectorInt method) emptyLatticeMask() (jLM.RegionBuilder.RegionBuilder method) end() (lm.stdVectorInt method) equal() (lm.SwigPyIterator method) erase() (lm.stdVectorInt method) erode() (jLM.RegionBuilder.RegionBuilder class method) estimateGPUMemory() (in module pySTDLM.CmdUtils) F File (class in jLM.RDME) FileJupyterMixin (class in jLM.JupyterDisplay) filename (jLM.RDME.File attribute) (jLM.RDME.Sim attribute) (jLM.RDME.SpatialModel attribute) fillWithRandomSpheres() (lm.LatticeBuilder method) finalize() (jLM.LmInteract.LmWriteMixin method) (jLM.RDME.Sim method) findParticles() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) float() (jLM.ColorGen.ColorGen method) floatFg() (jLM.ColorGen.ColorGen method) freeze() (jLM.BaseTypes.SimObjs method) front() (lm.stdVectorInt method) G get() (jLM.BaseTypes.SimObjs method) get_allocator() (lm.stdVectorInt method) getAutoNamespace() (jLM.BaseTypes.SimObjs method) getAvgVarTrace() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) getBoundingBox() (lm.Capsule method) (lm.CapsuleShell method) (lm.Cone method) (lm.Cuboid method) (lm.Cylinder method) (lm.Difference method) (lm.Ellipse method) (lm.Hemisphere method) (lm.Intersection method) (lm.Shape method) (lm.Sphere method) (lm.Torus method) (lm.Union method) (lm.UnionSet method) getCenter() (lm.Cone method) (lm.Ellipse method) (lm.Hemisphere method) (lm.Sphere method) (lm.Torus method) getCompiledLatticeMaxOccupancy() (in module lm) getDiffusionModel() (lm.SimulationFile method) getDiffusionModelLattice() (lm.SimulationFile method) getGPUMemoryDest() (lm.CudaByteLattice method) (lm.CudaIntLattice method) getGPUMemorySiteTypes() (lm.CudaByteLattice method) (lm.CudaIntLattice method) getGPUMemorySrc() (lm.CudaByteLattice method) (lm.CudaIntLattice method) getHeight() (lm.Cone method) getHistogram() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) getInnerRadius() (lm.CapsuleShell method) getLattice() (lm.SimulationFile method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) getLatticeHistogram() (jLM.Analysis.TrajAnalysisMixin method) (jLM.RDME.File method) (jLM.Types.TrajSpecies method) getLatticeSite() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) getLatticeTimes() (lm.SimulationFile method) getLatticeTrajectory() (jLM.Analysis.TrajAnalysisMixin method) (jLM.RDME.File method) (jLM.Types.TrajSpecies method) getMaxOccupancy() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) getNumberSites() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) getNumberTrajectory() (jLM.Analysis.TrajAnalysisMixin method) (jLM.RDME.File method) (jLM.Types.TrajSpecies method) getNumberTrajectoryFromRegion() (jLM.Analysis.TrajAnalysisMixin method) (jLM.RDME.File method) (jLM.Types.TrajRegion method) (jLM.Types.TrajSpecies method) getNumTrajectories() (in module jLM.CMEPostProcessing) getOccupancy() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) getOccupancyKymograph() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) getOrientation() (lm.Hemisphere method) getOuterRadius() (lm.CapsuleShell method) getP1() (lm.Capsule method) (lm.CapsuleShell method) (lm.Cuboid method) (lm.Cylinder method) getP2() (lm.Capsule method) (lm.CapsuleShell method) (lm.Cuboid method) (lm.Cylinder method) getParameter() (lm.SimulationFile method) getParticle() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) getParticleCounts() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) getParticleLatticeView() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) getPhaseSpace() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) getRadius() (lm.Capsule method) (lm.Cone method) (lm.Cylinder method) (lm.Hemisphere method) (lm.Sphere method) getRadius1() (lm.Ellipse method) (lm.Torus method) getRadius2() (lm.Ellipse method) (lm.Torus method) getRadius3() (lm.Ellipse method) getRate() (in module pySTDLM.SBMLReader) getReactionCount() (pyLM.RDME.RDMERegion method) getReactionModel() (lm.SimulationFile method) getReactionRateConstantsView() (lm.CMESolver method) (lm.GillespieDSolver method) (lm.NextReactionSolver method) getReactionString() (in module pyLM.ipyInterface) getSiteLatticeView() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) getSiteType() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) getSize() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) getSpacing() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) getSpatialModel() (lm.LatticeBuilder method) (lm.SimulationFile method) getSpecies() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) getSpeciesCounts() (lm.SimulationFile method) getSpeciesCountTimes() (lm.SimulationFile method) getSpeciesCountView() (lm.CMESolver method) (lm.GillespieDSolver method) (lm.NextReactionSolver method) getSpeciesNames() (lm.SimulationFile method) getSpecieTrace() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) getTimesteps() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) getTrajectory() (in module jLM.CMEPostProcessing) getType() (lm.Capsule method) (lm.CapsuleShell method) (lm.Cone method) (lm.Cuboid method) (lm.Cylinder method) (lm.Difference method) (lm.Ellipse method) (lm.Hemisphere method) (lm.Intersection method) (lm.Shape method) (lm.Sphere method) (lm.Torus method) (lm.Union method) (lm.UnionSet method) getVolume() (lm.Capsule method) (lm.CapsuleShell method) (lm.Cone method) (lm.Cuboid method) (lm.Cylinder method) (lm.Difference method) (lm.Ellipse method) (lm.Hemisphere method) (lm.Intersection method) (lm.Shape method) (lm.Sphere method) (lm.Torus method) (lm.Union method) (lm.UnionSet method) (pySTDLM.Cells.BoxCell method) (pySTDLM.Cells.CapsuleCell method) (pySTDLM.Cells.CapsuleShellCell method) (pySTDLM.Cells.CellShape method) (pySTDLM.Cells.SphereCell method) getXSize() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) getYSize() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) getZSize() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) GillespieDSolver (class in lm) greedyMesh() (in module jLM.Lattice) H h5() (jLM.LmInteract.LmWriteMixin method) (jLM.RDME.Sim method) hdf2lmRep() (in module jLM.Lattice) Hemisphere (class in lm) hookInterval (jLM.RDME.File property) (jLM.RDME.Sim property) (jLM.RDME.SpatialModel property) hookSimulation() (jLM.Solvers.ConstBoundaryConc method) (lm.GillespieDSolver method) (lm.IntMpdRdmeSolver method) (lm.MGPUIntMpdRdmeSolver method) (lm.MGPUMpdRdmeSolver method) (lm.MpdRdmeSolver method) (lm.NextReactionSolver method) hr() (in module pyLM.units) I importSBMLModel() (in module pySTDLM.SBMLReader) importSBMLModelL3V1() (in module pySTDLM.SBMLReader) incr() (lm.SwigPyIterator method) init_worker() (jLM.RDME.File method) initial_species_count_size() (lm.ReactionModel method) initialize() (lm.CMESolver method) (lm.GillespieDSolver method) (lm.IntMpdRdmeSolver method) (lm.MGPUIntMpdRdmeSolver method) (lm.MGPUMpdRdmeSolver method) (lm.MpdRdmeSolver method) (lm.NextReactionSolver method) insert() (lm.stdVectorInt method) internalAddToSim() (pySTDLM.Cells.BoxCell method) (pySTDLM.Cells.CapsuleCell method) (pySTDLM.Cells.CapsuleShellCell method) (pySTDLM.Cells.SphereCell method) internalModelCell() (pySTDLM.Cells.BoxCell method) (pySTDLM.Cells.CapsuleCell method) (pySTDLM.Cells.CapsuleShellCell method) (pySTDLM.Cells.SphereCell method) internalTranslateCell() (pySTDLM.Cells.BoxCell method) (pySTDLM.Cells.CapsuleCell method) (pySTDLM.Cells.CapsuleShellCell method) (pySTDLM.Cells.SphereCell method) Intersection (class in lm) intersects() (lm.Capsule method) (lm.CapsuleShell method) (lm.Cone method) (lm.Cuboid method) (lm.Cylinder method) (lm.Difference method) (lm.Ellipse method) (lm.Hemisphere method) (lm.Intersection method) (lm.Shape method) (lm.Sphere method) (lm.Torus method) (lm.Union method) (lm.UnionSet method) IntLattice (class in lm) IntMpdRdmeSolver (class in lm) intPackVolume() (pySTDLM.CellArranger.LooseGridArranger method) (pySTDLM.CellArranger.RandomArranger method) (pySTDLM.CellArranger.RandomSphericalArranger method) (pySTDLM.CellArranger.TightGridArranger method) IntRDMESimulation (class in pyLM.RDME) is_defined() (jLM.BaseTypes.SimObjs method) isValidFile() (lm.SimulationFile static method) iterator() (lm.stdVectorInt method) J j2render() (in module jLM.Template) jLM module jLM.Analysis module jLM.BaseTypes module jLM.CME module jLM.CMEPostProcessing module jLM.ColorGen module jLM.DisplayUtils module jLM.JupyterDisplay module jLM.Lattice module jLM.LmInteract module jLM.LMLogger module jLM.RDME module jLM.RegionBuilder module jLM.Solvers module jLM.Template module jLM.TexFmt module jLM.Types module joinWith() (lm.bounding_box method) JupyterDisplayMixin (class in jLM.JupyterDisplay) L Lattice (class in lm) lattice_spacing() (lm.DiffusionModel method) lattice_x_size() (lm.DiffusionModel method) lattice_y_size() (lm.DiffusionModel method) lattice_z_size() (lm.DiffusionModel method) LatticeAnalysisMixin (class in jLM.Analysis) LatticeBuilder (class in lm) latticeHistogram() (in module jLM.Lattice) latticeStatsAll() (in module jLM.Lattice) latticeStatsAll_h5fmt() (in module jLM.Lattice) latticeType (jLM.RDME.File attribute) (jLM.RDME.Sim attribute) (jLM.RDME.SpatialModel attribute) latticeWriteInterval (jLM.RDME.File property) (jLM.RDME.Sim property) (jLM.RDME.SpatialModel property) lm module lm::builder::Capsule (C++ class) lm::builder::Capsule::Capsule (C++ function) lm::builder::Capsule::contains (C++ function), [1] lm::builder::Capsule::getP1 (C++ function) lm::builder::Capsule::getP2 (C++ function) lm::builder::Capsule::getRadius (C++ function) lm::builder::Capsule::getVolume (C++ function) lm::builder::Capsule::intersects (C++ function) lm::builder::Capsule::~Capsule (C++ function) lm::builder::Cone (C++ class) lm::builder::Cone::Cone (C++ function) lm::builder::Cone::contains (C++ function), [1] lm::builder::Cone::getCenter (C++ function) lm::builder::Cone::getHeight (C++ function) lm::builder::Cone::getRadius (C++ function) lm::builder::Cone::getVolume (C++ function) lm::builder::Cone::intersects (C++ function) lm::builder::Cone::~Cone (C++ function) lm::builder::Cuboid (C++ class) lm::builder::Cuboid::contains (C++ function), [1] lm::builder::Cuboid::Cuboid (C++ function), [1] lm::builder::Cuboid::getP1 (C++ function) lm::builder::Cuboid::getP2 (C++ function) lm::builder::Cuboid::getVolume (C++ function) lm::builder::Cuboid::intersects (C++ function) lm::builder::Cuboid::~Cuboid (C++ function) lm::builder::Cylinder (C++ class) lm::builder::Cylinder::contains (C++ function), [1] lm::builder::Cylinder::Cylinder (C++ function) lm::builder::Cylinder::getP1 (C++ function) lm::builder::Cylinder::getP2 (C++ function) lm::builder::Cylinder::getRadius (C++ function) lm::builder::Cylinder::getVolume (C++ function) lm::builder::Cylinder::intersects (C++ function) lm::builder::Cylinder::~Cylinder (C++ function) lm::builder::Hemisphere (C++ class) lm::builder::Hemisphere::contains (C++ function), [1] lm::builder::Hemisphere::getCenter (C++ function) lm::builder::Hemisphere::getOrientation (C++ function) lm::builder::Hemisphere::getRadius (C++ function) lm::builder::Hemisphere::getVolume (C++ function) lm::builder::Hemisphere::Hemisphere (C++ function) lm::builder::Hemisphere::intersects (C++ function) lm::builder::Hemisphere::~Hemisphere (C++ function) lm::builder::LatticeBuilder (C++ class) lm::builder::LatticeBuilder::addParticles (C++ function) lm::builder::LatticeBuilder::addRegion (C++ function) lm::builder::LatticeBuilder::discretizeTo (C++ function) lm::builder::LatticeBuilder::fillWithRandomSpheres (C++ function) lm::builder::LatticeBuilder::getSpatialModel (C++ function) lm::builder::LatticeBuilder::LatticeBuilder (C++ function) lm::builder::LatticeBuilder::placeObject (C++ function) lm::builder::LatticeBuilder::placeRandomSphere (C++ function) lm::builder::LatticeBuilder::placeRandomSpheres (C++ function) lm::builder::LatticeBuilder::placeSphere (C++ function) lm::builder::LatticeBuilder::removeObject (C++ function) lm::builder::LatticeBuilder::removeSphere (C++ function) lm::builder::LatticeBuilder::~LatticeBuilder (C++ function) lm::builder::Shape (C++ class) lm::builder::Shape::boundingBoxesIntersect (C++ function) lm::builder::Shape::contains (C++ function), [1] lm::builder::Shape::discretizeTo (C++ function) lm::builder::Shape::getBoundingBox (C++ function) lm::builder::Shape::getShapeType (C++ function) lm::builder::Shape::getType (C++ function) lm::builder::Shape::getVolume (C++ function) lm::builder::Shape::intersects (C++ function) lm::builder::Shape::Shape (C++ function) lm::builder::Shape::ShapeType (C++ enum) lm::builder::Shape::ShapeType::CAPSULE (C++ enumerator) lm::builder::Shape::ShapeType::CAPSULE_SHELL (C++ enumerator) lm::builder::Shape::ShapeType::CONE (C++ enumerator) lm::builder::Shape::ShapeType::CUBOID (C++ enumerator) lm::builder::Shape::ShapeType::CYLINDER (C++ enumerator) lm::builder::Shape::ShapeType::DIFFERENCE (C++ enumerator) lm::builder::Shape::ShapeType::ELLIPSE (C++ enumerator) lm::builder::Shape::ShapeType::HEMISPHERE (C++ enumerator) lm::builder::Shape::ShapeType::INTERSECTION (C++ enumerator) lm::builder::Shape::ShapeType::MESH (C++ enumerator) lm::builder::Shape::ShapeType::SPHERE (C++ enumerator) lm::builder::Shape::ShapeType::TORUS (C++ enumerator) lm::builder::Shape::ShapeType::UNION (C++ enumerator) lm::builder::Shape::ShapeType::UNIONSET (C++ enumerator) lm::builder::Shape::~Shape (C++ function) lm::builder::Sphere (C++ class) lm::builder::Sphere::contains (C++ function), [1] lm::builder::Sphere::getCenter (C++ function) lm::builder::Sphere::getRadius (C++ function) lm::builder::Sphere::getVolume (C++ function) lm::builder::Sphere::intersects (C++ function) lm::builder::Sphere::setCenter (C++ function) lm::builder::Sphere::Sphere (C++ function) lm::builder::Sphere::~Sphere (C++ function) lm::me::MESolver (C++ class) lm::me::MESolver::generateTrajectory (C++ function) lm::me::MESolver::initialize (C++ function) lm::me::MESolver::MESolver (C++ function) lm::me::MESolver::needsDiffusionModel (C++ function) lm::me::MESolver::needsReactionModel (C++ function) lm::me::MESolver::~MESolver (C++ function) lm::rdme::CudaByteLattice (C++ class) lm::rdme::CudaByteLattice::addParticle (C++ function), [1] lm::rdme::CudaByteLattice::copyFromGPU (C++ function) lm::rdme::CudaByteLattice::copyToGPU (C++ function) lm::rdme::CudaByteLattice::CudaByteLattice (C++ function), [1] lm::rdme::CudaByteLattice::getGPUMemoryDest (C++ function) lm::rdme::CudaByteLattice::getGPUMemorySiteTypes (C++ function) lm::rdme::CudaByteLattice::getGPUMemorySrc (C++ function) lm::rdme::CudaByteLattice::getParticleLatticeView (C++ function) lm::rdme::CudaByteLattice::getParticleMemorySize (C++ function) lm::rdme::CudaByteLattice::getSiteLatticeView (C++ function) lm::rdme::CudaByteLattice::removeAllParticles (C++ function) lm::rdme::CudaByteLattice::removeParticles (C++ function), [1] lm::rdme::CudaByteLattice::setFromRowMajorByteData (C++ function) lm::rdme::CudaByteLattice::setSiteType (C++ function), [1] lm::rdme::CudaByteLattice::swapSrcDest (C++ function) lm::rdme::CudaByteLattice::~CudaByteLattice (C++ function) lm::rdme::CudaIntLattice (C++ class) lm::rdme::CudaIntLattice::addParticle (C++ function), [1] lm::rdme::CudaIntLattice::copyFromGPU (C++ function) lm::rdme::CudaIntLattice::copyToGPU (C++ function) lm::rdme::CudaIntLattice::CudaIntLattice (C++ function), [1] lm::rdme::CudaIntLattice::getGPUMemoryDest (C++ function) lm::rdme::CudaIntLattice::getGPUMemorySiteTypes (C++ function) lm::rdme::CudaIntLattice::getGPUMemorySrc (C++ function) lm::rdme::CudaIntLattice::removeAllParticles (C++ function) lm::rdme::CudaIntLattice::removeParticles (C++ function), [1] lm::rdme::CudaIntLattice::setFromRowMajorByteData (C++ function) lm::rdme::CudaIntLattice::setSiteType (C++ function), [1] lm::rdme::CudaIntLattice::swapSrcDest (C++ function) lm::rdme::CudaIntLattice::~CudaIntLattice (C++ function) lm::rdme::IntLattice (C++ class) lm::rdme::IntLattice::addParticle (C++ function), [1] lm::rdme::IntLattice::copyNativeToRowMajor (C++ function) lm::rdme::IntLattice::copyRowMajorToNative (C++ function) lm::rdme::IntLattice::copySitesRowMajorByteToNative (C++ function) lm::rdme::IntLattice::findParticles (C++ function) lm::rdme::IntLattice::getLatticeMemorySize (C++ function) lm::rdme::IntLattice::getMaxOccupancy (C++ function) lm::rdme::IntLattice::getMaxParticle (C++ function) lm::rdme::IntLattice::getMaxSiteType (C++ function) lm::rdme::IntLattice::getNeighboringSites (C++ function) lm::rdme::IntLattice::getOccupancy (C++ function), [1] lm::rdme::IntLattice::getParticle (C++ function), [1] lm::rdme::IntLattice::getParticleCounts (C++ function) lm::rdme::IntLattice::getParticleLatticeView (C++ function) lm::rdme::IntLattice::getSiteLatticeView (C++ function) lm::rdme::IntLattice::getSiteType (C++ function), [1] lm::rdme::IntLattice::getSiteTypes (C++ function) lm::rdme::IntLattice::IntLattice (C++ function), [1] lm::rdme::IntLattice::nativeSerialize (C++ function) lm::rdme::IntLattice::removeAllParticles (C++ function) lm::rdme::IntLattice::removeParticles (C++ function), [1] lm::rdme::IntLattice::setFromRowMajorByteData (C++ function) lm::rdme::IntLattice::setFromRowMajorData (C++ function) lm::rdme::IntLattice::setSitesFromRowMajorByteData (C++ function) lm::rdme::IntLattice::setSiteType (C++ function), [1] lm::rdme::IntLattice::~IntLattice (C++ function) lm::rdme::IntMpdRdmeSolver (C++ class) lm::rdme::IntMpdRdmeSolver::buildDiffusionModel (C++ function) lm::rdme::IntMpdRdmeSolver::buildModel (C++ function) lm::rdme::IntMpdRdmeSolver::generateTrajectory (C++ function) lm::rdme::IntMpdRdmeSolver::initialize (C++ function) lm::rdme::IntMpdRdmeSolver::IntMpdRdmeSolver (C++ function) lm::rdme::IntMpdRdmeSolver::needsDiffusionModel (C++ function) lm::rdme::IntMpdRdmeSolver::needsReactionModel (C++ function) lm::rdme::IntMpdRdmeSolver::setReactionRate (C++ function) lm::rdme::IntMpdRdmeSolver::~IntMpdRdmeSolver (C++ function) lm::rdme::MGPUIntMpdRdmeSolver (C++ class) lm::rdme::MGPUIntMpdRdmeSolver::buildDiffusionModel (C++ function) lm::rdme::MGPUIntMpdRdmeSolver::buildModel (C++ function) lm::rdme::MGPUIntMpdRdmeSolver::generateTrajectory (C++ function) lm::rdme::MGPUIntMpdRdmeSolver::initialize (C++ function) lm::rdme::MGPUIntMpdRdmeSolver::MGPUIntMpdRdmeSolver (C++ function) lm::rdme::MGPUIntMpdRdmeSolver::needsDiffusionModel (C++ function) lm::rdme::MGPUIntMpdRdmeSolver::needsReactionModel (C++ function) lm::rdme::MGPUIntMpdRdmeSolver::setReactionRate (C++ function) lm::rdme::MGPUIntMpdRdmeSolver::~MGPUIntMpdRdmeSolver (C++ function) lm::rdme::MGPUMpdRdmeSolver (C++ class) lm::rdme::MGPUMpdRdmeSolver::buildDiffusionModel (C++ function) lm::rdme::MGPUMpdRdmeSolver::buildModel (C++ function) lm::rdme::MGPUMpdRdmeSolver::generateTrajectory (C++ function) lm::rdme::MGPUMpdRdmeSolver::initialize (C++ function) lm::rdme::MGPUMpdRdmeSolver::MGPUMpdRdmeSolver (C++ function) lm::rdme::MGPUMpdRdmeSolver::needsDiffusionModel (C++ function) lm::rdme::MGPUMpdRdmeSolver::needsReactionModel (C++ function) lm::rdme::MGPUMpdRdmeSolver::setReactionRate (C++ function) lm::rdme::MGPUMpdRdmeSolver::~MGPUMpdRdmeSolver (C++ function) lm::rdme::MpdRdmeSolver (C++ class) lm::rdme::MpdRdmeSolver::buildDiffusionModel (C++ function) lm::rdme::MpdRdmeSolver::buildModel (C++ function) lm::rdme::MpdRdmeSolver::generateTrajectory (C++ function) lm::rdme::MpdRdmeSolver::initialize (C++ function) lm::rdme::MpdRdmeSolver::MpdRdmeSolver (C++ function) lm::rdme::MpdRdmeSolver::needsDiffusionModel (C++ function) lm::rdme::MpdRdmeSolver::needsReactionModel (C++ function) lm::rdme::MpdRdmeSolver::setReactionRate (C++ function) lm::rdme::MpdRdmeSolver::~MpdRdmeSolver (C++ function) lm::rdme::RDMESolver (C++ class) lm::rdme::RDMESolver::buildDiffusionModel (C++ function) lm::rdme::RDMESolver::RDMESolver (C++ function) lm::rdme::RDMESolver::setDiffusionModel (C++ function) lm::rdme::RDMESolver::~RDMESolver (C++ function) lm::thread::Thread (C++ class) lm::thread::Thread::getId (C++ function) lm::thread::Thread::setAffinity (C++ function) lm::thread::Thread::start (C++ function) lm::thread::Thread::stop (C++ function) lm::thread::Thread::Thread (C++ function) lm::thread::Thread::wake (C++ function) lm::thread::Thread::~Thread (C++ function) lm::thread::Worker (C++ class) lm::thread::Worker::abort (C++ function) lm::thread::Worker::checkpoint (C++ function) lm::thread::Worker::Worker (C++ function) lm::thread::Worker::~Worker (C++ function) lm::thread::WorkerManager (C++ class) lm::thread::WorkerManager::abortWorkers (C++ function) lm::thread::WorkerManager::addWorker (C++ function) lm::thread::WorkerManager::checkpointWorkers (C++ function) lm::thread::WorkerManager::getInstance (C++ function) lm::thread::WorkerManager::removeWorker (C++ function) lm::thread::WorkerManager::stopWorkers (C++ function) lm::thread::WorkerManager::WorkerManager (C++ function) lm::thread::WorkerManager::~WorkerManager (C++ function) LmReadMixin (class in jLM.LmInteract) LmWriteMixin (class in jLM.LmInteract) LooseGridArranger (class in pySTDLM.CellArranger) M makeSolver() (in module jLM.Solvers) matchRegex() (jLM.BaseTypes.SimObjs method) max (lm.bounding_box property) maxDiffusionRate() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) MESolver (class in lm) MGPUIntMpdRdmeSolver (class in lm) MGPUMpdRdmeSolver (class in lm) micron() (in module pyLM.units) microsecond() (in module pyLM.units) min (lm.bounding_box property) minute() (in module pyLM.units) mm() (in module pyLM.units) modelTables() (in module jLM.TexFmt) modifyRegion() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) module jLM jLM.Analysis jLM.BaseTypes jLM.CME jLM.CMEPostProcessing jLM.ColorGen jLM.DisplayUtils jLM.JupyterDisplay jLM.Lattice jLM.LmInteract jLM.LMLogger jLM.RDME jLM.RegionBuilder jLM.Solvers jLM.Template jLM.TexFmt jLM.Types lm pyLM pyLM.CME pyLM.ipyInterface pyLM.LMLogger pyLM.RDME pyLM.units pySTDLM pySTDLM.CellArranger pySTDLM.Cells pySTDLM.CmdUtils pySTDLM.Distributions pySTDLM.OnTheFly pySTDLM.PostProcessing pySTDLM.SBMLReader pySTDLM.StandardCells pySTDLM.StandardReactions pySTDLM.StandardReactionSystems MpdRdmeSolver (class in lm) ms() (in module pyLM.units) mutable_reaction() (lm.ReactionModel method) N NA (jLM.RDME.File attribute) (jLM.RDME.Sim attribute) (jLM.RDME.SpatialModel attribute) name (jLM.RDME.File attribute) (jLM.RDME.Sim attribute) (jLM.RDME.SpatialModel attribute) Namespace (class in jLM.BaseTypes) NAV (jLM.Types.BuilderRegion property) (jLM.Types.Region property) (jLM.Types.TrajRegion property) needsDiffusionModel() (lm.GillespieDSolver method) (lm.IntMpdRdmeSolver method) (lm.MGPUIntMpdRdmeSolver method) (lm.MGPUMpdRdmeSolver method) (lm.MpdRdmeSolver method) (lm.NextReactionSolver method) needsReactionModel() (lm.GillespieDSolver method) (lm.IntMpdRdmeSolver method) (lm.MGPUIntMpdRdmeSolver method) (lm.MGPUMpdRdmeSolver method) (lm.MpdRdmeSolver method) (lm.NextReactionSolver method) newBBox() (pySTDLM.CellArranger.RandomArranger method) next() (lm.SwigPyIterator method) NextReactionSolver (class in lm) nm() (in module pyLM.units) ns() (in module pyLM.units) number_reactions() (lm.ReactionModel method) number_site_types() (lm.DiffusionModel method) number_species() (lm.DiffusionModel method) (lm.ReactionModel method) numToStr() (in module jLM.DisplayUtils) O octoStructElem() (jLM.RegionBuilder.RegionBuilder static method) onBeginTrajectory() (lm.GillespieDSolver method) (lm.MpdRdmeSolver method) (lm.NextReactionSolver method) onEndTrajectory() (lm.GillespieDSolver method) (lm.MpdRdmeSolver method) (lm.NextReactionSolver method) onWriteLattice() (lm.MpdRdmeSolver method) opening() (jLM.RegionBuilder.RegionBuilder class method) openLMFile() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) outsideDomain() (pySTDLM.CellArranger.RandomArranger method) P packFastGrowingEcoli() (in module pySTDLM.StandardCells) packRegion() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) packSlowGrowingEcoli() (in module pySTDLM.StandardCells) packVolume() (pySTDLM.CellArranger.CellArranger method) (pySTDLM.CellArranger.LooseGridArranger method) (pySTDLM.CellArranger.RandomArranger method) (pySTDLM.CellArranger.RandomSphericalArranger method) (pySTDLM.CellArranger.TightGridArranger method) parameterTable() (in module jLM.TexFmt) ParticleGenerator (class in pySTDLM.Distributions) particles_per_site() (lm.DiffusionModel method) particleStatistics() (jLM.Analysis.LatticeAnalysisMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) peekFile() (in module pySTDLM.CmdUtils) perfPrintInterval (jLM.RDME.File property) (jLM.RDME.Sim property) (jLM.RDME.SpatialModel property) placeConcentrationInto() (jLM.Types.BuilderSpecies method) placeNumber() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) placeNumberInto() (jLM.Types.BuilderSpecies method) placeParticle() (jLM.Types.BuilderSpecies method) placeRandomSphere() (lm.LatticeBuilder method) placeRandomSpheres() (lm.LatticeBuilder method) placeSpeciesConcentration() (jLM.Types.BuilderRegion method) placeSpeciesNumber() (jLM.Types.BuilderRegion method) placeSphere() (lm.LatticeBuilder method) plotAvgVar() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) plotAvgVarFromFile() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) plotCMEReactionNetwork() (in module jLM.CMEPostProcessing) plotOccupancyKymograph() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) plotPhaseSpace() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) plotTrace() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) plotTraceFromFile() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) point (class in lm) pop() (lm.stdVectorInt method) pop_back() (lm.stdVectorInt method) populateLattice() (in module jLM.Lattice) previous() (lm.SwigPyIterator method) printCompiledOptions() (in module jLM) process_frame() (jLM.RDME.File method) push_back() (lm.stdVectorInt method) pyLM module pyLM.CME module pyLM.ipyInterface module pyLM.LMLogger module pyLM.RDME module pyLM.units module pySTDLM module pySTDLM.CellArranger module pySTDLM.Cells module pySTDLM.CmdUtils module pySTDLM.Distributions module pySTDLM.OnTheFly module pySTDLM.PostProcessing module pySTDLM.SBMLReader module pySTDLM.StandardCells module pySTDLM.StandardReactions module pySTDLM.StandardReactionSystems module R RandomArranger (class in pySTDLM.CellArranger) RandomSphericalArranger (class in pySTDLM.CellArranger) rate_constant_size() (lm.ReactionModel_Reaction method) RateConst (class in jLM.Types) rateConst() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) rbegin() (lm.stdVectorInt method) rc (jLM.RDME.Sim attribute) RDMERegion (class in pyLM.RDME) RDMESimulation (class in pyLM.RDME) Reaction (class in jLM.Types) reaction() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) (lm.ReactionModel method) reaction_location_matrix() (lm.DiffusionModel method) reaction_size() (lm.ReactionModel method) reactionList (jLM.RDME.Sim attribute) ReactionModel (class in lm) ReactionModel_Reaction (class in lm) reactionTable() (in module jLM.TexFmt) readSBMLtoCME() (in module pySTDLM.SBMLReader) readSBMLtoRDME() (in module pySTDLM.SBMLReader) readSBMLtoRegion() (in module pySTDLM.SBMLReader) reduce_trajectory_file() (jLM.RDME.File method) reg (jLM.RDME.Sim attribute) Region (class in jLM.Types) region() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) RegionBuilder (class in jLM.RegionBuilder) regionList (jLM.RDME.Sim attribute) regionTable() (in module jLM.TexFmt) removeParticles() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) removeSphere() (lm.LatticeBuilder method) rend() (lm.stdVectorInt method) reserve() (lm.stdVectorInt method) resize() (lm.stdVectorInt method) resizeLattice() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) run() (jLM.CME.CMESimulation method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) runMPI() (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) runSimulation() (in module lm) runSolver() (in module lm) (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) rxnRateList (jLM.RDME.Sim attribute) S sanitizeTex() (in module jLM.DisplayUtils) save() (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) se26 (jLM.RegionBuilder.RegionBuilder property) se6 (jLM.RegionBuilder.RegionBuilder property) second() (in module pyLM.units) set_bytes_per_particle() (lm.DiffusionModel method) set_diffusion_matrix() (lm.DiffusionModel method) set_initial_species_count() (lm.ReactionModel method) set_lattice_spacing() (lm.DiffusionModel method) set_lattice_x_size() (lm.DiffusionModel method) set_lattice_y_size() (lm.DiffusionModel method) set_lattice_z_size() (lm.DiffusionModel method) set_number_reactions() (lm.DiffusionModel method) (lm.ReactionModel method) set_number_site_types() (lm.DiffusionModel method) set_number_species() (lm.DiffusionModel method) (lm.ReactionModel method) set_particles_per_site() (lm.DiffusionModel method) set_rate_constant() (lm.ReactionModel_Reaction method) set_reaction_location_matrix() (lm.DiffusionModel method) set_type() (lm.ReactionModel_Reaction method) setBoundary() (jLM.Solvers.ConstBoundaryConc method) setCenter() (lm.Ellipse method) (lm.Sphere method) (lm.Torus method) setDefaultDiffusionRate() (pyLM.RDME.RDMERegion method) setDiffusionModel() (lm.SimulationFile method) setDiffusionModelLattice() (lm.SimulationFile method) setDiffusionRate() (pyLM.RDME.RDMERegion method) setHookInterval() (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) setLatticeSite() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) setLatticeWriteInterval() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) setLMLogConsole() (in module jLM.LMLogger) (in module pyLM.LMLogger) setLMLogFile() (in module jLM.LMLogger) (in module pyLM.LMLogger) setLMLoggerLevel() (in module jLM.LMLogger) (in module pyLM.LMLogger) setMaximumTimestep() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) setOverflowHandler() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) setParameter() (lm.SimulationFile method) setRandomSeed() (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) setReactionModel() (lm.SimulationFile method) setReactionRate() (lm.IntMpdRdmeSolver method) (lm.MGPUIntMpdRdmeSolver method) (lm.MGPUMpdRdmeSolver method) (lm.MpdRdmeSolver method) setRegions() (pySTDLM.Cells.BoxCell method) (pySTDLM.Cells.CapsuleCell method) (pySTDLM.Cells.CapsuleShellCell method) (pySTDLM.Cells.CellShape method) (pySTDLM.Cells.SphereCell method) setReplicate() (jLM.LmInteract.LmReadMixin method) (jLM.RDME.File method) setSimulationTime() (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) setSiteType() (lm.ByteLattice method) (lm.CudaByteLattice method) (lm.CudaIntLattice method) (lm.IntLattice method) (lm.Lattice method) setSpatialModel() (lm.SimulationFile method) setTimestep() (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) setTransitionRate() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) setTwoWayTransitionRate() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) setVerbosityLevel() (in module lm) setWriteInterval() (jLM.CME.CMESimulation method) (pyLM.CME.CMESimulation method) (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) Shape (class in lm) show() (jLM.Types.BuilderSpecies method) (jLM.Types.Species method) (jLM.Types.TrajSpecies method) showAllParameters() (jLM.JupyterDisplay.JupyterDisplayMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) showAllSpecies() (jLM.JupyterDisplay.JupyterDisplayMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) showAvgVar() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) showAvgVarFromFile() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) showBinaryLattices() (jLM.RegionBuilder.RegionBuilder static method) showDiffusionConstants() (jLM.JupyterDisplay.JupyterDisplayMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) showOccupancyKymograph() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) showRateConstants() (jLM.JupyterDisplay.JupyterDisplayMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) showReactions() (jLM.JupyterDisplay.JupyterDisplayMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) showRegion() (jLM.JupyterDisplay.JupyterDisplayMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) showRegionStack() (jLM.JupyterDisplay.JupyterDisplayMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) showSpecies() (jLM.JupyterDisplay.JupyterDisplayMixin method) (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) showStack() (jLM.RegionBuilder.RegionBuilder static method) showTrace() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) showTraceFromFile() (in module jLM.CMEPostProcessing) (in module pySTDLM.PostProcessing) showVolumeStack() (in module jLM.JupyterDisplay) Sim (class in jLM.RDME) SimObj (class in jLM.BaseTypes) SimObjs (class in jLM.BaseTypes) SimulationFile (class in lm) SimulationFile_create() (in module lm) SimulationFile_isValidFile() (in module lm) simulationTime (jLM.RDME.File property) (jLM.RDME.Sim property) (jLM.RDME.SpatialModel property) siteVolume() (pyLM.RDME.IntRDMESimulation method) (pyLM.RDME.RDMESimulation method) size() (lm.stdVectorInt method) sp (jLM.RDME.Sim attribute) SpatialModel (class in jLM.RDME) (class in lm) Species (class in jLM.Types) species() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) speciesList (jLM.RDME.Sim attribute) speciesWriteInterval (jLM.RDME.File property) (jLM.RDME.Sim property) (jLM.RDME.SpatialModel property) Sphere (class in lm) SphereCell (class in pySTDLM.Cells) sphereStructElem() (jLM.RegionBuilder.RegionBuilder static method) spoke() (jLM.RegionBuilder.RegionBuilder method) stdVectorInt (class in lm) stochasticRate (jLM.Types.RateConst property) str() (jLM.ColorGen.ColorGen method) strFg() (jLM.ColorGen.ColorGen method) swap() (lm.stdVectorInt method) swapSrcDest() (lm.CudaByteLattice method) (lm.CudaIntLattice method) SwigPyIterator (class in lm) T texfmt() (in module jLM.DisplayUtils) texUnits() (in module jLM.DisplayUtils) thisown (lm.bounding_box property) (lm.ByteLattice property) (lm.Capsule property) (lm.CapsuleShell property) (lm.CMESolver property) (lm.Cone property) (lm.Cuboid property) (lm.CudaByteLattice property) (lm.CudaIntLattice property) (lm.Cylinder property) (lm.Difference property) (lm.DiffusionModel property) (lm.Ellipse property) (lm.GillespieDSolver property) (lm.Hemisphere property) (lm.Intersection property) (lm.IntLattice property) (lm.IntMpdRdmeSolver property) (lm.Lattice property) (lm.LatticeBuilder property) (lm.MESolver property) (lm.MGPUIntMpdRdmeSolver property) (lm.MGPUMpdRdmeSolver property) (lm.MpdRdmeSolver property) (lm.NextReactionSolver property) (lm.point property) (lm.ReactionModel property) (lm.ReactionModel_Reaction property) (lm.Shape property) (lm.SimulationFile property) (lm.SpatialModel property) (lm.Sphere property) (lm.stdVectorInt property) (lm.SwigPyIterator property) (lm.Torus property) (lm.Union property) (lm.UnionSet property) (lm.vector property) TightGridArranger (class in pySTDLM.CellArranger) toHex() (in module jLM.DisplayUtils) Torus (class in lm) TrajAnalysisMixin (class in jLM.Analysis) TrajRegion (class in jLM.Types) TrajSpecies (class in jLM.Types) transformGrid() (jLM.RegionBuilder.RegionBuilder static method) transitionRate() (jLM.RDME.File method) (jLM.RDME.Sim method) (jLM.RDME.SpatialModel method) (jLM.Types.BuilderSpecies method) transitionRateIn() (jLM.Types.BuilderRegion method) transitionRateOut() (jLM.Types.BuilderRegion method) translateCell() (pySTDLM.Cells.BoxCell method) (pySTDLM.Cells.CapsuleCell method) (pySTDLM.Cells.CapsuleShellCell method) (pySTDLM.Cells.CellShape method) (pySTDLM.Cells.SphereCell method) type() (lm.ReactionModel_Reaction method) U unfreeze() (jLM.BaseTypes.SimObjs method) unicodeUnits() (in module jLM.DisplayUtils) Union (class in lm) UnionSet (class in lm) V value() (lm.SwigPyIterator method) vector (class in lm) visualizeRDMEInitialConditions() (in module pyLM.ipyInterface) vmd_precomp() (jLM.RDME.File method) volume (jLM.Types.BuilderRegion property) (jLM.Types.Region property) (jLM.Types.TrajRegion property) W write_to_h5() (jLM.RDME.File method) writeLatticeSites() (lm.MpdRdmeSolver method) writeTable() (in module pyLM.ipyInterface) X x (lm.point property) (lm.vector property) xs (jLM.RegionBuilder.RegionBuilder attribute) Y y (lm.point property) (lm.vector property) Z z (lm.point property) (lm.vector property)