Lattice Microbes
2.5
This is for whole cell modeling
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Class Index
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Z
|
_
B
bounding_box
(
lm::builder
)
BoxCell
(
pySTDLM.Cells
)
BuilderReaction
(
jLM.Types
)
BuilderRegion
(
jLM.Types
)
BuilderSpecies
(
jLM.Types
)
ByteLattice
(
lm::rdme
)
ByteLatticeExtended
(
lm::rdme
)
C
Capsule
(
lm::builder
)
CapsuleCell
(
pySTDLM.Cells
)
CapsuleShell
(
lm::builder
)
CapsuleShellCell
(
pySTDLM.Cells
)
CellArranger
(
pySTDLM.CellArranger
)
CellShape
(
pySTDLM.Cells
)
CheckpointSignaler
(
lm::main
)
CMESimulation
(
jLM.CME
)
CMESimulation
(
pyLM.CME
)
CMESolver
CMESolver
(
lm::cme
)
ColorGen
(
jLM.ColorGen
)
CommandLineArgumentException
(
lm
)
CMESolver::CompetitiveMMPropensityArgs
CMESolver::CompetitiveMMPropensityArgs
(
lm::cme
)
ResourceAllocator::ComputeResources
(
lm::main
)
ResourceAllocator::ComputeResources
Cone
(
lm::builder
)
ConstBoundaryConc
(
jLM.Solvers
)
Cuboid
(
lm::builder
)
CUDA
(
lm
)
CudaByteLattice
CudaByteLattice
(
lm::rdme
)
CudaByteLatticeExtended
CudaByteLatticeExtended
(
lm::rdme
)
CUDADriverException
(
lm
)
CUDAException
(
lm
)
CudaIntLattice
(
lm::rdme
)
Cylinder
(
lm::builder
)
D
DataOutputQueue
(
lm::main
)
DataOutputQueue::DataSet
(
lm::main
)
Difference
(
lm::builder
)
DiffusionConst
(
jLM.Types
)
Doxy2SWIG
(
doxy2swig
)
E
Ellipse
(
lm::builder
)
Exception
Exception
(
lm
)
F
File
(
jLM.RDME
)
FileExtended
(
jLM.RDMEExtended
)
FileJupyterMixin
(
jLM.JupyterDisplay
)
CMESolver::FirstOrderPropensityArgs
CMESolver::FirstOrderPropensityArgs
(
lm::cme
)
FluctuatingNRSolver
(
lm::cme
)
CMESolver::FPTTracking
CMESolver::FPTTracking
(
lm::cme
)
G
GillespieDSolver
(
lm::cme
)
gpu_info
gpu_worker_thread_int_params
(
lm::rdme
)
gpu_worker_thread_params
(
lm::rdme
)
H
H5Lookup
H5MetaData
HDF5Exception
(
lm::io::hdf5
)
Hemisphere
(
lm::builder
)
HillSwitch
(
lm::cme
)
I
Intersection
(
lm::builder
)
IntLattice
(
lm::rdme
)
IntMpdRdmeSolver
(
lm::rdme
)
IntMpdRdmeSolverExtended
(
lm::rdme
)
IntRDMESimulation
(
pyLM.RDME
)
InvalidArgException
(
lm
)
InvalidParticleException
(
lm::rdme
)
InvalidSiteException
(
lm::rdme
)
IOException
IOException
(
lm::io::hdf5
)
IOException
(
lm
)
J
JupyterDisplayMixin
(
jLM.JupyterDisplay
)
K
CMESolver::KHillPropensityArgs
CMESolver::KHillPropensityArgs
(
lm::cme
)
TwoStateHillSwitch::KHillPropensityArgs
(
lm::cme
)
CMESolver::KHillTransportPropensityArgs
CMESolver::KHillTransportPropensityArgs
(
lm::cme
)
L
LacHillSwitch
(
lm::cme
)
Lattice
Lattice
(
lm::rdme
)
lattice_coord_t
LatticeAnalysisMixin
(
jLM.Analysis
)
LatticeBuilder
(
lm::builder
)
LmReadMixin
(
jLM.LmInteract
)
LmWriteMixin
(
jLM.LmInteract
)
LocalDataOutputWorker
(
lm::main
)
LooseGridArranger
(
pySTDLM.CellArranger
)
M
matrix
(
lm::builder
)
Mesh
(
lm::builder
)
MESolver
(
lm::me
)
MESolver
MESolverFactory
(
lm::me
)
MESolverFactory
MGPUIntMpdRdmeSolver
(
lm::rdme
)
MGPUMpdRdmeSolver
(
lm::rdme
)
CMESolver::MichaelisMentenPropensityArgs
CMESolver::MichaelisMentenPropensityArgs
(
lm::cme
)
MpdRdmeSolver
(
lm::rdme
)
MpdRdmeSolver
MpdRdmeSolverExtended
(
lm
)
MpdTestHarness
(
lm::rdme
)
MPI
(
lm
)
MPIException
(
lm
)
MPIMpdRdmeSolver
(
lm::rdme
)
MPIRemoteDataOutputQueue
(
lm::main
)
MultiGPUMapper
N
Namespace
(
jLM.BaseTypes
)
neighbor_buffer
NextReactionSolver
(
lm::cme
)
NextSubvolumeSolver
(
lm::rdme
)
CMESolver::NoncompetitiveMMPropensityArgs
CMESolver::NoncompetitiveMMPropensityArgs
(
lm::cme
)
NullHandler
(
jLM.LMLogger
)
NullHandler
(
pyLM.LMLogger
)
O
SelfRegulatingGeneSwitch::OUKHillPropensityArgs
(
lm::cme
)
FluctuatingNRSolver::OUPropensityArgs
(
lm::cme
)
P
particle_loc_t
ParticleGenerator
(
pySTDLM.Distributions
)
LatticeBuilder::ParticlePlacement
(
lm::builder
)
ParticleSizeError
(
jLM.ParticleSizeSupport
)
ParticleSizeException
(
lm::rdme
)
ParticleSizeManager
(
lm::rdme
)
ParticleSizeMixin
(
jLM.ParticleSizeSupport
)
ParticleSizeValidator
(
jLM.ParticleSizeSupport
)
point
(
lm::builder
)
Print
(
lm
)
Print
CMESolver::PropensityArgs
CMESolver::PropensityArgs
(
lm::cme
)
PthreadException
(
lm::thread
)
PthreadException
R
RandomArranger
(
pySTDLM.CellArranger
)
RandomGenerator
(
lm::rng
)
RandomGenerator
RandomSphericalArranger
(
pySTDLM.CellArranger
)
RateConst
(
jLM.Types
)
RDMERegion
(
pyLM.RDME
)
RDMESimulation
(
pyLM.RDME
)
RDMESolver
(
lm::rdme
)
RDMESolver
Reaction
(
jLM.Types
)
ReactionQueue::ReactionEvent
(
lm::reaction
)
ReactionQueue::ReactionEvent
ReactionQueue
(
lm::reaction
)
ReactionQueue
Region
(
jLM.Types
)
RegionBuilder
(
jLM.RegionBuilder
)
SimulationFile::ReplicateHandles
(
lm::io::hdf5
)
SimulationFile::ReplicateHandles
ReplicateRunner
(
lm::main
)
ReplicateRunner
ResourceAllocator
(
lm::main
)
ResourceAllocator
S
CMESolver::SecondOrderPropensityArgs
CMESolver::SecondOrderPropensityArgs
(
lm::cme
)
CMESolver::SecondOrderSelfPropensityArgs
CMESolver::SecondOrderSelfPropensityArgs
(
lm::cme
)
segmentDescriptor
SelfRegulatingGeneSwitch
(
lm::cme
)
Shape
(
lm::builder
)
SignalHandler
(
lm::main
)
Sim
(
jLM.RDME
)
SimExtended
(
jLM.RDMEExtended
)
SimObj
(
jLM.BaseTypes
)
SimObjs
(
jLM.BaseTypes
)
SimulationFile
(
lm::io::hdf5
)
SimulationFile
SimulationParameters
(
lm::io
)
SpatialModel
(
jLM.RDME
)
SpatialModelExtended
(
jLM.RDMEExtended
)
Species
(
jLM.Types
)
CMESolver::SpeciesLimit
CMESolver::SpeciesLimit
(
lm::cme
)
Sphere
(
lm::builder
)
SphereCell
(
pySTDLM.Cells
)
SvgContext
(
jLM.ImageAnalysis
)
T
Thread
(
lm::thread
)
TightGridArranger
(
pySTDLM.CellArranger
)
Torus
(
lm::builder
)
CMESolver::TrackedParameter
CMESolver::TrackedParameter
(
lm::cme
)
TrajAnalysisMixin
(
jLM.Analysis
)
TrajRegion
(
jLM.Types
)
TrajSpecies
(
jLM.Types
)
TwoStateExpression
(
lm::cme
)
TwoStateHillLoopSwitch
(
lm::cme
)
TwoStateHillSwitch
(
lm::cme
)
U
CMESolver::UncompetitiveMMPropensityArgs
CMESolver::UncompetitiveMMPropensityArgs
(
lm::cme
)
Union
(
lm::builder
)
UnionSet
(
lm::builder
)
V
vector
(
lm::builder
)
W
Worker
(
lm::thread
)
Worker
WorkerManager
(
lm::thread
)
WorkerManager
X
XORShift
(
lm::rng
)
XORWow
(
lm::rng
)
Z
ZDivMPIGPUMapper
ZDivMultiGPUMapper
CMESolver::ZerothOrderHeavisidePropensityArgs
CMESolver::ZerothOrderHeavisidePropensityArgs
(
lm::cme
)
CMESolver::ZerothOrderPropensityArgs
CMESolver::ZerothOrderPropensityArgs
(
lm::cme
)
_
_Report
(
jLM.JupyterDisplay
)
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