Version 1.2 (June 2013)
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A
Complex
(
utils
)
HasReaction
(
simulator.agent
)
MultiEpisome
(
simulator.agent.zoo
)
SpatialGrid
(
simulator
)
ComplexArray
(
utils
)
HasSpecies
(
simulator.agent
)
MultiEpisomeParam
(
simulator.agent.zoo
)
SpecialisedAgent
(
simulator.agent
)
ActiveAgent
(
simulator.agent
)
ConnectedVolume
(
simulator.detachment
)
HillKinetic
(
simulator.reaction.kinetic
)
MultigridSolute
(
simulator.diffusionSolver.multigrid
)
Species
(
simulator.agent
)
ActiveParam
(
simulator.agent
)
ContinuousVector
(
simulator.geometry
)
I
MultigridUtils
(
simulator.diffusionSolver.multigrid
)
SpeciesParam
(
simulator.agent
)
Agent
(
simulator.agent
)
D
P
T
AgentContainer
(
simulator
)
Idynomics
(
idyno
)
AllBC
(
simulator.geometry.boundaryConditions
)
DiffusionSolver
(
simulator.diffusionSolver
)
InfoAgent
(
simulator.agent
)
ParticleWithCapsule
(
povray
)
TestUtils
(
test
)
B
DiscreteVector
(
simulator.geometry
)
InitialisationErrorLog
(
utils
)
ParticulateEPS
(
simulator.agent.zoo
)
U
Domain
(
simulator.geometry
)
IsBC
(
simulator.geometry.boundaryConditions
)
ParticulateEPSParam
(
simulator.agent.zoo
)
Background
(
povray
)
DS_Biomass
(
simulator.detachment
)
IsComputationDomain
(
simulator.geometry
)
Planar
(
simulator.geometry.shape
)
UnitConverter
(
utils
)
BactAdaptable
(
simulator.agent.zoo
)
DS_Proportional
(
simulator.detachment
)
IsKineticFactor
(
simulator.reaction.kinetic
)
Povray3DScene
(
povray
)
Update_IDynomics
(
soft_update
)
BactAdaptableParam
(
simulator.agent.zoo
)
DS_Quadratic
(
simulator.detachment
)
IsShape
(
simulator.geometry.shape
)
PovRayWriter
(
povray
)
V
BactEPS
(
simulator.agent.zoo
)
DS_SolGrad
(
simulator.detachment
)
J
R
BactEPSParam
(
simulator.agent.zoo
)
E
VectorizedArray
(
utils
)
Bacterium
(
simulator.agent.zoo
)
Jfilter
(
utils
)
Reaction
(
simulator.reaction
)
VectorProperty
(
povray
)
BacteriumParam
(
simulator.agent.zoo
)
Episome
(
simulator.agent.zoo
)
L
ReactionFactor
(
simulator.reaction
)
W
Biofilm3D
(
povray
)
EpisomeParam
(
simulator.agent.zoo
)
ReactionFactorWithConstant
(
simulator.reaction
)
BoundaryBulk
(
simulator.geometry.boundaryConditions
)
EpithelialGrid
(
simulator
)
LevelSet
(
simulator.detachment
)
ReactionGrowthFitness
(
simulator.reaction
)
World
(
simulator
)
BoundaryConstant
(
simulator.geometry.boundaryConditions
)
ExtraMath
(
utils
)
LightSource
(
povray
)
ResultFile
(
utils
)
X
BoundaryCyclic
(
simulator.geometry.boundaryConditions
)
F
LinearKinetic
(
simulator.reaction.kinetic
)
S
BoundaryGasMembrane
(
simulator.geometry.boundaryConditions
)
LocatedAgent
(
simulator.agent
)
XMLParser
(
utils
)
BoundaryZeroFlux
(
simulator.geometry.boundaryConditions
)
FftOperations
(
utils
)
LocatedGroup
(
simulator.agent
)
SimpleInhibition
(
simulator.reaction.kinetic
)
Z
Box
(
povray
)
FirstOrder
(
simulator.reaction
)
LocatedParam
(
simulator.agent
)
SimTimer
(
idyno
)
Bulk
(
simulator.geometry
)
FirstOrderKinetic
(
simulator.reaction.kinetic
)
LogFile
(
utils
)
Simulator
(
simulator
)
ZipArchive
(
utils
)
C
FluctEnv
(
simulator.geometry
)
M
SinglegridPressure
(
simulator.diffusionSolver.multigrid
)
G
SingleMonod
(
simulator.reaction
)
Camera
(
povray
)
MatrixOperations
(
utils
)
SoluteGrid
(
simulator
)
Chart
(
utils
)
GridElementFloat
(
simulator.geometry
)
ModelRuntimeException
(
exceptions
)
Solver_chemostat
(
simulator.diffusionSolver
)
Check_Release_Status
(
soft_update
)
GridOperations
(
utils
)
MonodKinetic
(
simulator.reaction.kinetic
)
Solver_multigrid
(
simulator.diffusionSolver
)
ColorMaps
(
povray
)
H
MTRandom
(
utils
)
Solver_pressure
(
simulator.diffusionSolver
)
HaldaneKinetic
(
simulator.reaction.kinetic
)
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