- a -

accept() : utils.Jfilter
ActiveAgent() : simulator.agent.ActiveAgent
add() : simulator.geometry.ContinuousVector , utils.Complex , simulator.geometry.ContinuousVector , utils.ComplexArray , simulator.agent.LocatedGroup , simulator.geometry.DiscreteVector , utils.ComplexArray , simulator.geometry.DiscreteVector , utils.ComplexArray
addActiveReaction() : simulator.agent.ActiveAgent , simulator.agent.HasReaction
addAgent() : simulator.reaction.Reaction
addAllReactions() : simulator.diffusionSolver.DiffusionSolver
addAllValues() : simulator.SpatialGrid
addBoundary() : simulator.geometry.Domain
addCell() : povray.Biofilm3D , povray.Povray3DScene
addMovement() : simulator.agent.LocatedAgent
addMoveToAgents() : simulator.agent.LocatedGroup
addPushMovement() : simulator.agent.LocatedAgent
addReaction() : simulator.agent.ActiveAgent , simulator.agent.HasReaction
addReactionWithSolutes() : simulator.diffusionSolver.DiffusionSolver
addSpringMovement() : simulator.agent.LocatedAgent
addTo() : utils.MatrixOperations , utils.GridOperations
addToZipArchiveAndDelete() : utils.ZipArchive
addToZipArchiveAndKeepLast() : utils.ZipArchive
addValueAt() : simulator.SpatialGrid
Agent() : simulator.agent.Agent
AgentContainer() : simulator.AgentContainer
agentFlushedAway() : simulator.AgentContainer
agentMoveBorderCheck() : simulator.agent.Species
alea() : simulator.geometry.ContinuousVector
applyAllBoundary() : simulator.geometry.Domain
applyBoundary() : simulator.geometry.boundaryConditions.AllBC , simulator.geometry.boundaryConditions.BoundaryCyclic , simulator.geometry.boundaryConditions.IsBC , simulator.geometry.boundaryConditions.BoundaryGasMembrane , simulator.geometry.boundaryConditions.BoundaryBulk , simulator.geometry.boundaryConditions.BoundaryCyclic , simulator.geometry.boundaryConditions.BoundaryZeroFlux , simulator.geometry.boundaryConditions.BoundaryConstant
applyComputation() : simulator.diffusionSolver.multigrid.MultigridSolute
applyReaction() : simulator.reaction.Reaction
applyTimeStep() : idyno.SimTimer
areaOfACircle() : utils.ExtraMath
average() : utils.ExtraMath