src/sys_def-types.jl

MEDYAN.AgentNames

The names of the agents in a simulation

  • diffusingspeciesnames::Vector{Symbol}
  • bulkspeciesnames::Vector{Symbol}
  • membranediffusingspeciesnames::Vector{Symbol}
  • fixedspeciesnames::Vector{Symbol}
  • filamentnames::Vector{Tuple{Symbol, Vector{Symbol}}}
  • vertexnames::Vector{Symbol}

MEDYAN.VertexName

  • membraneindex::Int64: membrane index
  • vid::Int64: vertex id

MEDYAN.SysDef

SysDef(agent_names::AgentNames)

A mutable struct mapping names to id numbers in a simulation

  • agent_names::MEDYAN.AgentNames
  • diffusing::MEDYAN.PropDictionary
  • diffusing_coeff::MEDYAN.PropDictionary
  • bulkspecies_indexmap::MEDYAN.PropDictionary
  • membranediffusing::MEDYAN.PropDictionary
  • fixedspecies::MEDYAN.PropDictionary
  • filament::MEDYAN.PropDictionary
  • filament_params::MEDYAN.PropDictionary
  • vertex::MEDYAN.PropDictionary
  • state::MEDYAN.PropDictionary
  • filamentsite::MEDYAN.PropDictionary
  • filamentendsite::MEDYAN.PropDictionary
  • membranesite::MEDYAN.PropDictionary: Each membrane site represents the membrane patches in each compartment together with some membrane diffusing species.
  • decimated_2mon_site::MEDYAN.PropDictionary
  • possiblecadherinsite::MEDYAN.PropDictionary
  • allfixedspeciesnames::Vector{String}
  • compartmentreactions::Vector{MEDYAN.CompartmentReaction}
  • compartmentreactioncallbacks::Vector{Any}
  • bulkreactions::Vector{MEDYAN.BulkReaction}
  • bulkreactioncallbacks::Vector{Any}: Context -> Nothing
  • link::MEDYAN.PropDictionary
  • total_num_link_types_places::Int64
  • link_reaction_site::MEDYAN.PropDictionary