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}
  • link_2mon_names::Vector{Symbol}
  • cadherinnames::Vector{Symbol}

MEDYAN.MonomerName

  • ftid::Int64: filament type id
  • fid::Int64: filament id
  • mid::Int64: monomer id

MEDYAN.VertexName

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

MEDYAN.Link2MonState

There is one instance of this per link_2mon.

  • chemstate::NamedTuple: Other state.
  • mechstate::NamedTuple: Used in link_2mon force calculation.
  • is_minimized::Bool: Set to true after minimization

MEDYAN.Link2MonParams

Link2mon Parameters, there is one instance of this per link2mon type

  • defaultstate::MEDYAN.Link2MonState
  • mechparams::Any
  • no_collide::Bool: if true, allows cylinders this link_2mon type connects and adjacent cylinders to clip

MEDYAN.CadherinState

There is one instance of this per cadherin.

  • chemstate::NamedTuple: Other state.
  • mechstate::NamedTuple: Used in link_2mon force calculation.
  • is_minimized::Bool: Set to true after minimization

MEDYAN.CadherinParams

Cadherin Parameters, there is one instance of this per cadherin type

  • defaultstate::MEDYAN.CadherinState
  • mechparams::Any

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
  • link_2mon::MEDYAN.PropDictionary
  • link_2mon_params::MEDYAN.PropDictionary
  • cadherin::MEDYAN.PropDictionary
  • cadherinparams::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.
  • link_2mon_site::MEDYAN.PropDictionary
  • mon_link_2mon_site::MEDYAN.PropDictionary
  • decimated_2mon_site::MEDYAN.PropDictionary
  • cadherinsite::MEDYAN.PropDictionary
  • possiblecadherinsite::MEDYAN.PropDictionary
  • allfixedspeciesnames::Vector{String}
  • compartmentreactions::Vector{MEDYAN.CompartmentReaction}
  • compartmentreactioncallbacks::Vector{Any}
  • bulkreactions::Vector{MEDYAN.BulkReaction}
  • bulkreactioncallbacks::Vector{Any}: Context -> Nothing
  • links::MEDYAN.PropDictionary