Table of Contents

Functions

Define a System

src/sysdefs.jl

• MEDYAN.AgentNames
• MEDYAN.SysDef
• add_diffusion_coeff!
• addreaction!
• addreactioncallback!
• add_filament_params!
• addfilamentsite!
• addfilament_reaction!
• addfilamentendsite!
• addfilamentend_reaction!

Contruct a Context

• MEDYAN.Context
• CubicGrid
• deepcopy, note: rng is shared

Mutate a Context

• Base.empty!

• load_snapshot!

• chem_adddiffusingcount!

• chem_addfixedcount!

• adddiffusingcount_rand!

• set_time!

• set_enable_cylinder_volume_exclusion!

• set_chemboundary!

• set_mechboundary!

Mutate filaments

• make_fila!
• make_fila_rand!
• remove_fila!
• update_fila_mono_state!
• polymerize_fila!
• depolymerize_fila!
• sever_fila!

Get data about filaments

• num_fila_types
• num_fila
• fila_mono_ids
• fila_mono_states
• fila_num_nodes
• fila_node_mids
• fila_node_positions
• fila_tip_tags
• fila_num_unmin_ends
• pick_rand_fila_mono_site
• pick_rand_fila_tip_site

Mutate links

• tag!
• make_link!
• remove_link!
• update_link!

Get data about links

• num_link_types
• link_type_name
• get_all_links
• get_all_tags
• tag2links
• place2links
• tag_exists
• place_exists
• link_exists
• link2tags
• tag2place
• place2tag
• has_tag
• get_position
• num_directions
• get_directions
• get_chem_state
• get_state
• get_bond_states
• get_bond_enabled
• get_reaction_enabled
• is_minimized
• get_link_mechanics

Run a simulation

• run_chemistry!
• minimize_energy!

Interfaces

Sites

• filament sites
• filament end sites
• decimated_2mon sites

Utilities

CubicGrid

• CubicGrid
• MEDYAN.grididat
• MEDYAN.filter_grididat
• MEDYAN.centerof