src/filament/functions.jl

`MEDYAN.num_fila`

num_fila(c::MEDYAN.Context; type) -> Int64

Return the number of filaments of a given type.

`MEDYAN.fila_mono_states`

fila_mono_states(
    c::MEDYAN.Context,
    f::MEDYAN.FilaIdx
) -> OffsetArrays.OffsetVector{UInt8, Vector{UInt8}}

Return a read only OffsetVector of monomer states on a filament.

This can be invalid after any mutations to context, so copy if needed.

`MEDYAN.fila_num_nodes`

fila_num_nodes(
    c::MEDYAN.Context,
    f::MEDYAN.FilaIdx
) -> Int64

Return the number of mechanical node positions of a filament.

`MEDYAN.fila_node_mids`

fila_node_mids(
    c::MEDYAN.Context,
    f::MEDYAN.FilaIdx
) -> Vector{Int64}

Return the node_mids of the filament.

The node_mids are the monomer ids at (slightly plus side of) the node_positions

                                 |
                      -----+-----|-----+-----
  minus end <----       M  |  M  | (M) |  M        ----> plus end
                      -----+-----|-----+-----
                                 |
                                 ^ A node position is indicated by the line.

The monomer id with parenthesis (M) will in `node_mids`

The first monomer id is the first monomer id on the filament. The last monomer id is the last monomer id on the filament + 1

`MEDYAN.fila_node_positions`

fila_node_positions(
    c::MEDYAN.Context,
    f::MEDYAN.FilaIdx
) -> Vector{StaticArraysCore.SVector{3, Float64}}

Return the mechanical node positions of the filament.

`MEDYAN.fila_tip_tags`

fila_tip_tags(
    c::MEDYAN.Context,
    f::MEDYAN.FilaIdx
) -> Pair{MEDYAN.Tag{MEDYAN.FilaTipIdx}, MEDYAN.Tag{MEDYAN.FilaTipIdx}}

Return the pair of minus end, plus end filament tip tags.

`MEDYAN.fila_num_unmin_ends`

fila_num_unmin_ends(
    c::MEDYAN.Context,
    fila_idx::MEDYAN.FilaIdx
) -> Pair{Int64, Int64}

Return a pair (minus => plus) of the number of unminimized monomers on the minus and plus end of a filament.

This will be reset to (0 => 0) by minimize_energy!

When an end is depolymerized this will decrease, but saturate at 0. When an end is polymerized this will increase.

For example if after minimization a filament has a plus end depolymerization, this function will return (0 => 0). Then if a plus end polymerization happens, this function will return (0 => 1), even though the net change in filament length is zero.

`MEDYAN.is_minimized`

is_minimized(c::Context, p::Union{FilaMonoIdx, FilaTipIdx, Tag})::Bool

Return true iff the monomer or tip has been minimized. Throw an error if p doesn’t exist.

`MEDYAN.pick_rand_fila_mono_site`

pick_rand_fila_mono_site(c::Context, chem_voxel, fila_typeid, fsid)::Union{FilaMonoIdx, Nothing}

Return a FilaMonoIdx of a random filamonosite, or return nothing if rejected weighted by counts, using the default RNG.

`MEDYAN.pick_rand_fila_tip_site`

pick_rand_fila_tip_site(c::Context, chem_voxel, fila_typeid, fesid)::Union{FilaTipIdx, Nothing}

Return a FilaTipIdx of a random filaendsite, or return nothing if rejected weighted by counts, using the default RNG.