MEDYAN.update_link!

Tuple{MEDYAN.Context, MEDYAN.Link}

update_link!(c::Context, link::Link; kwargs...)::Nothing

Update the link.

Keyword Arguments

• places=(): places or tags to attach to the link.

  Set an element to nothing to not change the attached place. Set an element to a null place or tag to detach that place.

• state=(;): state properties to change.

  A NamedTuple of changes. For example, state = (;k1 = 3.6, k7 = 2.0,) to change state.k1 to 3.6 and state.k7 to 2.0.

• bond_states=(): bond state properties to change.

  A Tuple of NamedTuple or nothing. If an element in the tuple is nothing, the corresponding bond state isn’t changed. For example, bond_states = (nothing, (;L0 = 3.6,)) to change bond_states[2].L0 to 3.6.

• colvar_thresholds=(): colvar thresholds to change.

  A Tuple of nothing, Real, or AbstractVector. If an element in the tuple is nothing, the corresponding colvar threshold isn’t changed. A Real is accepted for a 1-dimensional colvar; otherwise a length-D vector is required. For example, colvar_thresholds = (nothing, 2.7) to leave colvar 1’s threshold unchanged and set colvar 2’s threshold to 2.7. See get_colvar_thresholds.

• bond_enabled=(): bond enable flags to change.

  A Tuple of Union{Bool, Nothing}. If an element in the tuple is nothing, the corresponding bond enable flag isn’t changed. For example, bond_enabled = (nothing, true, false) to not change bond 1, enable bond 2, and disable bond 3.

• reaction_enabled=(): reaction enable flags to change.

  A Tuple of NamedTuple or nothing. If an element in the tuple is nothing, the corresponding reaction enable flags aren’t changed. For example, reaction_enabled = (nothing, (;a=true, b=false)) to not change any reactions on place 1, enable reaction a on place 2, and disable reaction b on place 2.

• is_minimized::Bool=false: is the link marked as minimized.

  By default links are marked as minimized at the end of mechanics when updated.

• reset_colvar_stats::Bool=false: reset the link’s ColVarStats to NaN, discarding the stats collected by the last baoab! run.

  By default the stats are kept. See get_colvar_stats.