Custom reference energy

Similarly to the logic behind TorchANI reference energy EnergyFunctionComponent, it is often useful to attribute a custom reference energy to a Residue type (by name). This can be, for example, to promote a positive bias towards a certain sub-set of aminoacids during mutation/design processes. The following methods allow the introduction of custom reference energies in ProtoSyn energy evaluations.

ProtoSyn.Calculators.calc_custom_ref_energy — Function

Calculators.calc_custom_ref_energy([::A], pose::Pose, selection::Opt{AbstractSelection}, update_forces::Bool = false; [map::Opt{Dict{AbstractSelection, T}} = nothing]) where {A, T <: AbstractFloat}

Calculate and return the Pose pose energy according to the given map. The map is a 1 to 1 correspondence between AbstractSelection instances and energy values. If provided, an AbstractSelection selection limits the selected range of Atom instances considered for this EnergyFunctionComponent calculation. Note that any provided selection and map AbstractSelection type are promoted to the biggest value: selection is promoted to the AbstractSelection type of map if the map type is larger or vice-versa. update_forces Bool has no effect in this EnergyFunctionComponent calculation and is only included to provide a standard function signature between all EnergyFunctionComponent instances. If no map is provided, returns 0.0.

Examples

julia> ProtoSyn.Calculators.calc_custom_ref_energy(pose, nothing, false)
(0.0, nothing)

julia> ProtoSyn.Calculators.calc_custom_ref_energy(pose, nothing, false, map = Dict{AbstractSelection, Float64}(rn"ALA" => 3.0, rn"GLU" => 2.4))
(71.4, nothing)

source

ProtoSyn.Calculators.get_default_custom_ref_energy — Function

get_default_custom_ref_energy(;[α::T = 1.0]) where {T <: AbstractFloat}

Return the default custom reference energy EnergyFunctionComponent. α sets the component weight (on an EnergyFunction instance). This component employs the calc_custom_ref_energy method, therefore defining a Pose energy based on a user-defined map between AbstractSelection instances and energy values.

Settings

map::Dict{AbstractSelection, T} - Defines which map the custom reference energy should use;

Examples

julia> ProtoSyn.Calculators.get_default_custom_ref_energy()
🞧  Energy Function Component:
+---------------------------------------------------+
| Name           | Custom_Ref_Energy                |
| Alpha (α)      | 1.0                              |
| Update forces  | true                             |
| Calculator     | calc_custom_ref_energy           |
+---------------------------------------------------+
 |    +----------------------------------------------------------------------------------+
 ├──  ● Settings                      | Value                                            |
 |    +----------------------------------------------------------------------------------+
 |    | map                           | Dict{AbstractSelection, Float64}(0 components)   |
 |    +----------------------------------------------------------------------------------+
 |    
 └──  ○  Selection: nothing

source