Common

default_energy_function(::Type{T}) where {T <: AbstractFloat}
default_energy_function()

Returns a default EnergyFunction for ProtoSyn. If no Type{T} is provided, will use ProtoSyn.Units.defaultFloat. This EnergyFunction is optimized for evaluating protein systems.

Examples

julia> ProtoSyn.Common.default_energy_function()
🗲  Energy Function (7 components):
+----------------------------------------------------------------------+
| Index | Component name                                | Weight (α)   |
+----------------------------------------------------------------------+
| 1     | TorchANI_ML_Model                             |       1.00   |
| 2     | All_Atom_Clash_Rest                           |       1.00   |
| 3     | Hydrogen_Bonds                                |       0.50   |
| 4     | Coulomb                                       |       0.60   |
| 5     | TorchANI_Ref_Energy                           |       1.00   |
| 6     | GB_Solvation                                  |       1.00   |
| 7     | SASA_Solvation                                |   5.00e-04   |
+----------------------------------------------------------------------+
 ● Update forces: false
 ● Selection: Set
 └── TrueSelection (Atom)

default_energy_step_callback(n::Int)::Callback

Returns a simple Callback that prints the current step and total energy value of the Pose every n steps.

Examples

julia> ProtoSyn.Common.default_energy_step_callback(100)
✉  Callback:
+----------------------------------------------------------------------+
| Index | Field                     | Value                            |
+----------------------------------------------------------------------+
| 1     | Event                     | energy_step                      |
| 2     | Frequency                 | 100                              |
+----------------------------------------------------------------------+

default_energy_step_frame_callback(n::Int, filename::String)::Callback

Returns a simple Callback that prints the current step and total energy value of the Pose every n steps, while printing the current structure to the given filename (format infered from filename extension).

Examples

julia> ProtoSyn.Common.default_energy_step_frame_callback(100, "test.pdb")
✉  Callback:
+----------------------------------------------------------------------+
| Index | Field                     | Value                            |
+----------------------------------------------------------------------+
| 1     | Event                     | energy_step_frame                |
| 2     | Frequency                 | 100                              |
+----------------------------------------------------------------------+

default_energy_step_detailed(n::Int, msg::String = "Callback", color::Symbol = :none, file_out::Opt{String} = nothing, print_to_sdtout::Bool = true)::Callback

Returns a detailed Callback that prints the current step and all energy components of the Pose every n steps. An optional msg String can be provided as a header. Output can be colored by setting the color flag. For a list of available colors, check the printstyled documentation. By default, default_energy_step_detailed prints the output to the stdout. This can be toggled by setting the print_to_sdtout flag. Optionally, if a file_out is provided (as a String), output is also printed to that file.

Examples

julia> ProtoSyn.Common.default_energy_step_detailed(1)
✉  Callback:
+----------------------------------------------------------------------+
| Index | Field                     | Value                            |
+----------------------------------------------------------------------+
| 1     | Event                     | energy_step_detailed             |
| 2     | Frequency                 | 1                                |
+----------------------------------------------------------------------+

default_energy_step_frame_detailed(n::Int, output_frame::String, msg::String = "Callback", color::Symbol = :none, output_log::Opt{String} = nothing, print_to_sdtout::Bool = true)::Callback

Returns a detailed Callback that prints the current step and all energy components of the Pose every n steps, while printing the current structure to the given filename (format infered from filename extension). An optional msg String can be provided as a header. Output can be colored by setting the color flag. For a list of available colors, check the printstyled documentation. By default, default_energy_step_detailed prints the output to the stdout. This can be toggled by setting the print_to_sdtout flag. Optionally, if a file_out is provided (as a String), output is also printed to that file.

Examples

julia> ProtoSyn.Common.default_energy_step_detailed(1)
✉  Callback:
+----------------------------------------------------------------------+
| Index | Field                     | Value                            |
+----------------------------------------------------------------------+
| 1     | Event                     | energy_step_detailed             |
| 2     | Frequency                 | 1                                |
+----------------------------------------------------------------------+

detailed_message(msg::String; color::Symbol = :none, file_out::Opt{String} = nothing, print_to_sdtout::Bool = true, N::Int = 100)

Print a detailed message msg in the same style as default_energy_step_detailed, with the given color (uses the printstyled method). If file_out is set to a String (nothing, by default), also print to a file with the given file name. If print_to_stdout is set to false (true, by default), skip printing to the stdout. N sets the length of the final stylized message.

Examples

julia> ProtoSyn.Common.detailed_message("Simulation (Stage 3) ...", color = :blue, N = 120)
| --------------------------------------------- Simulation (Stage 3) ... --------------------------------------------- |