class SamplingProtocol
- SamplingProtocol
- Reference
- Object
Overview
Define colvar bounds, windows and time for the collective variables.
Included Modules
- YAML::Serializable
Defined in:
moltiverse/protocols.crConstructors
-
.create_from_properties(base_protocol : SamplingProtocol, properties : Hash(String, Int32 | Float64 | Bool)) : SamplingProtocol
Create a new protocol based on the properties of a molecule
- .from_file(path : String | Path) : self
- .new(colvars : Array(Colvar::Windowed), simulation_time : Float64, fullsamples : Int32, metadynamics : Bool, hillweight : Float64, hillwidth : Float64, newhillfrequency : Int32, structure_generator : String = "cdpkit", protonation_ph : Float64 = 7.0, name : String = "default", description : String = "", output_frequency : Int = 500)
- .new(ctx : YAML::ParseContext, node : YAML::Nodes::Node)
- .new(name : String, version : Int32 = 1) : self
Instance Method Summary
- #calculate_iterations_and_step : Tuple(Int32, Int32)
- #clone : SamplingProtocol
- #colvars : Array(Colvar::Windowed)
- #describe
- #description : String
- #description=(description : String)
- #execute(lig : Ligand, cpus : Int = System.cpu_count)
- #fullsamples : Int32
- #hillweight : Float64
- #hillwidth : Float64
- #loaded_from_file : Bool
- #loaded_from_file=(loaded_from_file : Bool)
- #metadynamics : Bool
- #name : String
- #name=(name : String)
- #newhillfrequency : Int32
- #output_frequency : Int32
- #output_frequency=(output_frequency : Int32)
- #protocol_type : String
- #protocol_type=(protocol_type : String)
- #protonation_ph : Float64
- #protonation_ph=(protonation_ph : Float64)
- #simulation_time : Float64
- #smiles_conversion_timeout : Int32
- #smiles_conversion_timeout=(smiles_conversion_timeout : Int32)
- #structure_generator : String
- #structure_generator=(structure_generator : String)
- #user_selected : Bool
- #user_selected=(user_selected : Bool)
- #version : Int32
- #version=(version : Int32)
Constructor Detail
def self.create_from_properties(base_protocol : SamplingProtocol, properties : Hash(String, Int32 | Float64 | Bool)) : SamplingProtocol
#
Create a new protocol based on the properties of a molecule
def self.new(colvars : Array(Colvar::Windowed), simulation_time : Float64, fullsamples : Int32, metadynamics : Bool, hillweight : Float64, hillwidth : Float64, newhillfrequency : Int32, structure_generator : String = "cdpkit", protonation_ph : Float64 = 7.0, name : String = "default", description : String = "", output_frequency : Int = 500)
#