Top Level Namespace

Included Modules

• Chem

Extended Modules

• Chem

Defined in:

Constant Summary

AQUA = Colorize::ColorRGB.new(0, 255, 255)

ELECTRIC_BLUE = Colorize::ColorRGB.new(30, 144, 255)

GREEN = Colorize::ColorRGB.new(0, 163, 131)

ORANGE = Colorize::ColorRGB.new(255, 165, 0)

PURPLE = Colorize::ColorRGB.new(128, 0, 128)

RED = Colorize::ColorRGB.new(214, 69, 80)

TURQUOISE = Colorize::ColorRGB.new(64, 224, 208)

WHITE = Colorize::ColorRGB.new(255, 255, 255)

XTB_ENERGY_PATTERN = /\s*\|\s+TOTAL ENERGY\s+(\-?\d+\.\d+)\s+Eh\s+\|/

XTB_EXEC = "xtb"

YELLOW = Colorize::ColorRGB.new(255, 191, 0)

Method Summary

• abort(message : String, status : Int = 1) : NoReturn
• append_content(source_path : String, destination_path : String)

  Function to concatenate files

• check_dependencies
• n_frames(dcd : String)
• print_banner
• rand_conf(input_mol : String) : Chem::Structure
• run(cmd : String, args : Array, output path : Path | String | Nil = nil, retries : Int = 1, env : Process::Env = nil) : Bool
• run_cmd(cmd : String, args : Array(String), output_file : Nil.class | String, stage : String | Colorize::Object(String), verbose : Bool = true)

  run_cmd is a function for general purpuse.

• run_cmd(cmd : String, args : Array, output_file : String)
• run_cmd(cmd, args)
• run_cmd_silent(cmd : String, args : Array(String), output_file : Nil.class | String)
• run_cmd_version(cmd : String, args : Array(String)) : String
• run_namd(cmd : String, args : Array(String), output_file : String, stage : String | Colorize::Object(String), window : String)
• write_geometrical_data(st : Chem::Structure, index : Int64, pdb_names : Array(String), bonds_file : File, angles_file : File, dihedrals_file : File, hydrogen : Bool, printing_full : Bool)
• write_getidx(outfile : String)

Method Detail