3.3. ligandparam.recipes.buildligand

class ligandparam.recipes.buildligand.BuildLigand(*args, **kwargs)

Bases: Recipe

This is a recipe for doing a parametrization of a ligand using the RESP method, and then building the ligand in gas, aqueous, and target environments.

This recipe has a default list of stages that are run, and the stages can be disable by passing a dictionary of stages to disable to the disable stages method defined in the Recipe class.

default_stage_list = { “Initialize”: True, “Normalize1”: True, “Minimize”: True, “Rotate”: True, “GrabGaussianCharge”: True, “MultiRespFit”: True, “UpdateCharge”: True, “Normalize2”: True, “UpdateNames”: True, “UpdateTypes”: True, “ParmChk”: True, “Leap”: True, “BuildGas”: True, “BuildAq”: True, “BuildTarget”: True }

Methods

add_stage(stage)	Add a stage to the list of stages to run.
apply_stage_list([stage_list])	Apply the stage list to the recipe.
check_validity()	Check the validity of the stages in the list of stages to run.
clean()	Clean up the files created by the stages.
execute([dry_run])	Execute the stages in the list of stages to run.
insert_stage(newstage, stage_name)	Insert a stage into the list of stages to run before the specified stage.
list_stages()	Print out the list of stages to run.
remove_stage(stage_name)	Remove a stage from the list of stages to run.

add_leaprc
setup

setup()