3.2. ligandparam.recipes.freeligand

class ligandparam.recipes.freeligand.FreeLigand(*args, **kwargs)[source]

Bases: Recipe

This is a recipe for doing a parametrization of a ligand using the RESP method with multi-state fitting.

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, }

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()[source]