3.3. ligandparam.recipes.buildligand

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

Bases: Recipe

The rough approach to using this class is to generate a new Parametrization class, and then generate self.stages as a list of stages that you want to run. :param in_filename: The in_filename of the ligand. :type in_filename: str :param cwd: The current working directory. :type cwd: Union[Path, str] :param *args: Additional positional arguments. :param **kwargs: Additional keyword arguments.

Keyword Arguments:

  • name (str) – The base name for the ligand.

  • inputoptions (dict) – A dictionary of input options, which should include ‘name’ or ‘pdb_filename’.

Raises:

ValueError – If neither ‘name’ nor ‘pdb_filename’ is provided in inputoptions.

Methods

add_stage(stage)

Add a stage to the list of stages to run.

clean()

Clean up the files created by the stages.

execute([dry_run, nproc, mem])

Execute the stages in the list of stages to run.

insert_stage(newstage, stage_name[, print_info])

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