3.1. ligandparam.recipes.lazyligand

class ligandparam.recipes.lazyligand.LazyLigand(in_filename: Path | str, cwd: Path | str, *args, **kwargs)

Bases: Recipe

This is a class for parametrizing a simple ligand using Gaussian and Antechamber.

This class is designed to do a quick parametrization of a very standard ligand. If your ligand is weird in any way, you should use a different class. This class does a very simple parametrization using Gaussian and Antechamber. The steps are: 1. Initialize the ligand using the PDB file. 2. Minimize the ligand using Gaussian at a low level of theory. 3. Minimize the ligand using Gaussian at a high level of theory. 4. Calculate the RESP charges using Gaussian at the low level of theory. 5. Check the parameters using ParmChk. 6. Generate the Leap input files.

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
setup

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
setup

execute(dry_run=False, nproc: int | None = None, mem: int | None = None) → Any

Execute the stages in the list of stages to run.

This function executes the stages in the list of stages to run. The stages are executed in the order that they were added to the list. If a stage fails, the function will print an error message and exit. The stages are

Parameters:

dry_run (bool, optional) – If True, the stages will not be executed, but the function will print the commands that would be executed.

Return type:

None

setup()