3.1. ligandparam.recipes.lazyligand

class ligandparam.recipes.lazyligand.LazyLigand(*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])	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
initial_coordinates
print_info
setup

This is the base class for all parametrizations, that is a sub class of the ligand_param.driver.Driver class.

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.

Parameters:

• pdb_file (str, optional) – The path to a PDB file containing the ligand structure.

• netcharge (int, optional) – The net charge of the ligand.

• atom_type (str, optional) – The atom type to use for the ligand. Default is ‘gaff2’.

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])	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
initial_coordinates
print_info
setup

setup()