3.3. ligandparam.recipes.buildligand

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

Bases: Recipe

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()