4.9. ligandparam.stages.abstractstage

class ligandparam.stages.abstractstage.AbstractStage(name, **kwargs)

Bases: object

This is an abstract class for all the stages.

Methods

list_files_in_directory(directory)	List all the files in a directory.
print_docs()	Print the documentation for the stage.

append_stage
clean
execute

_abc_impl = <_abc._abc_data object>

_add_output(output)

Add the output to the stage.

Parameters:

output (str) – The output file to add to the stage.

_add_required(filename)

Add a required file to the stage.

Parameters:

filename (str) – The file to add to the required list.

abstract _append_stage(stage: AbstractStage) → AbstractStage

_check_required()

Check if the required files are present.

_check_self()

abstract _clean()

abstract _execute(dry_run=False)

_generate_implied()

Generate the implied options.

This function generates the implied options, such as the base_name from the pdb_filename.

_parse_inputoptions(inputoptions=None, **kwargs)

Parse the input options.

Parameters:

• inputoptions (dict) – A dictionary of input options.

• **kwargs (dict) – A dictionary of input options

append_stage(stage: AbstractStage) → AbstractStage

clean() → None

default_options = {'atom_type': 'gaff2', 'base_name': None, 'force_gaussian_rerun': False, 'leaprc': ['leaprc.gaff2'], 'mem': '8GB', 'net_charge': 0.0, 'nproc': 6, 'pdb_filename': None, 'target_pdb': None, 'theory': {'high': 'PBE1PBE/6-31G*', 'low': 'HF/6-31G*'}}

execute(dry_run=False) → None

list_files_in_directory(directory)

List all the files in a directory.

Parameters:

directory (str) – The directory to list the files from.

print_docs()

Print the documentation for the stage.