Topo

TopoGen()

Bases: ABC

Standardized framework for generating topology files.

dry_run(path_structure, simlify_config)

Perform a dry run to obtain any preliminary information needed before run.

PARAMETER	DESCRIPTION
path_structure	Path structure file for topology generation. TYPE: str
simlify_config	Simlify configuration. TYPE: SimlifyConfig

RETURNS	DESCRIPTION
dict[str, Any]	Keyword arguments to be passed into run.

run(path_structure, simlify_config, **kwargs)

Generate a topology file.

PARAMETER	DESCRIPTION
path_structure	Path structure file for topology generation. TYPE: str
simlify_config	Simlify configuration. TYPE: SimlifyConfig

cli_run_gen_topo()

Command-line interface for generating a topology file

run_gen_topo(path_structure, import_string, simlify_config)

Diver function for generating a topology file.

PARAMETER	DESCRIPTION
path_structure	Path structure file for topology generation. TYPE: str
import_string	Import string to a topology generation class. For example, "simlify.simulation.amber.topo.AmberTopoGen". TYPE: str
simlify_config	Simlify configuration. TYPE: SimlifyConfig