4.4. ligandparam.stages.resp

class ligandparam.stages.resp.StageLazyResp(stage_name: str, main_input: Path | str, cwd: Path | str, *args, **kwargs)

Bases: AbstractStage

This class runs a ‘lazy’ resp calculation based on only a single gaussian output file.

Methods

add_required(filename)	Add a required file to the stage.
execute([dry_run, nproc, mem])	Execute antechamber to convert the gaussian output to a mol2 file.
list_files_in_directory(directory)	List all the files in a directory.

append_stage
clean

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

Execute antechamber to convert the gaussian output to a mol2 file.

Parameters:

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

class ligandparam.stages.resp.StageMultiRespFit(stage_name: str, main_input: Path | str, cwd: Path | str, *args, **kwargs)

Bases: AbstractStage

This class runs a multi-state resp fitting calculation, based on multiple gaussian output files.

TODO: Implement this class. TODO: Implement the clean method. TODO: Implement the execute method. TODO: Add a check that a multistate resp fit is possible.

Methods

add_required(filename)	Add a required file to the stage.
execute([dry_run, nproc, mem])	Execute a multi-state respfitting calculation.
list_files_in_directory(directory)	List all the files in a directory.

append_stage
clean

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

Execute a multi-state respfitting calculation.

if __name__ == “__main__”: comp = parmutils.BASH( 12 ) model = rf.ResidueResp( comp, 1 )

model.add_state( “$base”, “$base.log.mol2”, glob.glob(“gaussianCalcs/$base_*.log”), qmmask=”@*” )

model.multimolecule_fit(True) model.perform_fit(“@*”,unique_residues=False) #model.preserve_residue_charges_by_shifting() model.print_resp()

Parameters:

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