4.4. ligandparam.stages.resp

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

Runs a ‘lazy’ RESP calculation based on a single Gaussian output file.

Parameters:

stage_name (str) – Name of the stage.
main_input (Union[Path, str]) – Path to the input Gaussian log file.
cwd (Union[Path, str]) – Current working directory.
out_mol2 (str) – Path to the output mol2 file (from kwargs).
net_charge (float, optional) – Net charge for the molecule (default is 0.0).
atom_type (str, optional) – Atom type for antechamber (default is ‘gaff2’).
molname (str, optional) – Molecule name (from kwargs).

Methods

`add_required`(filename)	Add a required file to the stage.
`append_stage`(stage)	Append a stage to the current stage.
`clean`()	Clean up 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.

Initialize the StageLazyResp.

Parameters:

Methods

`add_required`(filename)	Add a required file to the stage.
`append_stage`(stage)	Append a stage to the current stage.
`clean`()	Clean up 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.

execute(dry_run=False, nproc: int | None = None, mem: int | None = None) → Any[source]

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 be run.
nproc (int, optional) – Number of processors to use (default is None).
mem (int, optional) – Memory to use in MB (default is None).

Returns:

None

Return type:

Any

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

Runs a multi-state RESP fitting calculation based on multiple Gaussian output files.

Parameters:

stage_name (str) – Name of the stage.
main_input (Union[Path, str]) – Path to the input mol2 file.
cwd (Union[Path, str]) – Directory containing Gaussian output files.
in_gaussian_label (str) – Label for Gaussian output files (from kwargs).
out_respfit (str) – Path to the output RESP fit file (from kwargs).
net_charge (float, optional) – Net charge for the molecule (default is 0.0).

Methods

`add_required`(filename)	Add a required file to the stage.
`append_stage`(stage)	Append a stage to the current stage.
`clean`()	Clean up the stage.
`execute`([dry_run, nproc, mem])	Execute a multi-state RESP fitting calculation.
`list_files_in_directory`(directory)	List all the files in a directory.

Initialize the StageMultiRespFit.

Parameters:

stage_name (str) – Name of the stage.
main_input (Union[Path, str]) – Path to the input mol2 file.
cwd (Union[Path, str]) – Directory containing Gaussian output files.
*args – Additional positional arguments.
**kwargs – Additional keyword arguments. Must include ‘in_gaussian_label’ and ‘out_respfit’.

Methods

`add_required`(filename)	Add a required file to the stage.
`append_stage`(stage)	Append a stage to the current stage.
`clean`()	Clean up the stage.
`execute`([dry_run, nproc, mem])	Execute a multi-state RESP fitting calculation.
`list_files_in_directory`(directory)	List all the files in a directory.

execute(dry_run=False, nproc: int | None = None, mem: int | None = None) → Any[source]

Execute a multi-state RESP fitting calculation.

Parameters:

dry_run (bool, optional) – If True, the stage will not be executed, but the function will print the commands that would be run.
nproc (int, optional) – Number of processors to use (default is None).
mem (int, optional) – Memory to use in MB (default is None).

Returns:

None

Return type:

Any