4.3. ligandparam.stages.gaussian

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

Bases: AbstractStage

This is class to run a basic Gaussian calculation on the ligand. This does 2 gaussian steps, a minimization and an ESP calculation for RESP charges.

Parameters:

inputoptions (dict) – The input options for the stage

Return type:

None

Methods

add_required(filename)

Add a required file to the stage.

execute([dry_run, nproc, mem])

Execute the Gaussian calculations.

list_files_in_directory(directory)

List all the files in a directory.

append_stage

clean

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

Execute the Gaussian calculations.

Parameters:

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

Return type:

None

setup(name_template: str) → bool[source]
class ligandparam.stages.gaussian.StageGaussianRotation(stage_name: str, main_input: Path | str, cwd: Path | str, *args, **kwargs)[source]

Bases: AbstractStage

This is class to rotate the ligand and run Gaussian calculations of the resp charges for each rotated ligand.

Parameters:

  • name (str) – The name of the stage

  • alpha (list) – The list of alpha angles to rotate the ligand

  • beta (list) – The list of beta angles to rotate the ligand

  • gamma (list) – The list of gamma angles to rotate the ligand

  • inputoptions (dict) – The input options for the stage

Methods

add_required(filename)

Add a required file to the stage.

execute([dry_run, nproc, mem])

Execute the Gaussian calculations for the rotated ligands.

list_files_in_directory(directory)

List all the files in a directory.

write_rotation(coords, name_template)

Write the rotation to a file.

append_stage

clean

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

Execute the Gaussian calculations for the rotated ligands.

Parameters:

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

setup(name_template: str) → bool[source]
write_rotation(coords, name_template: str)[source]

Write the rotation to a file.

class ligandparam.stages.gaussian.StageGaussiantoMol2(stage_name: str, main_input: Path | str, cwd: Path | str, *args, **kwargs)[source]

Bases: AbstractStage

Convert Gaussian output to mol2 format.

This class converts the Gaussian output to mol2 format, and assigns the charges to the mol2 file.

Parameters:

  • name (str) – The name of the stage

  • inputoptions (dict) – The input options for the stage

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

Return type:

None

Methods

add_required(filename)

Add a required file to the stage.

execute([dry_run, nproc, mem])

Execute the Gaussian to mol2 conversion.

list_files_in_directory(directory)

List all the files in a directory.

remove_blank_lines(file_path)

Remove blank lines from a file.

append_stage

clean

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

Execute the Gaussian to mol2 conversion.

Parameters:

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

Return type:

None

remove_blank_lines(file_path)[source]

Remove blank lines from a file.

Parameters:

file_path (str) – The path to the file to remove blank lines from

Return type:

None

setup(name_template: str) → bool[source]