4.3. ligandparam.stages.gaussian

class ligandparam.stages.gaussian.StageGaussian(name, inputoptions=None)[source]

Bases: AbstractStage

This is class to run a basic Gaussian calculations on the ligand.

This does three gaussian steps, one at a low level of theory, one at a higher level of theory, and one for the resp calculation.

Parameters:

  • name (str) – The name of the stage

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

Return type:

None

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>
_append_stage(stage: AbstractStage) → AbstractStage[source]

Appends the stage.

Parameters:

stage (AbstractStage) – _description_

Returns:

_description_

Return type:

AbstractStage

_clean()[source]

Clean the files generated during the stage.

_execute(dry_run=False)[source]

This class writes the Gaussian input files, and runs the Gaussian calculations.

This function creates a gaussianCalcs directory, and writes the Gaussian input files to that directory. It then runs the Gaussian calculations in that directory. By default, if it finds a Gaussian log file in the directory, it will not rerun the Gaussian calculations. This can be overridden by setting the force_gaussian_rerun option to True.

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

class ligandparam.stages.gaussian.StageGaussianRotation(name, alpha=[0.0], beta=[0.0], gamma=[0.0], inputoptions=None)[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

list_files_in_directory(directory)

List all the files in a directory.

print_docs()

Print the documentation for the stage.

write_rotation(coords)

Write the rotation to a file.

append_stage

clean

execute
_abc_impl = <_abc._abc_data object>
_append_stage(stage: AbstractStage) → AbstractStage[source]

Append the stage to the current stage.

Parameters:

stage (AbstractStage) – The stage to append to the current stage

_clean()[source]
_execute(dry_run=False)[source]

Executes a gaussian roation resp calculation on the ligand.

This stage rotates the ligand by the alpha, beta, and gamma angles, and then runs a Gaussian RESP calculation on the rotated ligand. The rotated ligand is written to a trajectory file, and the Gaussian calculations are run in the gaussianCalcs directory.

Parameters:

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

_print_rotation(alpha, beta, gamma)[source]

Print the rotation to the user.

_print_status(count, alphas, betas, gammas)[source]

Print the status of the stage.

Parameters:

  • count (int) – The current count of the rotations

  • alphas (list) – The list of alpha angles

  • betas (list) – The list of beta angles

  • gammas (list) – The list of gamma angles

write_rotation(coords)[source]

Write the rotation to a file.

class ligandparam.stages.gaussian.StageGaussiantoMol2(name, inputoptions=None, dry_run=None)[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

list_files_in_directory(directory)

List all the files in a directory.

print_docs()

Print the documentation for the stage.

remove_blank_lines(file_path)

Remove blank lines from a file.

append_stage

clean

execute
_abc_impl = <_abc._abc_data object>
_append_stage(stage: AbstractStage) → AbstractStage[source]

Append the stage to the current stage.

_clean()[source]
_execute(dry_run=False)[source]

Converts the gaussian output to mol2 format and assigns the charges.

This script converts the Gaussian output to mol2 format, and then assigns the charges to the mol2 file. Antechamber is used to clean up the mol2 file format written by MDAnalysis.

Parameters:

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

Returns:

  • None

  • To Do

  • —–

  • - Remove extraneous antechamber calls.

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