4.3. ligandparam.stages.gaussian

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

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:

Return type:

None

Methods

`add_required`(filename)	Add a required file to the stage.
`list_files_in_directory`(directory)	List all the files in a directory.

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

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

Parameters:

Methods

`add_required`(filename)	Add a required file to the stage.
`list_files_in_directory`(directory)	List all the files in a directory.
`write_rotation`(coords)	Write the rotation to a file.

class ligandparam.stages.gaussian.StageGaussiantoMol2(name, base_cls=None, dry_run=None)[source]

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
base_cls (Ligand) – The base class of the ligand
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.
`list_files_in_directory`(directory)	List all the files in a directory.
`remove_blank_lines`(file_path)	Remove blank lines from a file.

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