4.1. ligandparam.stages.initialize

class ligandparam.stages.initialize.StageInitialize(name, inputoptions=None)[source]

Bases: AbstractStage

This class is used to initialize from pdb to mol2 file using Antechamber.

Parameters:

name (str) – The name of the stage
inputoptions (dict) – The input options

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.

_clean()[source]: Clean the files generated during the stage.

_execute(dry_run=False)[source]

This function sets up a run in antechamber to generate a mol2 file from a pdb file with bcc charges.

This function does a few things to get ready for a parametrization. It first removes the CONECT lines from the pdb file and then runs antechamber to generate a mol2 file with bcc charges and the specified atom type.

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