4.4. ligandparam.stages.resp

class ligandparam.stages.resp.StageLazyResp(name, inputoptions=None)[source]

Bases: AbstractStage

This class runs a ‘lazy’ resp calculation based on only a single gaussian output file.

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

Initialize the StageLazyResp class.

Parameters:

name (str) – The name of the stage
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.

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]

Execute antechamber to convert the gaussian output to a mol2 file.

This stage will convert the gaussian output file to a mol2 file using antechamber, and will incorporate the resp charges calculated by gaussian into the mol2 file.

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

class ligandparam.stages.resp.StageMultiRespFit(name, inputoptions=None)[source]

Bases: AbstractStage

This class runs a multi-state resp fitting calculation, based on multiple gaussian output files.

TODO: Implement this class. TODO: Implement the clean method. TODO: Implement the execute method. TODO: Add a check that a multistate resp fit is possible.

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

Initialize the StageMultiRespFit class.

Parameters:

namestr: The name of the stage
: Ligand: The base class of the ligand

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]

Execute a multi-state respfitting calculation.

This stage will execute a multi-state resp fitting calculation based on the gaussian output files created with the gaussian stage.

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