4.7. ligandparam.stages.build_system

class ligandparam.stages.build_system.StageBuild(stage_name: str, name: Path | str, cwd: Path | str, *args, **kwargs)

Bases: AbstractStage

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

Parameters:

• name (str) – The name of the stage

• build_type (str) – The type of build to perform [aq, gas, or target]

• target_pdb (str) – The target pdb file

• concentration (float) – The concentration of the ions

• rbuffer (float) – The buffer radius

• inputoptions (dict) – The input options

Methods

Get_Num_Ions(parm7[, wat_resname])	Get the number of ions needed for the system.
add_required(filename)	Add a required file to the stage.
check_target()	Check that the target pdb file is correct.
execute([dry_run, nproc, mem])	Execute the Gaussian calculations.
list_files_in_directory(directory)	List all the files in a directory.

append_stage
clean

Get_Num_Ions(parm7, wat_resname='WAT')

Get the number of ions needed for the system.

check_target()

Check that the target pdb file is correct.

execute(dry_run=False, nproc: int | None = None, mem: int | None = None) → Any

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