4.7. ligandparam.stages.build_system

class ligandparam.stages.build_system.StageBuild(name, base_cls=None, build_type='aq', target_pdb=None, concentration=0.14, rbuffer=9.0)

Bases: AbstractStage

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

Parameters:

• name (str) – Name of the stage.

• base_cls (object) – Object of the base class.

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.
list_files_in_directory(directory)	List all the files in a directory.

append_stage
clean
execute

Initialize the StageInitialize class.

Parameters:

• name (str) – The name of the stage

• base_cls (Ligand) – The base class of the ligand

• 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

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.
list_files_in_directory(directory)	List all the files in a directory.

append_stage
clean
execute

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.