4.7. ligandparam.stages.build_system

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

Bases: AbstractStage

Parameters:

namestr

Name of the stage.

: object

Object of the base class.

Methods

Get_Num_Ions(parm7[, wat_resname])	Get the number of ions needed for the system.
check_target()	Check that the target pdb file is correct.
list_files_in_directory(directory)	List all the files in a directory.
print_docs()	Print the documentation for the stage.

append_stage
clean
execute

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.
check_target()	Check that the target pdb file is correct.
list_files_in_directory(directory)	List all the files in a directory.
print_docs()	Print the documentation for the stage.

append_stage
clean
execute

Get_Num_Ions(parm7, wat_resname='WAT')

Get the number of ions needed for the system.

_abc_impl = <_abc._abc_data object>

_append_stage(stage: AbstractStage) → AbstractStage

Appends the stage.

_aq_build(dry_run=False)

Build the ligand in aqueous environment.

This function will build the ligand in an aqueous environment. The ligand will be solvated in a box of water molecules and ions will be added to neutralize the system. The concentration of the ions can be specified for addition to the system after the solvent is added.

Parameters:

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

• Do (To)

• -----

• solvating) (- Add options for different neutralization schemes (before or after)

_clean()

Clean the files generated during the stage.

_execute(dry_run=False)

Builds the ligand in the specified environment.

This function will build the ligand in the specified environment. The environment can be aqueous (aq), gas (gas), or target (target).

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

_gas_build(dry_run=False)

Build the ligand in gas environment.

_target_build(dry_run=False)

Build the ligand in the target environment.

check_target()

Check that the target pdb file is correct.