luna.interaction.fp.view module

class ShellViewer(show_cartoon=False, bg_color='white', add_directional_arrows=True, show_res_labels=True, inter_color=<luna.util.ColorPallete object>, pse_export_version='1.8')

Bases: luna.wrappers.pymol.PymolSessionManager

Class that inherits from PymolSessionManager and implements set_view() to depict shells (IFP features) and interactions in Pymol and save the view as a Pymol session.

This class can be used to visualize multiple complexes into the same Pymol session, for instance, to compare binding modes and analyze similar shells. To do so, it is recommended that the protein structures are in the same coordinate system, i.e., they should be aligned first. This can be achieved with luna.align.tmalign.align_2struct() or any other tool of your preference.

Examples

In the below example, we will assume a LUNA project object named proj_obj already exists.

To visualize shells, we first need to generate them. So, let’s define a ShellGenerator object that will create shells over 2 iterations (levels). At each iteration, the shell radius will be increased by 3 and substructural information will be encoded following EIFP definition. Here, as an example, we will generate shells for the first AtomGroupsManager object at proj_obj.

>>> from luna.interaction.fp.shell import ShellGenerator
>>> from luna.interaction.fp.type import IFPType
>>> num_levels, radius_step = 2, 3
>>> sg = ShellGenerator(num_levels, radius_step, ifp_type=IFPType.EIFP)
>>> atm_grps_mngr = list(proj_obj.atm_grps_mngrs)[0]
>>> sm = sg.create_shells(atm_grps_mngr)

The function create_shells() returns a ShellManager object, which provides built-in methods to access the created shells. Therefore, you can interact with it to select the shells you want to visualize in Pymol. As an example, let’s select all unique shells at the last level:

>>> shells = sm.get_shells_by_level(num_levels - 1, unique_shells=True)

Note

Levels are 0-indexed. So, the first level is 0, second is 1, etc. That means if num_levels is 5, the last level will be 4.

As ShellViewer expects a list of tuples, we will define it now. The first item of the tuple is the Entry instance, which represents a ligand. This can be obtained directly from the AtomGroupsManager object. The second item is the list of shells you want to visualize. Finally, the third item can be either a PDB file or a directory. In this example, we will use the PDB directory defined during the LUNA project initialization.

>>> shell_tuples = [(atm_grps_mngr.entry, shells, proj_obj.pdb_path)]

To finish, we now create a new ShellViewer object and call new_session(), which will initialize the session, depict shells and interactions, and save the session to an output PSE file.

>>> from luna.interaction.fp.view import ShellViewer
>>> sv = ShellViewer()
>>> sv.new_session(shell_tuples, "example.pse")

set_view(shell_tuples)

Depict shells (IFP features) and interactions into the current Pymol session.

Parameters

shell_tuples (iterable of tuple) – Each tuple must contain three items: an Entry instance, an iterable of Shell, and a PDB file or the directory where the PDB file is located.