from luna.mol.entry import MolFileEntry
from luna.wrappers.pymol import PymolWrapper, PymolSessionManager
from luna.MyBio.util import entity_to_string
from luna.util.exceptions import PymolSessionNotInitialized
from luna.util.file import is_file_valid
import logging
logger = logging.getLogger()
[docs]class ShellViewer(PymolSessionManager):
"""Class that inherits from :class:`~luna.wrappers.pymol.PymolSessionManager` and implements :meth:`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 :func:`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
:class:`~luna.interaction.fp.shell.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 :class:`~luna.mol.groups.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 :meth:`~luna.interaction.fp.shell.ShellGenerator.create_shells` returns a
:class:`~luna.interaction.fp.shell.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 :class:`~luna.mol.entry.Entry` instance, which represents a ligand. This can be obtained directly from
the :class:`~luna.mol.groups.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
:meth:`~luna.wrappers.pymol.PymolSessionManager.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")
"""
[docs] def set_view(self, 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 :class:`~luna.mol.entry.Entry` instance,
an iterable of :class:`~luna.interaction.fp.shell.Shell`,
and a PDB file or the directory where the PDB file is located.
"""
if not isinstance(self.wrapper, PymolWrapper):
raise PymolSessionNotInitialized("No session was initialized.")
for target_entry, shells, pathname in shell_tuples:
if is_file_valid(pathname):
pdb_file = pathname
else:
pdb_file = "%s/%s.pdb" % (pathname, target_entry.pdb_id)
main_grp = target_entry.to_string(sep="-")
mol_block = (entity_to_string(target_entry.get_biopython_structure())
if isinstance(target_entry, MolFileEntry) else None)
# Load PDB and extract hetatm.
self.load_pdb(pdb_file, main_grp, mol_block)
residue_selections = set()
for index, shell in enumerate(shells):
sphere_obj = "%s.spheres.s%d_lvl%d_center%d" % (main_grp, index, shell.level, hash(shell.central_atm_grp))
centroid_obj = "%s.centroid" % (sphere_obj)
self.wrapper.add_pseudoatom(centroid_obj, {"color": "white", "pos": list(shell.central_atm_grp.centroid)})
self.wrapper.hide([("nonbonded", centroid_obj)])
self.wrapper.show([("spheres", centroid_obj), ("nb_spheres", centroid_obj), ("dots", centroid_obj)])
self.wrapper.set("dot_color", "red")
self.wrapper.set("sphere_scale", shell.radius, {"selection": centroid_obj})
self.wrapper.set("sphere_transparency", 0.85, {"selection": centroid_obj})
self.wrapper.run_cmds([("center", {"selection": centroid_obj})])
self.wrapper.label([(centroid_obj, '"%s"' % "+".join([a.name for a in sorted(shell.central_atm_grp.atoms)]))])
# Add interactions and styles.
interacting_residue_sels = self.set_interactions_view(shell.interactions, main_grp, sphere_obj)
residue_selections.update(interacting_residue_sels)
if residue_selections:
self.wrapper.select(name="%s.inter_residues" % main_grp, selection=" or ".join(residue_selections))
self.set_last_details_to_view()