from luna.mol.entry import MolFileEntry
from luna.interaction.calc import InteractionsManager
from luna.wrappers.pymol import PymolWrapper, PymolSessionManager, mybio_to_pymol_selection
from luna.util.file import is_file_valid
from luna.util.exceptions import PymolSessionNotInitialized
from luna.MyBio.util import entity_to_string
[docs]class InteractionViewer(PymolSessionManager):
"""Class that inherits from :class:`~luna.wrappers.pymol.PymolSessionManager` and implements :meth:`set_view`
to depict 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. 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.
Parameters
----------
show_hydrop_surface : bool
If True, highlight hydrophobic surfaces. The default value is False
**kwargs : dict, optional
Extra arguments to `InteractionViewer`. Refer to :class:`~luna.wrappers.pymol.PymolSessionManager`
documentation for a list of all possible arguments.
Examples
--------
In the below examples, we will assume a LUNA project object named ``proj_obj`` already exists.
**Example 1)** In the first example, we will visualize all interactions identified in the first protein-ligand complex.
To do so, we will provide a tuple containing an :class:`~luna.interaction.calc.InteractionsManager` from where
the interactions will be recovered.
First access the property ``interactions_mngrs`` to get an iterable of
:class:`~luna.interaction.calc.InteractionsManager` objects and get the first one.
>>> interactions_mngr = list(proj_obj.interactions_mngrs)[0]
As `InteractionViewer` 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.interaction.calc.InteractionsManager` object.
The :class:`~luna.mol.entry.Entry` instance is necessary because the second item in the tuple (interactions)
may be an iterable of :class:`~luna.interaction.type.InteractionType` from where such information
cannot be recovered. 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.
>>> inter_tuples = [(interactions_mngr.entry, interactions_mngr, proj_obj.pdb_path)]
Now, we create a new `InteractionViewer` object and call
:meth:`~luna.wrappers.pymol.PymolSessionManager.new_session`, which will initialize the session, depict the interactions, and save
the session to an output PSE file.
>>> inter_view = InteractionViewer()
>>> inter_view.new_session(inter_tuples, "output.pse")
**Example 2)** In this example, we will create a new Pymol session where a given set of interactions will be shown.
Let's say, for instance, we only want to visualize hydrogen bonds.
To do so, instead of defining a tuple with an :class:`~luna.interaction.calc.InteractionsManager` instance, we will
define a list of :class:`~luna.interaction.type.InteractionType` objects, which will contain only hydrogen bonds.
Let's start with the selection of hydrogen bonds. Here, we will use the built-in method
:meth:`luna.interaction.calc.InteractionsManager.filter_by_types`, which permits to filter interactions by type.
>>> interactions_mngr = list(proj_obj.interactions_mngrs)[0]
>>> hydrogen_bonds = interactions_mngr.filter_by_types(['Hydrogen bond'])
Now, we just create the tuple as we did before and define the list of interactions we want to depict in the Pymol session.
>>> inter_tuples = [(interactions_mngr.entry, hydrogen_bonds, proj_obj.pdb_path)]
Finally, we create a new `InteractionViewer` object and call
:meth:`InteractionViewer.new_session`, which will initialize the session, depict the interactions, and save
the session to an output PSE file.
>>> inter_view = InteractionViewer()
>>> inter_view.new_session(inter_tuples, "output.pse")
**Example 3)** In this final example, we will create a new Pymol session to visualize all complexes in a LUNA project.
To do so, we create a list with one tuple for each complex:
>>> inter_tuples = [(im.entry, im, proj_obj.pdb_path) for im in proj_obj.interactions_mngrs]
Then, as we did before, just create a new `InteractionViewer` object and call :meth:`InteractionViewer.new_session`.
>>> inter_view = InteractionViewer()
>>> inter_view.new_session(inter_tuples, "output.pse")
**Note:** it is recommended that all complexes have the same atomic coordinates to make the analysis and comparisons easier.
If that's not the case, you may want to align the structures first. To do so, you can use :func:`luna.align.tmalign.align_2struct`
or any other tool of your preference.
"""
def __init__(self, show_hydrop_surface=False, **kwargs):
self.show_hydrop_surface = show_hydrop_surface
super().__init__(**kwargs)
[docs] def set_view(self, inter_tuples):
"""Depict interactions into the current Pymol session.
Parameters
----------
inter_tuples : iterable of tuple
Each tuple must contain three items: an :class:`~luna.mol.entry.Entry` instance,
an iterable of :class:`~luna.interaction.type.InteractionType` or an :class:`~luna.interaction.calc.InteractionsManager`,
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, inter_data, pathname in inter_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="-").replace("'", "-")
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)
if isinstance(inter_data, InteractionsManager):
interactions = inter_data.interactions
else:
interactions = inter_data
# Add interactions and styles.
interacting_residue_sels = self.set_interactions_view(interactions, main_grp)
if interacting_residue_sels:
self.wrapper.select(name="%s.inter_residues" % main_grp, selection=" or ".join(interacting_residue_sels))
if self.show_hydrop_surface:
self.wrapper.color([("white", "%s and !name PS*" % main_grp)])
# It will display all hydrophobic groups if an AtomGroupsManager is available.
atm_grp_mngr = interactions[0].src_grp.manager
if atm_grp_mngr is not None:
interacting_atms = set()
for atm_grp in atm_grp_mngr.filter_by_types(["Hydrophobe", "Hydrophobic"], must_contain_all=False):
inters = [i for i in atm_grp.interactions if i.type == "Hydrophobic"]
for comp in atm_grp.compounds:
comp_sel = "%s and %s" % (main_grp, mybio_to_pymol_selection(comp))
self.wrapper.show([("sticks", comp_sel)])
if len(inters) > 0:
for inter in inters:
for atm in inter.src_grp.atoms + inter.trgt_grp.atoms:
if atm not in interacting_atms:
self.wrapper.color([("pink", "%s and %s" % (main_grp, mybio_to_pymol_selection(atm)))])
for atm in inter.src_interacting_atms + inter.trgt_interacting_atms:
self.wrapper.color([("hotpink", "%s and %s" % (main_grp, mybio_to_pymol_selection(atm)))])
interacting_atms.add(atm)
else:
for atm in atm_grp.atoms:
self.wrapper.color([("wheat", "%s and %s" % (main_grp, mybio_to_pymol_selection(atm)))])
self.wrapper.hide([("sticks", "%s and not hetatm" % main_grp)])
self.wrapper.show([("sticks", "%s.inter_residues" % main_grp)])
self.wrapper.color([("white", "%s and not hetatm and not %s.inter_residues and !name PS*" % (main_grp, main_grp))])
# Otherwise, it will display only hydrophobic groups comprising the interacting groups.
else:
interacting_atms = set()
for inter in interactions:
if inter.type != "Hydrophobic":
continue
for atm in inter.src_grp.atoms + inter.trgt_grp.atoms:
if atm not in interacting_atms:
self.wrapper.color([("pink", "%s and %s" % (main_grp, mybio_to_pymol_selection(atm)))])
for atm in inter.src_interacting_atms + inter.trgt_interacting_atms:
self.wrapper.color([("hotpink", "%s and %s" % (main_grp, mybio_to_pymol_selection(atm)))])
interacting_atms.add(atm)
self.set_last_details_to_view()