#!/usr/bin/env python3
import os
import re
from fretraj import _nglview_found
if _nglview_found:
import nglview
import ipywidgets
else:
print("nglview is not available. Please install with pip or conda")
[docs]def connect2pymol():
"""Establish an RPC connection to run PyMOL commands from the command line or from a Jupyter notebook
Notes
-----
Start a PyMOL server session from a terminal:
>>> pymol -R
On Windows you may create a shortcut that executes the command C:\path\to\PyMOLWin.exe -R
"""
import xmlrpc.client as xmlrpclib
cmd = xmlrpclib.ServerProxy("http://localhost:9123")
curr_wd = os.getcwd()
try:
cmd.cd(curr_wd)
except:
cmd.cd(re.sub(r"/mnt/([a-z])", r"\1:", curr_wd))
return cmd
[docs]def nglview_trajectory(traj_biomol):
"""Create a nglview trajectory scene
Parameters
----------
traj_biomol : mdtraj.Trajectory
trajectory of the biomolecule
Returns
-------
view : nglview.NGLWidget
"""
view = nglview.NGLWidget()
view.add_trajectory(traj_biomol)
view.clear_representations(component=0)
view.add_simplified_base(component=0, selection="/0", disablePicking=True, colorScheme="atomindex")
view.add_cartoon(component=0, selection="/0", aspectRatio=4, disablePicking=True, colorScheme="atomindex")
view.stage.set_parameters(mouse_preset="pymol")
return view
[docs]def nglview_trajectory_AV(traj_biomol, traj_volume1, traj_volume2, surface_representation=False):
"""Create a nglview trajectory scene with donor and acceptor accessible volumes (AV)
Parameters
----------
traj_biomol : mdtraj.Trajectory
trajectory of the biomolecule
traj_volume1, traj_volume2 : mdtraj.Trajectory
trajectory of the donor and acceptor accessible volume
surface_representation : bool (default: False)
show a surface representation (instead of spacefill, which is faster)
Returns
-------
view : nglview.NGLWidget
"""
view = nglview.NGLWidget()
view.add_trajectory(traj_biomol)
view.add_trajectory(traj_volume1)
view.add_trajectory(traj_volume2)
view.clear_representations(component=0)
view.clear_representations(component=1)
view.clear_representations(component=2)
view.add_simplified_base(component=0, selection="/0", disablePicking=True, colorScheme="atomindex")
view.add_cartoon(component=0, selection="/0", aspectRatio=4, disablePicking=True, colorScheme="atomindex")
if surface_representation:
view.add_surface(
color="#6cb381", wireframe=True, opacity=0.4, isolevel=0, component=1, disablePicking=True, selection="all"
)
view.add_surface(
color="#c25449", wireframe=True, opacity=0.4, isolevel=0, component=2, disablePicking=True, selection="all"
)
else:
view.add_spacefill(color="#6cb381", component=1, disablePicking=True, selection="all")
view.add_spacefill(color="#c25449", component=2, disablePicking=True, selection="all")
view.stage.set_parameters(mouse_preset="pymol")
return view
[docs]def nglview_trajectory_ACV(traj_biomol, traj_volume1_FV, traj_volume2_FV, traj_volume1_CV, traj_volume2_CV):
"""Create a nglview trajectory scene with donor and acceptor accessible-contact volumes (ACV)
Parameters
----------
traj_biomol : mdtraj.Trajectory
trajectory of the biomolecule
traj_volume1_FV, traj_volume2_FV : mdtraj.Trajectory
trajectory of the donor and acceptor free volume
traj_volume1_CV, traj_volume2_CV : mdtraj.Trajectory
trajectory of the donor and acceptor contact volume
Returns
-------
view : nglview.NGLWidget
"""
view = nglview.NGLWidget()
view.add_trajectory(traj_biomol)
view.add_trajectory(traj_volume1_CV)
view.add_trajectory(traj_volume2_CV)
view.add_trajectory(traj_volume1_FV)
view.add_trajectory(traj_volume2_FV)
view.clear_representations(component=0)
view.clear_representations(component=1)
view.clear_representations(component=2)
view.clear_representations(component=3)
view.clear_representations(component=4)
view.add_simplified_base(component=0, selection="/0", disablePicking=True, colorScheme="atomindex")
view.add_cartoon(component=0, selection="/0", aspectRatio=4, disablePicking=True, colorScheme="atomindex")
view.add_surface(
color="#6cb381", wireframe=False, opacity=0.4, isolevel=0, component=1, disablePicking=True, selection="all"
)
view.add_surface(
color="#c25449", wireframe=False, opacity=0.4, isolevel=0, component=2, disablePicking=True, selection="all"
)
view.add_surface(
color="#6cb381", wireframe=True, opacity=0.4, isolevel=0, component=3, disablePicking=True, selection="all"
)
view.add_surface(
color="#c25449", wireframe=True, opacity=0.4, isolevel=0, component=4, disablePicking=True, selection="all"
)
view.stage.set_parameters(mouse_preset="pymol")
return view
[docs]def nglview_multimodel_ACV(biomol_filename, volume1_filename, volume2_filename):
"""Create a nglview multi-model structure scene with donor and acceptor accessible-contact volumes (ACV)
Parameters
----------
structure_filename : str
multi-model PDB of the biomolecule
volume1_filename, volume2_filename : str
multi-model PDB of the donor and acceptor accessible-contact volume
Returns
-------
view : nglview.NGLWidget
n_model : int
"""
global view
view = nglview.NGLWidget()
struct = nglview.FileStructure(biomol_filename)
acv_D = nglview.FileStructure(volume1_filename)
acv_A = nglview.FileStructure(volume2_filename)
struct_str = struct.get_structure_string()
n_models = struct_str.count("MODEL")
view.add_component(struct)
view.add_component(acv_D)
view.add_component(acv_A)
view.clear_representations(component=0)
view.clear_representations(component=1)
view.clear_representations(component=2)
view.add_simplified_base(component=0, selection="/0", disablePicking=True, colorScheme="atomindex")
view.add_cartoon(component=0, selection="/0", aspectRatio=4, disablePicking=True, colorScheme="atomindex")
view.add_surface(
color="#6cb381", wireframe=False, opacity=0.4, isolevel=0, component=1, disablePicking=True, selection="CV"
)
view.add_surface(
color="#c25449", wireframe=False, opacity=0.4, isolevel=0, component=2, disablePicking=True, selection="CV"
)
view.add_surface(
color="#6cb381", wireframe=True, opacity=0.4, isolevel=0, component=1, disablePicking=True, selection="all"
)
view.add_surface(
color="#c25449", wireframe=True, opacity=0.4, isolevel=0, component=2, disablePicking=True, selection="all"
)
view.stage.set_parameters(mouse_preset="pymol")
return view, n_models
[docs]def _change_model(model):
"""Change the current model
Parameters
----------
model : int
"""
for i in range(view.n_components):
view._remote_call("setSelection", target="compList", args=[f"/{model}"], kwargs=dict(component_index=i))
n_representations = 5 # more than 5 representations are unlikely
for i in range(n_representations):
view._remote_call(
"setSelection",
target="Representation",
args=[f"/{model}"],
kwargs=dict(component_index=0, repr_index=i),
)
[docs]def model_slider(n_models):
"""A slider widget for multi-model structures
Parameters
----------
n_models : int
number of models in the structure
Returns
-------
int_slider: ipywidgets.IntSlider
Notes
-----
See also: https://ipywidgets.readthedocs.io/en/stable/examples/Widget%20List.html
"""
int_slider = ipywidgets.IntSlider(
value=0,
min=0,
max=n_models - 1,
step=1,
description="Frame:",
disabled=False,
continuous_update=False,
orientation="horizontal",
readout=True,
readout_format="d",
)
int_slider.observe(_on_slider_value_change, names="value")
return int_slider
[docs]def _on_slider_value_change(change):
"""Updates the view upon changing the slider value
Parameters
----------
change : dict
Notes
-----
See also: https://ipywidgets.readthedocs.io/en/latest/examples/Widget%20Events.html
"""
output = ipywidgets.Output()
with output:
_change_model(change["new"])
[docs]def render_view(view, gui=False):
"""Display an nglview scene with or without a GUI
Parameters
----------
view : nglview.NGLWidget
gui : bool
display the scene within a GUI window
(useful for interacting with components and representations)
"""
print("Building scene, please wait...")
return view.display(gui)
