def _create_view(self, system=None, view=None, gui=True):
"""Helper function to create the NGLview object.
Parameters
----------
system : Sire.System.System
A Sire molecular system.
view : int
The index of an existing view.
gui : bool
Whether to display the gui.
"""
if system is None and view is None:
raise ValueError("Both 'system' and 'view' cannot be 'None'.")
elif system is not None and view is not None:
raise ValueError("One of 'system' or 'view' must be 'None'.")
# Make sure gui flag is valid.
if gui not in [True, False]:
gui = True
# Default to the most recent view.
if view is None:
index = self._num_views
else:
index = view
# Create the file name.
filename = "%s/view_%04d.pdb" % (self._work_dir, index)
# Increment the number of views.
if view is None:
self._num_views += 1
# Create a PDB object and write to file.
if system is not None:
try:
pdb = _SireIO.PDB2(system)
pdb.writeToFile(filename)
except Exception as e:
msg = "Failed to write system to 'PDB' format."
if _isVerbose():
print(msg)
raise IOError(e) from None
else:
raise IOError(msg) from None
# Import NGLView when it is used for the first time.
import nglview as _nglview
# Create the NGLview object.
view = _nglview.show_file(filename)
# Return the view and display it.
return view.display(gui=gui)
def view_presets_multiple(struct, traj):
#print(f'Image for {concentration} and state {state_name} ({iterable}), iso {iso}.')
if os.path.exists(struct):
view = nglview.show_file(struct, default=False)
else:
print(f'Structure file not found: {struct}')
view.add_component(traj)
#Set color schemes
colors = {
'normal': 'whitesmoke',
'helix5': 'royalblue',
'helix10': 'mediumspringgreen',
'density': 'plum',
'activeSite': 'darkorange'
}
#Set residues ranges
normal = ['1-101', '109-139', '148-223', '226-266', '288-317']
activeSite = ['103-107', '223-226']
muts = ['140', '285', '278']
#Representations
for res in normal:
view.add_cartoon(res, color=colors['normal'], opacity=1)
for res in activeSite:
view.add_cartoon(res, color=colors['activeSite'])
view.add_cartoon('139-148', color=colors['helix5'])
view.add_cartoon('266-288', color=colors['helix10'])
view.add_licorice('224') #, color=colors['activeSite'])
view.add_licorice('105') #, color=colors['activeSite'])
view.add_ball_and_stick('MeO') #, color=colors['activeSite'])
for res in muts:
view.add_licorice(res) #, color=colors['density'])
view.center()
view.stage.set_parameters(
**{
"clipNear": 0,
"clipFar": 100,
"clipDist": 10,
"fogNear": 20,
"fogFar": 100,
"backgroundColor": "white",
})
return view
def view_presets_density(self, struct, dens, iso):
view = nglview.show_file(struct, default=False)
view.add_component(dens)
#Set color schemes
colors = {
'normal': 'whitesmoke',
'helix5': 'royalblue',
'helix10': 'mediumspringgreen',
'density': 'plum',
'activeSite': 'darkorange'
}
#Set residues ranges
normal = ['1-101', '109-139', '148-223', '226-266', '288-317']
activeSite = ['103-107', '223-226']
#Representations
for res in normal:
view.add_cartoon(res, color=colors['normal'], opacity=0.3)
for res in activeSite:
view.add_cartoon(res, color=colors['activeSite'])
view.add_cartoon('139-148', color=colors['helix5'])
view.add_cartoon('266-288', color=colors['helix10'])
view.add_licorice('224', color=colors['activeSite'])
view.add_licorice('105', color=colors['activeSite'])
##surface density
view.clear_representations(component=1)
view.add_surface(component=1,
color=colors['density'],
isolevelType='level',
isolevel=iso)
view.center()
view.stage.set_parameters(
**{
"clipNear": 0,
"clipFar": 100,
"clipDist": 10,
"fogNear": 20,
"fogFar": 100,
"backgroundColor": "white",
})
return view
def __init__(self, filename, atom_index=39):
self.atom_index = atom_index
self.view = nv.show_file(filename, default=False)
self.u = mda.Universe(filename)
self.cutoff = widgets.FloatText(value=0, description='Cutoff (nm):')
self._n = widgets.Label(value='0')
self._atom = widgets.Label(value='atoms within cutoff')
self.natom_label = widgets.HBox(children=[self._n, self._atom])
self.cutoff.observe(self.update, names='value')
self.hbox = widgets.HBox(children=[self.cutoff, self.natom_label])
self.widget = widgets.VBox(
children=[self.cutoff, self.natom_label, self.view])
self.update()
def _show_structure(pdb_path):
"""
Show the ligand-bound structure that belongs to the dynophore. Could be the starting frame of
the MD simulation.
Parameters
----------
pdb_path : str or pathlib.Path
Path to PDB file (structure/topology)
Returns
-------
nglview.widget.NGLWidget
Visualization with the NGL Viewer.
"""
view = nv.show_file(str(pdb_path), ext="pdb")
return view
def show_file(fp, **kwargs):
"""
Return a structure view.
Parameters
----------
fp : filename or list of filenames
kwargs : dict
Molecular representation of selections, e.g. protein='cartoon'
Returns
-------
View object
"""
view = nglview.show_file(fp)
setup_view(view, **kwargs)
return view
def viewer(self, base_name='superposed', stride=1):
import nglview
c = input('Value of parameter: ')
it = input('Value of iterable: ')
base_name = f'{self.results}/{base_name}'
print(f'{base_name}_{c}-it{it}-s{stride}.xtc')
view = nglview.show_file(f'{base_name}_{c}-it{it}-s{stride}.pdb')
view.add_component(f'{base_name}_{c}-it{it}-s{stride}-Molar.dx')
view.add_component(f'{base_name}_{c}-it{it}-s{stride}.xtc')
view.clear_representations()
view.add_representation('cartoon')
view.add_representation('licorice', selection='not hydrogen')
return view
def protein(input_type, input_value, output_image_filename=None):
"""
Visualizing protein data.
Parameters
----------
input_type : str
Either "pdb_code" or a file extension e.g. "pdb".
input_value: str or pathlib.Path
Either the PDB code of the protein or a local filepath.
output_image_filename : str
Optional; default: None.
Filename to save a static image of the protein.
Returns
-------
nglview.widget.NGLWidget
Interactive NGL viewer visualizing a given protein and (if available) its co-crystallized
ligand.
"""
if input_type == "pdb_code":
viewer = nv.show_pdbid(input_value, height="600px")
else:
with open(input_value) as f:
viewer = nv.show_file(f,
ext=input_type,
height="600px",
default_representation=False)
viewer.add_representation("cartoon", selection="protein")
viewer.add_representation(repr_type="ball+stick",
selection="hetero and not water")
viewer.center("protein")
if output_image_filename is not None:
viewer.render_image(trim=True, factor=2)
viewer._display_image()
viewer.download_image(output_image_filename)
return viewer
def test_show_file():
view = nv.show_file(nv.datafiles.PDB)
def visualize(self, show_pocket_centroid=True, show_anchor_residues=True):
"""
Visualize the pocket (subpockets, regions, and anchor residues).
Parameters
----------
show_pocket_centroid : bool
Show the pocket centroid as sphere (default) or not.
show_anchor_residues : bool
Show the anchor residues as spheres (default) or not.
Returns
-------
nglview.widget.NGLWidget
Pocket visualization.
"""
filepath = str(self._filepath)
# Load structure from file in nglview # TODO in the future: show_file > show_text?
view = nglview.show_file(filepath)
view._remote_call("setSize", target="Widget", args=["1000px", "600px"])
view.clear()
# Get file format (this is important to know how nglview will index residues)
file_format = filepath.split(".")[-1]
# Get residue ID > nglview index mapping
residue_id2ix = self._map_residue_id2ix(file_format)
# Show regions
scheme_regions_list = []
for index, region in self.regions.iterrows():
color = region["region.color"]
residue_id = region["residue.id"]
residue_ngl_ix = residue_id2ix.loc[residue_id]
scheme_regions_list.append([color, residue_ngl_ix])
scheme_regions = nglview.color._ColorScheme(scheme_regions_list,
label="scheme_regions")
view.add_representation("cartoon",
selection="protein",
color=scheme_regions)
# Show pocket centroids
if show_pocket_centroid:
view.shape.add_sphere(list(self.centroid), [0, 0, 1], 2,
"centroid")
# Show subpockets
for index, subpocket in self.subpockets.iterrows():
center = list(subpocket["subpocket.center"])
name = subpocket["subpocket.name"]
color_rgb = colors.to_rgb(subpocket["subpocket.color"])
view.shape.add_sphere(center, color_rgb, 2, name)
# Show anchor points
if show_anchor_residues:
for index, anchor_residue in self.anchor_residues.iterrows():
center = list(anchor_residue["anchor_residue.center"])
color_rgb = colors.to_rgb(anchor_residue["subpocket.color"])
view.shape.add_sphere(center, color_rgb, 0.5)
# Show
return view