def view_estrogen_receptor():
"""
load receptor structure and display with ngl
"""
view = nv.show_pdbid("1g50", default=False)
view._set_size("800px", "400px")
view.add_cartoon(":B or :C")
view.add_ball_and_stick("(:B or :C) and EST")
view.center(":B or :C")
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_API_promise_to_have():
# for Jupyter notebook extension
nv._jupyter_nbextension_paths()
view = nv.demo()
# trigger _set_size
with patch.object(view, '_remote_call') as mock_call:
view.layout.width = '100px'
view.layout.height = '500px'
mock_call.assert_called_with('setSize',
args=['', '500px'],
target='Widget')
# Structure
structure = nv.Structure()
structure.get_structure_string
assert hasattr(structure, 'id')
assert hasattr(structure, 'ext')
assert hasattr(structure, 'params')
# Widget
nv.NGLWidget._set_coordinates
nv.NGLWidget.add_component
nv.NGLWidget.add_trajectory
nv.NGLWidget._coordinates_dict
nv.NGLWidget.set_representations
nv.NGLWidget.clear
nv.NGLWidget.center
# add component
view.add_component('rcsb://1tsu.pdb')
view.add_pdbid('1tsu')
# display
js_utils.clean_error_output()
display(view.player.widget_repr)
view.player._display()
view._display_image()
# show
try:
nv.show_pdbid('1tsu')
except:
pass
nv.show_url('https://dummy.pdb')
# other backends will be tested in other sections
# constructor
ngl_traj = nv.PyTrajTrajectory(pt.datafiles.load_ala3())
nv.NGLWidget(ngl_traj, parameters=dict(background_color='black'))
nv.NGLWidget(ngl_traj, representations=[dict(type='cartoon', params={})])
view.parameters
view.camera
view.camera = 'perspective'
view._request_stage_parameters()
view._ngl_repr_dict = REPR_DICT
view._handle_repr_dict_changed(dict(new=dict(c0={})))
# dummy
class DummWidget():
value = ''
view.player.picked_widget = DummWidget()
view._update_background_color(change=dict(new='blue'))
tab = view.player._display()
view.player.widget_repr = view.player._make_widget_repr()
view._handle_n_components_changed(change=dict(new=2, old=1))
view._handle_n_components_changed(change=dict(new=1, old=1))
view._handle_n_components_changed(change=dict(new=1, old=0))
view.on_loaded(change=dict(new=True))
view.on_loaded(change=dict(new=False))
view._first_time_loaded = False
view
view._first_time_loaded = True
view
view._init_gui = True
view
view._theme = 'dark'
view
view.display(gui=True, style='ngl')
view.display(gui=False)
view.display(gui=True, style='ipywidgets')
view._set_sync_camera([view])
view._set_unsync_camera([view])
view._set_selection('.CA')
view.color_by('atomindex')
representations = [dict(type='cartoon', params=dict())]
view.representations = representations
repr_parameters = dict(opacity=0.3, params=dict())
view.update_representation(parameters=repr_parameters)
view._remove_representation()
view.clear()
view.add_representation('surface', selection='*', useWorker=True)
view.add_representation('surface', selection='*', component=1)
view.center()
view._on_render_image(change=dict(new='xyz'))
view.render_image()
view.render_image(frame=2)
view.download_image()
assert view._dry_run(view._set_sync_camera,
[view])['methodName'] == 'setSyncCamera'
msg = dict(type='request_frame', data=dict())
view._ngl_handle_msg(view, msg=msg, buffers=[])
msg = dict(type='repr_parameters', data=dict(name='hello'))
view._ngl_handle_msg(view, msg=msg, buffers=[])
view.loaded = True
msg = dict(type='request_loaded', data=True)
view._ngl_handle_msg(view, msg=msg, buffers=[])
view.loaded = False
msg = dict(type='request_loaded', data=True)
view._ngl_handle_msg(view, msg=msg, buffers=[])
msg = dict(type='all_reprs_info', data=REPR_DICT)
view._ngl_handle_msg(view, msg=msg, buffers=[])
msg = dict(type='stage_parameters', data=dict())
view._ngl_handle_msg(view, msg=msg, buffers=[])
# test negative frame (it will be set to self.count - 1)
view.frame = -1
msg = dict(type='request_frame', data=dict())
# async_message
msg = {'type': 'async_message', 'data': 'ok'}
view._ngl_handle_msg(view, msg, [])
# render_image
r = view.render_image()
Widget.widgets[r.model_id] = r
msg = {'type': 'image_data', 'ID': r.model_id, 'data': b'YmxhIGJsYQ=='}
view._ngl_handle_msg(view, msg, [])
view.loaded = True
view.show_only([
0,
])
view._js_console()
view._get_full_params()
# iter
for c in view:
assert isinstance(c, nv.widget.ComponentViewer)
def show(self):
"""return a 3D view of the protein within the notebook"""
view = nglview.show_pdbid(self.pdbid)
return view
def test_API_promise_to_have():
# for Jupyter notebook extension
nv._jupyter_nbextension_paths()
view = nv.demo()
# Structure
structure = nv.Structure()
structure.get_structure_string
assert hasattr(structure, 'id')
assert hasattr(structure, 'ext')
assert hasattr(structure, 'params')
# Widget
nv.NGLWidget._set_coordinates
nv.NGLWidget.add_component
nv.NGLWidget.add_trajectory
nv.NGLWidget.coordinates_dict
nv.NGLWidget.set_representations
nv.NGLWidget.clear
nv.NGLWidget.center
# add component
view.add_component('rcsb://1tsu.pdb')
view.add_pdbid('1tsu')
# display
js_utils.clean_error_output()
display.display(view.player.widget_repr)
view.player._display()
view._display_image()
# show
try:
nv.show_pdbid('1tsu')
except:
pass
nv.show_url('https://dummy.pdb')
# other backends will be tested in other sections
# constructor
ngl_traj = nv.PyTrajTrajectory(pt.datafiles.load_ala3())
nv.NGLWidget(ngl_traj, parameters=dict(background_color='black'))
nv.NGLWidget(ngl_traj, representations=[dict(type='cartoon')])
view.parameters
view.camera
view.camera = 'perspective'
view._request_stage_parameters()
view._repr_dict = REPR_DICT
view._handle_repr_dict_changed(dict(new=dict(c0={})))
# dummy
class DummWidget():
value = ''
view.player.picked_widget = DummWidget()
view._update_background_color(change=dict(new='blue'))
view.on_update_dragged_file(change=dict(new=2, old=1))
view.on_update_dragged_file(change=dict(new=1, old=1))
tab = view.player._display()
view.player.widget_repr = view.player._make_widget_repr()
view._handle_n_components_changed(change=dict(new=2, old=1))
view._handle_n_components_changed(change=dict(new=1, old=1))
view._handle_n_components_changed(change=dict(new=1, old=0))
view.on_loaded(change=dict(new=True))
view.on_loaded(change=dict(new=False))
view._refresh_render()
view.sync_view()
view._first_time_loaded = False
view._ipython_display_()
view._first_time_loaded = True
view._ipython_display_()
view._init_gui = True
view._ipython_display_()
view._theme = 'dark'
view._ipython_display_()
view.display(gui=True)
view.display(gui=False)
view.display(gui=True, use_box=True)
view._set_draggable(True)
view._set_draggable(False)
view._set_sync_frame()
view._set_sync_camera()
view._set_spin([0, 1, 0], 0.5)
view._set_selection('.CA')
view.color_by('atomindex')
representations = [dict(type='cartoon', params=dict())]
view.representations = representations
repr_parameters = dict(opacity=0.3, params=dict())
view.update_representation(parameters=repr_parameters)
view._remove_representation()
view.clear()
view.add_representation('surface', selection='*', useWorker=True)
view.add_representation('surface', selection='*', component=1)
view.center()
view._hold_image = True
view._on_render_image(change=dict(new=u'xyz'))
view._hold_image = False
view._on_render_image(change=dict(new=u'xyz'))
view.render_image()
view.render_image(frame=2)
view.download_image()
msg = dict(type='request_frame', data=dict())
view._ngl_handle_msg(view, msg=msg, buffers=[])
msg = dict(type='repr_parameters', data=dict(name='hello'))
view._ngl_handle_msg(view, msg=msg, buffers=[])
view.loaded = True
msg = dict(type='request_loaded', data=True)
view._ngl_handle_msg(view, msg=msg, buffers=[])
view.loaded = False
msg = dict(type='request_loaded', data=True)
view._ngl_handle_msg(view, msg=msg, buffers=[])
msg = dict(type='all_reprs_info', data=REPR_DICT)
view._ngl_handle_msg(view, msg=msg, buffers=[])
msg = dict(type='stage_parameters', data=dict())
view._ngl_handle_msg(view, msg=msg, buffers=[])
# test negative frame (it will be set to self.count - 1)
view.frame = -1
msg = dict(type='request_frame', data=dict())
view.loaded = True
view.show_only([
0,
])
view._js_console()
view._get_full_params()
view.detach(split=False)
view.detach(split=True)
# view._set_place_proxy(HBox())
# iter
for c in view:
assert isinstance(c, nv.widget.ComponentViewer)
def test_API_promise_to_have():
# for Jupyter notebook extension
nv._jupyter_nbextension_paths()
view = nv.demo()
# Structure
structure = nv.Structure()
structure.get_structure_string
assert hasattr(structure, 'id')
assert hasattr(structure, 'ext')
assert hasattr(structure, 'params')
# Widget
nv.NGLWidget._set_coordinates
nv.NGLWidget.add_component
nv.NGLWidget.add_trajectory
nv.NGLWidget.coordinates_dict
nv.NGLWidget.set_representations
nv.NGLWidget.clear
nv.NGLWidget.center
# add component
view.add_component('rcsb://1tsu.pdb')
view.add_pdbid('1tsu')
# display
js_utils.clean_error_output()
display.display(view.player.widget_repr)
view.player._display()
view._display_image()
# show
try:
nv.show_pdbid('1tsu')
except:
pass
nv.show_url('https://dummy.pdb')
# other backends will be tested in other sections
# constructor
ngl_traj = nv.PyTrajTrajectory(pt.datafiles.load_ala3())
nv.NGLWidget(ngl_traj, parameters=dict(background_color='black'))
nv.NGLWidget(ngl_traj, representations=[dict(type='cartoon')])
view.parameters
view.camera
view.camera = 'perspective'
view._request_stage_parameters()
view._repr_dict = REPR_DICT
view._handle_repr_dict_changed(dict(new=dict(c0={})))
# dummy
class DummWidget():
value = ''
view.player.picked_widget = DummWidget()
view._update_background_color(change=dict(new='blue'))
view.on_update_dragged_file(change=dict(new=2, old=1))
view.on_update_dragged_file(change=dict(new=1, old=1))
tab = view.player._display()
view.player.widget_repr = view.player._make_widget_repr()
view._handle_n_components_changed(change=dict(new=2, old=1))
view._handle_n_components_changed(change=dict(new=1, old=1))
view._handle_n_components_changed(change=dict(new=1, old=0))
view.on_loaded(change=dict(new=True))
view.on_loaded(change=dict(new=False))
view._refresh_render()
view.sync_view()
view._first_time_loaded = False
view._ipython_display_()
view._first_time_loaded = True
view._ipython_display_()
view._init_gui = True
view._ipython_display_()
view._theme = 'dark'
view._ipython_display_()
view.display(gui=True)
view.display(gui=False)
view.display(gui=True, use_box=True)
view._set_draggable(True)
view._set_draggable(False)
view._set_sync_frame()
view._set_sync_camera()
view._set_spin([0, 1, 0], 0.5)
view._set_selection('.CA')
view.color_by('atomindex')
representations = [dict(type='cartoon', params=dict())]
view.representations = representations
repr_parameters = dict(opacity=0.3, params=dict())
view.update_representation(parameters=repr_parameters)
view._remove_representation()
view.clear()
view.add_representation('surface', selection='*', useWorker=True)
view.add_representation('surface', selection='*', component=1)
view.center()
view._hold_image = True
view._on_render_image(change=dict(new=u'xyz'))
view._hold_image = False
view._on_render_image(change=dict(new=u'xyz'))
view.render_image()
view.render_image(frame=2)
view.download_image()
msg = dict(type='request_frame', data=dict())
view._ngl_handle_msg(view, msg=msg, buffers=[])
msg = dict(type='repr_parameters', data=dict(name='hello'))
view._ngl_handle_msg(view, msg=msg, buffers=[])
view.loaded = True
msg = dict(type='request_loaded', data=True)
view._ngl_handle_msg(view, msg=msg, buffers=[])
view.loaded = False
msg = dict(type='request_loaded', data=True)
view._ngl_handle_msg(view, msg=msg, buffers=[])
msg = dict(type='all_reprs_info', data=REPR_DICT)
view._ngl_handle_msg(view, msg=msg, buffers=[])
msg = dict(type='stage_parameters', data=dict())
view._ngl_handle_msg(view, msg=msg, buffers=[])
# test negative frame (it will be set to self.count - 1)
view.frame = -1
msg = dict(type='request_frame', data=dict())
view.loaded = True
view.show_only([0,])
view._js_console()
view._get_full_params()
view.detach(split=False)
view.detach(split=True)
# view._set_place_proxy(HBox())
# iter
for c in view:
assert isinstance(c, nv.widget.ComponentViewer)
def colored_struct(
*,
pdb,
prop_df,
chain_col='chain',
site_col='site',
color_col='color',
representation='cartoon',
highlight_col=None,
highlight_representation='spacefill',
show_other=False,
other_color='#FFFFFF',
orientation=None,
):
"""Create widget showing a colored structure.
Parameters
------------
pdb : str
Existing PDB file, or ID to be downloaded from PDB.
prop_df : pandas DataFrame
Data on sites to show and how to color them. You are responsible for
ensuring that chaing / site labels are consistent with those in `pdb`,
no automatic checks of this are performed.
chain_col: str
Column in `prop_df` with PDB chain ID.
site_col : str
Column in `prop_df` with PDB site numbers.
color_col : str
Column in `prop_df` with color for each site.
representation : str or list
Protein representation (e.g., 'cartoon', 'surface', 'spacefill',
or other `nglview <https://github.com/arose/nglview>`_ representation;
or a list of such representations.
highlight_col : str or `None`
Optional column of boolean values in `prop_df` indicating
sites to also draw in `highlight_representation`.
highlight_representation : str
Additional representation for sites specified in `highlight_col`.
show_other : `False` or str
Show selections **not** listed as sites in `prop_df`? If so, specify
those selections. Can be 'all', 'protein', or other selection string
(`see here <https://github.com/arose/ngl/tree/master/doc/usage>`_).
other_color : str
Color for any sites not in `prop_df` but shown via `show_other`.
orientation : `None` or list of 16 numbers
Orientation to show the structure, can be obtained via the
`_camera_orientation` property of a structure widget
(https://github.com/arose/nglview/issues/785#issuecomment-487409212).
Returns
--------
nglview.widget.NGLWidget
The widget can be shown in a Jupyter notebook.
"""
# error checking on `prop_df` and its columns
cols = []
for colname, col, optional in [
('color_col', color_col, False),
('site_col', site_col, False),
('chain_col', chain_col, False),
('highlight_col', highlight_col, True),
]:
if col is None:
if not optional:
raise ValueError(f"must specify `{colname}`")
elif col not in prop_df.columns:
raise ValueError(f"`prop_df` lacks `{colname}` of {col}")
elif col in cols:
raise ValueError(f"duplicate column names of {col}")
else:
cols.append(col)
prop_df = (prop_df[cols].drop_duplicates())
if len(prop_df) != len(prop_df.groupby([chain_col, site_col])):
raise ValueError('Inconsistent duplicated rows for some sites in '
'`prop_df`. For each chain and site, entries must '
f"be the same for all rows in these columns: {cols}")
# get PDB into a widget; use `default_representation=False` as here:
# https://github.com/arose/nglview/issues/802#issuecomment-492760630
if os.path.isfile(pdb):
w = nglview.show_structure_file(
pdb,
default_representation=False,
)
else:
try:
w = nglview.show_pdbid(
pdb,
default_representation=False,
)
except HTTPError: # noqa: F821
raise ValueError(f"`pdb` {pdb} does not specify an existing "
'PDB file or an ID that can be downloaded')
# Set up color schemes as here:
# https://github.com/arose/nglview/pull/755
# For details on selection strings, see here:
# https://github.com/arose/ngl/blob/master/doc/usage/selection-language.md
colorscheme = []
selectionlist = []
highlight_colorscheme = []
highlight_selectionlist = []
for row in prop_df.itertuples():
color = getattr(row, color_col)
sel_str = f":{getattr(row, chain_col)} and {getattr(row, site_col)}"
selectionlist.append(f"({sel_str})")
colorscheme.append([color, sel_str])
if highlight_col and getattr(row, highlight_col):
highlight_selectionlist.append(f"({sel_str})")
highlight_colorscheme.append([color, sel_str])
colorscheme.append([other_color, '*'])
selection = ', '.join(selectionlist)
if show_other:
selection = f"({show_other}) or ({selection})"
# uniquely label color schemes as here:
# https://github.com/arose/nglview/issues/802#issuecomment-492501051
colorscheme = nglview.color._ColorScheme(
colorscheme,
label=f"colorscheme_{secrets.token_hex(10)}",
)
highlight_selection = ', '.join(highlight_selectionlist)
highlight_colorscheme = nglview.color._ColorScheme(
highlight_colorscheme,
label=f"colorscheme_{secrets.token_hex(10)}",
)
# color and style widget; set assembly to BU1 (biological unit 1) as here:
# https://github.com/arose/ngl/blob/master/doc/usage/selection-language.md
w.clear_representations()
if isinstance(representation, str):
representation = [representation]
for r in representation:
w.add_representation(
r,
selection=selection,
color=colorscheme,
assembly='BU1',
)
if highlight_representation and highlight_selection:
w.add_representation(
highlight_representation,
selection=highlight_selection,
color=highlight_colorscheme,
assembly='BU1',
)
if orientation:
if len(orientation) != 16:
raise ValueError('`orientation` not list of 16 numbers')
w._set_camera_orientation(orientation)
return w
