def test_trim_messages():
view = nv.demo()
view.remove_component(view[0])
assert view._ngl_msg_archive == []
view.add_component(nv.datafiles.ALA3)
assert len(view._ngl_msg_archive) == 1
assert view._ngl_msg_archive[0]['methodName'] == 'loadFile'
view = nv.demo()
c = view.add_component(nv.datafiles.ALA3)
view.remove_component(c)
assert len(view._ngl_msg_archive) == 1
assert view._ngl_msg_archive[0]['methodName'] == 'loadFile'
def test_player_click_button():
""" test_player_click_button """
view = nv.demo(gui=True)
view._ipython_display_()
view._repr_dict = REPR_DICT
view.player._create_all_widgets()
view.player.widget_export_image = view.player._make_button_export_image()
button_iter = chain.from_iterable([
view.player.widget_repr_control_buttons.children,
view.player.widget_theme.children,
view.player.widget_drag.children,
[
view.player._show_download_image(),
view.player._make_button_url("", ""),
view.player._make_button_center(),
view.player._make_button_qtconsole(),
view.player.widget_export_image.children[0].children[0],
view.player.widget_repr_add.children[0],
],
view.player.widget_drag.children,
[
w for w in view.player.widget_preference.children
if isinstance(w, Button)
],
])
for button in button_iter:
click(button)
def test_API_promise_to_have():
view = nv.demo()
# Structure
structure = nv.Structure()
structure.get_structure_string
nt.assert_true(hasattr(structure, 'id'))
nt.assert_true(hasattr(structure, 'ext'))
nt.assert_true(hasattr(structure, 'params'))
# Widget
nv.NGLWidget._set_coordinates
nv.NGLWidget._set_initial_structure
nv.NGLWidget.add_component
nv.NGLWidget.add_trajectory
nv.NGLWidget.coordinates_dict
nv.NGLWidget.set_representations
nv.NGLWidget.clear
nv.NGLWidget.center
nv._get_notebook_info()
# display
display.Javascript(jsutils.js_clean_error_output)
display.display(view.player.repr_widget)
view.player._display()
def test_layout_BoxNGL():
view = nv.demo()
box = nv.widget_box.BoxNGL([view])
box._ipython_display_()
box.layout = Layout()
box._gui_style = 'row'
box._gui_style = 'column'
box._gui_style = 'row'
def test_layout_BoxNGL():
view = nv.demo()
box = nv.widget_box.BoxNGL([view])
box._ipython_display_()
box.layout = Layout()
box._gui_style = 'row'
box._gui_style = 'column'
box._gui_style = 'row'
def test_representation_control():
view = nv.demo()
repr_control = view._display_repr()
repr_control.name = 'surface'
repr_control.name = 'cartoon'
repr_control.repr_index = 1
repr_control.component_index = 1
def test_representation_control():
view = nv.demo()
repr_control = view._display_repr()
repr_control.name = 'surface'
repr_control.name = 'cartoon'
repr_control.repr_index = 1
repr_control.component_index = 1
def test_fullscreen():
v = nv.demo()
fs = nv.widget.Fullscreen(v, [v])
fs.fullscreen()
with patch.object(v, 'handle_resize'):
fs._fullscreen_changed(MagicMock(new=True, old=False))
assert v.handle_resize.called
# just run the code
fs._fullscreen_changed(MagicMock(new=True, old=False))
fs._fullscreen_changed(MagicMock(new=False, old=True))
def test_player_click_tab():
view = nv.demo()
gui = view.player._display()
assert isinstance(gui, ipywidgets.Tab)
for i, child in enumerate(gui.children):
try:
gui.selected_index = i
assert isinstance(child, ipywidgets.Box)
except TraitError:
pass
def test_player_click_tab():
view = nv.demo()
gui = view.player._display()
assert isinstance(gui, ipywidgets.Tab)
for i, child in enumerate(gui.children):
try:
gui.selected_index = i
assert isinstance(child, ipywidgets.Box)
except TraitError:
pass
def test_just_runs_and_exits_gracefully(self):
from matplotlib.widgets import AxesWidget
from ipywidgets.widgets import HBox
ifig = plt.figure()
iax = plt.gca()
nglwdg = nglview.demo()
mplw = AxesWidget(iax)
box_out = visualize._box_me((ifig, iax, nglwdg, mplw))
assert isinstance(box_out, HBox)
assert None is visualize._box_me((ifig, iax, nglwdg, mplw, 1))
def test_widget_box():
# empty
box = nv.widget_box.BoxNGL()
try:
box.layout = Layout()
except traitlets.TraitError:
pass
box._update_size()
view = nv.demo()
box = nv.widget_box.BoxNGL([view])
box._update_size()
box._is_beautified = True
box._beautify()
box._is_beautified = False
box._beautify()
def test_widget_box():
# empty
box = nv.widget_box.BoxNGL()
try:
box.layout = Layout()
except traitlets.TraitError:
pass
box._update_size()
view = nv.demo()
box = nv.widget_box.BoxNGL([view])
box._update_size()
box._is_beautified = True
box._beautify()
box._is_beautified = False
box._beautify()
def test_viewer_control():
view = nv.demo()
view
mat = [11, 12, 13, 14, 21, 22, 23, 24, 31, 32, 33, 34, 41, 42, 43, 44]
vector = [0, 1, 2]
view.control.align(mat)
view.control.rotate(mat)
view.control.translate(vector)
view.control.apply_matrix(mat)
view.control.center(vector)
view.control.orient(mat)
view.control.zoom(0.3)
view.control.rotate(mat)
view.control.spin(vector, 0.1)
def test_player_click_button():
""" test_player_click_button """
view = nv.demo(gui=True)
view._ipython_display_()
view._repr_dict = REPR_DICT
view.player._create_all_widgets()
view.player.widget_export_image = view.player._make_button_export_image()
button_iter = chain.from_iterable([
view.player.widget_repr_control_buttons.children,
view.player.widget_theme.children,
view.player.widget_drag.children,
[view.player._show_download_image(),
view.player._make_button_url("", ""),
view.player._make_button_center(),
view.player._make_button_qtconsole(),
view.player.widget_export_image.children[0].children[0],
view.player.widget_repr_add.children[0],
],
view.player.widget_drag.children,
[w for w in view.player.widget_preference.children if isinstance(w, Button)],
])
for button in button_iter:
click(button)
def test_layout_DraggableBox():
view = nv.demo()
box = nv.widget_box.DraggableBox([view])
box._ipython_display_()
box._dialog = 'on'
box._dialog = 'off'
def test_player_picked():
view = nv.demo()
s = dict(x=3)
view.player.widget_picked = view.player._make_text_picked()
view.picked = s
assert view.player.widget_picked.value == '{"x": 3}'
def test_player_submit_text():
""" test_player_click_button """
view = nv.demo(gui=True)
submit(view.player._make_command_box())
def test_add_new_shape():
view = nv.demo()
view
view.stage.set_parameters(mousePreset='default')
def test_color_scheme():
view = nv.demo()
scheme = nv.color._ColorScheme([['red', '1-6'], ['yellow', '20-30']],
'what')
view.clear()
view.add_cartoon(color=scheme)
def test_player_submit_text():
""" test_player_click_button """
view = nv.demo(gui=True)
submit(view.player._make_command_box())
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 test_player_picked():
view = nv.demo()
s = dict(x=3)
view.player.widget_picked = view.player._make_text_picked()
view.picked = s
nt.assert_equal(view.player.widget_picked.value, '{"x": 3}')
def test_player_picked():
view = nv.demo()
s = dict(x=3)
view.player.widget_picked = view.player._make_text_picked()
view.picked = s
assert view.player.widget_picked.value == '{"x": 3}'
def test_layout_DraggableBox():
view = nv.demo()
box = nv.widget_box.DraggableBox([view])
box._ipython_display_()
box._dialog = 'on'
box._dialog = 'off'
def test_representation_control():
view = nv.demo()
repr_control = view._display_repr()
# interact(f, x=10);
# +
# import nglview as np
# from nglview.datafiles import ASE_Traj
# ASE_Traj
# +
# import MDAnalysis as mda
import nglview as nv
from nglview.datafiles import PDB, XTC
# u = mda.Universe(PDB, XTC)
# protein = u.select_atoms('protein')
# +
# w = nv.ASEStructure(atoms)
# nv.ASEStructure?
# w
# -
nv.__version__
nv.show_ase(atoms)
nv.demo()
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_player_picked():
view = nv.demo()
s = dict(x=3)
view.player.widget_picked = view.player._make_text_picked()
view.picked = s
nt.assert_equal(view.player.widget_picked.value, '{"x": 3}')
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)
