def test_component_for_duck_typing():
view = NGLWidget()
traj = pt.load(nv.datafiles.PDB)
view.add_component(get_fn('tz2.pdb'))
view.add_component(get_fn('tz2_2.pdb.gz'))
view.add_trajectory(nv.PyTrajTrajectory(traj))
view.component_0.add_representation('cartoon')
c0 = view[0]
c1 = view[1]
assert hasattr(view, 'component_0')
assert hasattr(view, 'component_1')
assert hasattr(view, 'trajectory_0')
assert hasattr(view.trajectory_0, 'n_frames')
assert hasattr(view.trajectory_0, 'get_coordinates')
assert hasattr(view.trajectory_0, 'get_structure_string')
c0.show()
c0.hide()
view.remove_component(c0.id)
assert not hasattr(view, 'component_2')
# negative indexing
assert view[-1]._index == c1._index
def test_component_for_duck_typing():
# FIXME: deprecate duck typing?
# syntax looks ugly.
view = NGLWidget()
traj = pt.load(nv.datafiles.PDB)
# add 3 components (trajectory is a component)
view.add_component(get_fn('tz2.pdb'))
view.add_component(get_fn('tz2_2.pdb.gz'))
view.add_trajectory(nv.PyTrajTrajectory(traj))
view.component_0.add_representation('cartoon')
c0 = view[0]
c1 = view[1]
assert hasattr(view, 'component_0')
assert hasattr(view, 'component_1')
assert hasattr(view, 'trajectory_0')
assert hasattr(view.trajectory_0, 'n_frames')
assert hasattr(view.trajectory_0, 'get_coordinates')
assert hasattr(view.trajectory_0, 'get_structure_string')
c0.show()
c0.hide()
# 2 components left
view.remove_component(c0.id)
# c1 become 1st component
assert not hasattr(view, 'component_2')
assert len(view._ngl_component_ids) == 2
# negative indexing
assert view[0]._index == c1._index
def test_handling_n_components_changed():
view = nv.NGLWidget()
n_traj = nv.PyTrajTrajectory(pt.load(nv.datafiles.PDB))
view.add_trajectory(n_traj)
# fake updating n_components and _repr_dict from front-end
view._ngl_repr_dict = REPR_DICT
view.n_components = 1
view.player.widget_repr = view.player._make_widget_repr()
view.remove_component(n_traj.id)
# fake updating n_components from front-end
view._ngl_repr_dict = {'c0': {}}
view.n_components = 0
def test_load_data():
view = nv.show_pytraj(pt.datafiles.load_tz2())
# load blob with ext
blob = open(nv.datafiles.PDB).read()
view._load_data(blob, ext='pdb')
# raise if passing blob but does not provide ext
nt.assert_raises(ValueError, view._load_data, blob)
# load PyTrajectory
t0 = nv.PyTrajTrajectory(pt.datafiles.load_ala3())
view._load_data(t0)
def test_component_for_duck_typing():
view = NGLWidget()
traj = pt.load(nv.datafiles.PDB)
view.add_component('data/tz2.pdb')
view.add_component('data/tz2_2.pdb.gz')
view.add_trajectory(nv.PyTrajTrajectory(traj))
c0 = view[0]
c1 = view[1]
nt.assert_true(hasattr(view, 'component_0'))
nt.assert_true(hasattr(view, 'component_1'))
nt.assert_true(hasattr(view, 'trajectory_0'))
nt.assert_true(hasattr(view.trajectory_0, 'n_frames'))
nt.assert_true(hasattr(view.trajectory_0, 'get_coordinates'))
nt.assert_true(hasattr(view.trajectory_0, 'get_structure_string'))
c0.show()
c0.hide()
view.remove_component(c0.id)
nt.assert_false(hasattr(view, 'component_2'))
def test_load_data():
view = nv.show_pytraj(pt.datafiles.load_tz2())
# load blob with ext
blob = open(nv.datafiles.PDB).read()
view._load_data(blob, ext='pdb')
# raise if passing blob but does not provide ext
with pytest.raises(ValueError):
view._load_data(blob)
# raise if passing dummy name
with pytest.raises(NameError):
view._load_data(hahahaha)
# load PyTrajectory
t0 = nv.PyTrajTrajectory(pt.datafiles.load_ala3())
view._load_data(t0)
# load current folder
view._load_data(get_fn('tz2.pdb'))
def test_loaded_attribute():
traj = pt.datafiles.load_tz2()
structure = nv.FileStructure(nv.datafiles.PDB)
# False, empty constructor
view = nv.NGLWidget()
view.loaded = False
view.add_structure(structure)
view.add_trajectory(traj)
view
# False, constructor with a single Structure
view = nv.NGLWidget(structure)
view.loaded = False
view.add_trajectory(traj)
view
# True
view = nv.NGLWidget()
view.loaded = True
view.add_structure(structure)
view.add_trajectory(traj)
view
# False then True, empty constructor
view = nv.NGLWidget()
view.loaded = False
view.add_structure(structure)
view.loaded = True
view.add_trajectory(traj)
view
# False then True, constructor with a Trajectory
view = nv.NGLWidget(nv.PyTrajTrajectory(traj))
view.loaded = False
view.add_structure(structure)
view.loaded = True
view.add_trajectory(traj)
view
def test_trajectory_show_hide_sending_cooridnates():
view = NGLWidget()
traj0 = pt.datafiles.load_tz2()
traj1 = pt.datafiles.load_trpcage()
view.add_trajectory(nv.PyTrajTrajectory(traj0))
view.add_trajectory(nv.PyTrajTrajectory(traj1))
for traj in view._trajlist:
nt.assert_true(traj.shown)
view.frame = 1
def copy_coordinate_dict(view):
# make copy to avoid memory free
return dict((k, v.copy()) for k, v in view.coordinates_dict.items())
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide 0
view.hide([
0,
])
nt.assert_false(view._trajlist[0].shown)
nt.assert_true(view._trajlist[1].shown)
# update frame so view can update its coordinates
view.frame = 2
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
aa_eq(coordinates_dict[1], traj1[2].xyz)
# hide 0, 1
view.hide([0, 1])
nt.assert_false(view._trajlist[0].shown)
nt.assert_false(view._trajlist[1].shown)
view.frame = 3
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
nt.assert_equal(coordinates_dict[1].shape[0], 0)
# slicing, show only component 1
view[1].show()
view.frame = 0
nt.assert_false(view._trajlist[0].shown)
nt.assert_true(view._trajlist[1].shown)
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
aa_eq(coordinates_dict[1], traj1[0].xyz)
# show all
view[1].show()
view[0].show()
view.frame = 1
nt.assert_true(view._trajlist[0].shown)
nt.assert_true(view._trajlist[1].shown)
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide all
view[1].hide()
view[0].hide()
view.frame = 2
nt.assert_false(view._trajlist[0].shown)
nt.assert_false(view._trajlist[1].shown)
coordinates_dict = copy_coordinate_dict(view)
nt.assert_equal(coordinates_dict[0].shape[0], 0)
nt.assert_equal(coordinates_dict[1].shape[0], 0)
def test_interpolate():
# dummy test
traj = pt.datafiles.load_tz2()
ngl_traj = nv.PyTrajTrajectory(traj)
interpolate.linear(0, 0.4, ngl_traj, step=1)
def test_trajectory_show_hide_sending_cooridnates():
view = NGLWidget()
traj0 = pt.datafiles.load_tz2()
traj1 = pt.datafiles.load_trpcage()
view.add_trajectory(nv.PyTrajTrajectory(traj0))
view.add_trajectory(nv.PyTrajTrajectory(traj1))
for traj in view._trajlist:
assert traj.shown
view.frame = 1
def copy_coordinate_dict(view):
# make copy to avoid memory free
return {k: v.copy() for k, v in view._coordinates_dict.items()}
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide 0
view.hide([
0,
])
assert not view._trajlist[0].shown
assert view._trajlist[1].shown
# update frame so view can update its coordinates
view.frame = 2
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
aa_eq(coordinates_dict[1], traj1[2].xyz)
# hide 0, 1
view.hide([0, 1])
assert not view._trajlist[0].shown
assert not view._trajlist[1].shown
view.frame = 3
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
assert coordinates_dict[1].shape[0] == 0
# slicing, show only component 1
view[1].show()
view.frame = 0
assert not view._trajlist[0].shown
assert view._trajlist[1].shown
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
aa_eq(coordinates_dict[1], traj1[0].xyz)
# show all
view[1].show()
view[0].show()
view.show(indices='all')
view.show(indices=[
0,
])
view.show(indices=[0, 1])
view.frame = 1
assert view._trajlist[1].shown
coordinates_dict = copy_coordinate_dict(view)
aa_eq(coordinates_dict[0], traj0[1].xyz)
aa_eq(coordinates_dict[1], traj1[1].xyz)
# hide all
view[1].hide()
view[0].hide()
view.frame = 2
assert not view._trajlist[0].shown
assert not view._trajlist[1].shown
coordinates_dict = copy_coordinate_dict(view)
assert coordinates_dict[0].shape[0] == 0
assert coordinates_dict[1].shape[0] == 0
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_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)