def viewtrj(self):
path = self.path+'/TMPQCEIMS/TMP.'+self.trj
file_list = os.listdir(path)
probes = []
for file in file_list:
if ('trj' in file)&('pdb' not in file):
trajectory = path+'/'+file
command = 'sed -i \'\' \'s/SI/Si/g\' ' + trajectory
print('running comman:',command)
os.system(command)
command = 'obabel -ixyz ' + trajectory + ' -opdb -O' + trajectory +'.pdb'
print('running comman:',command)
os.system(command)
#mol = openbabel.OBMol()
#obConversion.ReadFile(mol, trajectory)
#obConversion.WriteFile(mol, trajectory+'.pdb')
probes.append(trajectory+'.pdb')
#traj = pt.load(trajectory+'.pdb')
#self.view.add_trajectory(traj)
self.view = []
for p in probes:
traj = pt.load(p)
self.view.append(nv.show_pytraj(traj))
def test_representations():
view = nv.show_pytraj(pt.datafiles.load_tz2())
view.representations = DEFAULT_REPR
view.add_cartoon()
representations_2 = DEFAULT_REPR[:]
representations_2.append({'type': 'cartoon', 'params': {'sele': 'all'}})
_assert_dict_list_equal(view.representations, representations_2)
# accept dict too (to specify seperate reprs for different component
def func():
view.representations = {'0': MagicMock()}
assert view._dry_run(
func)['methodName'] == '_set_representation_from_repr_dict'
# Representations
# make fake params
try:
view._ngl_repr_dict = {'c0': {'0': {'parameters': {}}}}
except (KeyError, TraitError):
# in real application, we are not allowed to assign values
pass
view._ngl_repr_dict = REPR_DICT
representation_widget = RepresentationControl(view, 0, 0)
representation_widget
representation_widget._on_parameters_changed(change=dict(new=dict()))
def test_coordinates_meta():
from mdtraj.testing import get_fn
fn, tn = [get_fn('frame0.pdb'),] * 2
trajs = [pt.load(fn, tn), md.load(fn, top=tn), pmd.load_file(tn, fn)]
N_FRAMES = trajs[0].n_frames
from MDAnalysis import Universe
u = Universe(tn, fn)
trajs.append(Universe(tn, fn))
views = [nv.show_pytraj(trajs[0]), nv.show_mdtraj(trajs[1]), nv.show_parmed(trajs[2])]
views.append(nv.show_mdanalysis(trajs[3]))
for index, (view, traj) in enumerate(zip(views, trajs)):
view.frame = 3
nt.assert_equal(view.trajlist[0].n_frames, N_FRAMES)
nt.assert_equal(len(view.trajlist[0].get_coordinates_dict().keys()), N_FRAMES)
if index in [0, 1]:
# pytraj, mdtraj
if index == 0:
aa_eq(view.coordinates[0], traj.xyz[3], decimal=4)
else:
aa_eq(view.coordinates[0],10*traj.xyz[3], decimal=4)
view.coordinates = traj.xyz[2]
def test_caching_bool():
view = nv.show_pytraj(pt.datafiles.load_tz2())
nt.assert_false(view.cache)
view.caching()
nt.assert_true(view.cache)
view.uncaching()
nt.assert_false(view.cache)
def test_remote_call():
# how to test JS?
view = nv.show_pytraj(pt.datafiles.load_tz2())
view._remote_call('centerView', target='stage')
fn = 'notebooks/tz2.pdb'
kwargs = {'defaultRepresentation': True}
view._remote_call('loadFile', target='stage', args=[fn,], kwargs=kwargs)
def test_remote_call():
# how to test JS?
view = nv.show_pytraj(pt.datafiles.load_tz2())
view._remote_call('centerView', target='stage')
fn = 'notebooks/tz2.pdb'
kwargs = {'defaultRepresentation': True}
view._remote_call('loadFile', target='stage', args=[fn,], kwargs=kwargs)
def test_representations():
view = nv.show_pytraj(pt.datafiles.load_tz2())
nt.assert_equal(view.representations, DEFAULT_REPR)
view.add_cartoon()
representations_2 = DEFAULT_REPR[:]
representations_2.append({'type': 'cartoon', 'params': {'sele': 'all'}})
print(representations_2)
print(view.representations)
_assert_dict_list_equal(view.representations, representations_2)
def test_representations():
view = nv.show_pytraj(pt.datafiles.load_tz2())
nt.assert_equal(view.representations, DEFAULT_REPR)
view.add_cartoon()
representations_2 = DEFAULT_REPR[:]
representations_2.append({'type': 'cartoon', 'params': {'sele': 'all'}})
print(representations_2)
print(view.representations)
_assert_dict_list_equal(view.representations, representations_2)
def visualize(self, *args, **kwargs):
"""require NGLView
Parameters
----------
args and kwargs : NGLView's arguments
"""
import nglview
return nglview.show_pytraj(self, *args, **kwargs)
def test_coordinates_dict():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view = nv.show_pytraj(traj)
view.frame = 1
coords = view.coordinates_dict[0]
aa_eq(coords, traj[1].xyz)
# dummy
view._send_binary = False
view.coordinates_dict = {0: coords}
def test_player_simple():
traj = pt.datafiles.load_tz2()
view = nv.show_pytraj(traj)
nt.assert_false(view.player.sync_frame)
# dummy
component_slider = ipywidgets.IntSlider()
repr_slider = ipywidgets.IntSlider()
# dummy test
player = nv.player.TrajectoryPlayer(view)
player.smooth()
player.camera = 'perspective'
player.camera = 'orthographic'
player.frame
player.frame = 10
player.count
player.sync_frame = False
player.sync_frame = True
player.parameters = dict(step=2)
player._display()
player._make_button_center()
player._make_button_theme()
player._make_button_reset_theme()
player._make_widget_preference()
player._show_download_image()
player._make_button_url('dummy_url', description='dummy_url')
player._show_website()
player._make_button_qtconsole()
player._make_text_picked()
player._refresh(component_slider, repr_slider)
player._make_widget_repr()
player._make_resize_notebook_slider()
player._make_button_export_image()
player._make_repr_playground()
player._make_drag_widget()
player._make_spin_box()
player._make_widget_picked()
player._make_export_image_widget()
player._make_theme_box()
player._make_general_box()
player._update_padding()
player.on_spin_changed(change=dict(new=True))
player.on_spin_x_changed(change=dict(new=1))
player.on_spin_y_changed(change=dict(new=1))
player.on_spin_z_changed(change=dict(new=1))
player.on_spin_speed_changed(change=dict(new=0.5))
player._real_time_update = True
player._make_widget_repr()
player.widget_component_slider
player.widget_repr_slider
player._create_all_tabs()
player._create_all_widgets()
player.widget_tab = None
player._create_all_widgets()
def test_coordinates_dict():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view = nv.show_pytraj(traj)
view.frame = 1
coords = view.coordinates_dict[0]
aa_eq(coords, traj[1].xyz)
# dummy
view._send_binary = False
view.coordinates_dict = {0: coords}
# increase coverage for IndexError: make index=1000 (which is larger than n_frames)
view._set_coordinates(1000)
def test_coordinates_dict():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view = nv.show_pytraj(traj)
view.frame = 1
coords = view.coordinates_dict[0]
aa_eq(coords, traj[1].xyz)
# dummy
view._send_binary = False
view.coordinates_dict = {0: coords}
# increase coverage for IndexError: make index=1000 (which is larger than n_frames)
view._set_coordinates(1000)
def test_player_simple():
traj = pt.datafiles.load_tz2()
view = nv.show_pytraj(traj)
# dummy
component_slider = ipywidgets.IntSlider()
repr_slider = ipywidgets.IntSlider()
# dummy test
player = nv.player.TrajectoryPlayer(view)
player.smooth()
player.camera = 'perspective'
player.camera = 'orthographic'
player.frame
player.frame = 10
player.parameters = dict(step=2)
player._display()
player._make_button_center()
w = player._make_widget_preference()
w.children[0].value = 1.
player.widget_preference = None
w = player._make_widget_preference()
w.children[0].value = 1.
player._show_download_image()
player._make_text_picked()
player._refresh(component_slider, repr_slider)
player._make_widget_repr()
player._make_resize_notebook_slider()
player._make_button_export_image()
player._make_repr_playground()
player._make_widget_picked()
player._make_export_image_widget()
player._make_general_box()
player._update_padding()
player._real_time_update = True
player._make_widget_repr()
player.widget_component_slider
player.widget_repr_slider
player._create_all_tabs()
player._create_all_widgets()
player.widget_tab = None
player._create_all_widgets()
player._simplify_repr_control()
player._real_time_update = True
player.widget_repr_slider.value = 0
player.widget_repr_slider.value = 1
slider_notebook = player._make_resize_notebook_slider()
slider_notebook.value = 300
player.widget_repr_name.value = 'surface'
player.widget_repr_name.value = 'cartoon'
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(AssertionError, view._load_data, blob)
# load PyTrajectory
t0 = nv.PyTrajTrajectory(pt.datafiles.load_ala3())
view._load_data(t0)
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_movie_maker(mock_image, ImageSequenceClip):
from nglview.contrib.movie import MovieMaker
ImageSequenceClip.write_gif = MagicMock()
ImageSequenceClip.write_videofile = MagicMock()
traj = pytraj.datafiles.load_tz2()
view = nglview.show_pytraj(traj)
movie = MovieMaker(view,
in_memory=True,
download_folder='here',
render_params={'factor': 4},
moviepy_params={},
stop=2)
movie.make()
def test_representations():
view = nv.show_pytraj(pt.datafiles.load_tz2())
nt.assert_equal(view.representations, DEFAULT_REPR)
view.add_cartoon()
representations_2 = DEFAULT_REPR[:]
representations_2.append({'type': 'cartoon', 'params': {'sele': 'all'}})
print(representations_2)
print(view.representations)
_assert_dict_list_equal(view.representations, representations_2)
# Representations
# make fake params
view._repr_dict = {'c0': {'0': {'parameters': {}}}}
representation_widget = Representation(view, 0, 0)
representation_widget._display()
def test_add_repr_shortcut():
view = nv.show_pytraj(pt.datafiles.load_tz2())
assert isinstance(view, nv.NGLWidget), 'must be instance of NGLWidget'
# add
view.add_cartoon(color='residueindex')
view.add_rope(color='red')
# update
view.update_cartoon(opacity=0.4)
view.update_rope(coor='blue')
# remove
view.remove_cartoon()
view.remove_rope()
def test_add_repr_shortcut():
view = nv.show_pytraj(pt.datafiles.load_tz2())
assert isinstance(view, nv.NGLWidget), 'must be instance of NGLWidget'
# add
view.add_cartoon(color='residueindex')
view.add_rope(color='red')
# update
view.update_cartoon(opacity=0.4)
view.update_rope(coor='blue')
# remove
view.remove_cartoon()
view.remove_rope()
def to_nglview(traj, **kwd): # pragma: no cover
'''convert to nglview object
Parameters
----------
traj : pytraj.TrajectoryIterator or Trajectory
**kwd : additional arguments for nglview
Returns
-------
nglview.NGLWidget
'''
import nglview as nv
return nv.show_pytraj(traj, **kwd)
def test_coordinates_meta():
from mdtraj.testing import get_fn
fn, tn = [get_fn('frame0.pdb'),] * 2
trajs = [pt.load(fn, tn), md.load(fn, top=tn), pmd.load_file(tn, fn)]
N_FRAMES = trajs[0].n_frames
from MDAnalysis import Universe
u = Universe(tn, fn)
trajs.append(Universe(tn, fn))
views = [nv.show_pytraj(trajs[0]), nv.show_mdtraj(trajs[1]), nv.show_parmed(trajs[2])]
views.append(nv.show_mdanalysis(trajs[3]))
for index, (view, traj) in enumerate(zip(views, trajs)):
view.frame = 3
nt.assert_equal(view._trajlist[0].n_frames, N_FRAMES)
def test_coordinates_meta():
from mdtraj.testing import get_fn
fn, tn = [get_fn('frame0.pdb'),] * 2
trajs = [pt.load(fn, tn), md.load(fn, top=tn), pmd.load_file(tn, fn)]
N_FRAMES = trajs[0].n_frames
from MDAnalysis import Universe
u = Universe(tn, fn)
trajs.append(Universe(tn, fn))
views = [nv.show_pytraj(trajs[0]), nv.show_mdtraj(trajs[1]), nv.show_parmed(trajs[2])]
views.append(nv.show_mdanalysis(trajs[3]))
for index, (view, traj) in enumerate(zip(views, trajs)):
view.frame = 3
nt.assert_equal(view._trajlist[0].n_frames, N_FRAMES)
def test_player_link_to_ipywidgets():
traj = pt.datafiles.load_tz2()
view = nv.show_pytraj(traj)
int_text = IntText(2)
float_text = BoundedFloatText(40, min=10)
HBox([int_text, float_text])
link((int_text, 'value'), (view.player, 'step'))
link((float_text, 'value'), (view.player, 'delay'))
assert view.player.step == 2
assert view.player.delay == 40
float_text.value = 100
assert view.player.delay == 100
float_text.value= 0.00
# we set min=10
assert view.player.delay == 10
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)
# raise if passing dummy name
nt.assert_raises(NameError, lambda : 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_player_link_to_ipywidgets():
traj = pt.datafiles.load_tz2()
view = nv.show_pytraj(traj)
int_text = IntText(2)
float_text = BoundedFloatText(40, min=10)
HBox([int_text, float_text])
link((int_text, 'value'), (view.player, 'step'))
link((float_text, 'value'), (view.player, 'delay'))
nt.assert_equal(view.player.step, 2)
nt.assert_equal(view.player.delay, 40)
float_text.value = 100
nt.assert_equal(view.player.delay, 100)
float_text.value = 0.00
# we set min=10
nt.assert_equal(view.player.delay, 10)
def test_representations():
view = nv.show_pytraj(pt.datafiles.load_tz2())
assert view.representations == DEFAULT_REPR
view.add_cartoon()
representations_2 = DEFAULT_REPR[:]
representations_2.append({'type': 'cartoon', 'params': {'sele': 'all'}})
_assert_dict_list_equal(view.representations, representations_2)
# Representations
# make fake params
try:
view._repr_dict = {'c0': {'0': {'parameters': {}}}}
except (KeyError, TraitError):
# in real application, we are not allowed to assign values
pass
view._repr_dict = REPR_DICT
representation_widget = RepresentationControl(view, 0, 0)
representation_widget
representation_widget._on_parameters_changed(change=dict(new=dict()))
def test_representations():
view = nv.show_pytraj(pt.datafiles.load_tz2())
assert view.representations == DEFAULT_REPR
view.add_cartoon()
representations_2 = DEFAULT_REPR[:]
representations_2.append({'type': 'cartoon', 'params': {'sele': 'all'}})
_assert_dict_list_equal(view.representations, representations_2)
# Representations
# make fake params
try:
view._repr_dict = {'c0': {'0': {'parameters': {}}}}
except (KeyError, TraitError):
# in real application, we are not allowed to assign values
pass
view._repr_dict = REPR_DICT
representation_widget = RepresentationControl(view, 0, 0)
representation_widget
representation_widget._on_parameters_changed(change=dict(new=dict()))
def test_movie_maker(ImageSequenceClip):
from nglview.contrib.movie import MovieMaker
ImageSequenceClip.write_gif = MagicMock()
ImageSequenceClip.write_videofile = MagicMock()
traj = pytraj.datafiles.load_tz2()
view = nglview.show_pytraj(traj)
movie = MovieMaker(view, in_memory=False)
movie.download_folder = os.path.join(os.path.dirname(__file__), 'data')
# fake _event
movie._event = FakeEvent()
movie._event._event_set = True
movie.make()
movie._event._event_set = False
movie.make()
movie = MovieMaker(view, in_memory=False)
movie.skip_render = True
movie.make()
movie.output = 'hello.mp4'
movie.make()
movie.interupt()
movie._event = None
movie.interupt()
movie.in_memory = True
movie.make()
movie._event._event_set = False
movie.make()
movie = MovieMaker(view,
download_folder='here',
render_params=dict(factor=4),
moviepy_params={},
stop=2)
movie.make()
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_speed():
import pytraj as pt
from pytraj.testing import get_fn, Timer
traj = pt.datafiles.load_tz2_ortho()
fname_tuple = ([traj.filename, traj.top.filename, 100],
[nv.datafiles.TRR, nv.datafiles.PDB, 10])
for (fn, tn, n_files) in fname_tuple:
traj = pt.load([fn,]*n_files, tn)
print('trajectory', traj)
view = nv.show_pytraj(traj)
xyz = traj.xyz
xyz_bytes = traj.xyz.tobytes()
xyz_base64 = nv.encode_numpy(xyz)
with Timer() as t:
view.caching()
print('caching', t.time_gap())
with Timer() as t:
view.send(xyz_bytes)
print('send bytes', t.time_gap())
with Timer() as t:
view.send(xyz_base64)
print('send base64', t.time_gap())
with Timer() as t:
nv.encode_numpy(xyz)
print('encode_numpy', t.time_gap())
with Timer() as t:
xyz.tobytes()
print('tobytes', t.time_gap())
def test_add_repr_shortcut():
view = nv.show_pytraj(pt.datafiles.load_tz2())
assert isinstance(view, nv.NGLWidget), 'must be instance of NGLWidget'
view.add_cartoon(color='residueindex')
view.add_rope(color='red')
def test_player():
traj = pt.datafiles.load_tz2()
view = nv.show_pytraj(traj)
nt.assert_false(view.player.sync_frame)
def default_view():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
return nv.show_pytraj(traj)
def test_download_image():
"""just make sure it can be called
"""
view = nv.show_pytraj(pt.datafiles.load_tz2())
view.download_image('myname.png', 2, False, False, True)
def test_add_repr_shortcut():
view = nv.show_pytraj(pt.datafiles.load_tz2())
assert isinstance(view, nv.NGLWidget), 'must be instance of NGLWidget'
view.add_cartoon(color='residueindex')
view.add_rope(color='red')
import pytraj as pt
import nglview as nv
traj = pt.load('sim.nc', top='sim.prmtop')
traj.strip(":TIP3")
view = nv.show_pytraj(traj)
view.clear()
view.add_cartoon('protein', color_scheme='residueindex')
view.add_ball_and_stick('not protein', opacity=0.5)
view
def test_coordinates_dict():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view = nv.show_pytraj(traj)
view.frame = 1
coords = view.coordinates_dict[0]
aa_eq(coords, traj[1].xyz)
def test_player_simple():
traj = pt.datafiles.load_tz2()
view = nv.show_pytraj(traj)
assert not view.player.sync_frame
# dummy
component_slider = ipywidgets.IntSlider()
repr_slider = ipywidgets.IntSlider()
# dummy test
player = nv.player.TrajectoryPlayer(view)
player.smooth()
player.camera = 'perspective'
player.camera = 'orthographic'
player.frame
player.frame = 10
player.count
player.sync_frame = False
player.sync_frame = True
player.parameters = dict(step=2)
player._display()
player._make_button_center()
player._make_button_theme()
player._make_button_reset_theme()
w = player._make_widget_preference()
w.children[0].value = 1.
player.widget_preference = None
w = player._make_widget_preference()
w.children[0].value = 1.
player._show_download_image()
player._make_button_url('dummy_url', description='dummy_url')
player._show_website()
player._make_button_qtconsole()
player._make_text_picked()
player._refresh(component_slider, repr_slider)
player._make_widget_repr()
player._make_resize_notebook_slider()
player._make_button_export_image()
player._make_repr_playground()
player._make_drag_widget()
player._make_spin_box()
player._make_widget_picked()
player._make_export_image_widget()
player._make_theme_box()
player._make_general_box()
player._update_padding()
player.spin = True
player.on_spin_changed(change=dict(new=True))
player.on_spin_x_changed(change=dict(new=1))
player.on_spin_y_changed(change=dict(new=1))
player.on_spin_z_changed(change=dict(new=1))
player.on_spin_speed_changed(change=dict(new=0.5))
player._spin_x = 2
player._spin_y = 2
player._spin_z = 2
player.spin = False
player.on_spin_changed(change=dict(new=True))
player.on_spin_x_changed(change=dict(new=1))
player.on_spin_y_changed(change=dict(new=1))
player.on_spin_z_changed(change=dict(new=1))
player.on_spin_speed_changed(change=dict(new=0.5))
player._on_widget_built(change=dict(new=player))
player._on_widget_built(change=dict(new=None))
player._real_time_update = True
player._make_widget_repr()
player.widget_component_slider
player.widget_repr_slider
player._create_all_tabs()
player._create_all_widgets()
player.widget_tab = None
player._create_all_widgets()
player._simplify_repr_control()
player._real_time_update = True
player.widget_repr_slider.value = 0
player.widget_repr_slider.value = 1
slider_notebook = player._make_resize_notebook_slider()
slider_notebook.value = 300
player.widget_repr_name.value = 'surface'
player.widget_repr_name.value = 'cartoon'
def default_view():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
return nv.show_pytraj(traj)
def test_coordinates_dict():
traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
view = nv.show_pytraj(traj)
view.frame = 1
coords = view.coordinates_dict[0]
aa_eq(coords, traj[1].xyz)
def test_download_image():
"""just make sure it can be called
"""
view = nv.show_pytraj(pt.datafiles.load_tz2())
view.download_image('myname.png', 2, False, False, True)