def __init__(self, structure=None, representations=None, parameters=None, **kwargs):
super(NGLWidget, self).__init__(**kwargs)
self._gui = None
self._init_gui = kwargs.pop('gui', False)
self._theme = kwargs.pop('theme', 'default')
self._widget_image = widget_image.Image()
self._widget_image.width = 900.
self._image_array = []
# do not use _displayed_callbacks since there is another Widget._display_callbacks
self._event = threading.Event()
self._ngl_displayed_callbacks_before_loaded = []
self._ngl_displayed_callbacks_after_loaded = []
_add_repr_method_shortcut(self, self)
self.shape = Shape(view=self)
self._handle_msg_thread = threading.Thread(target=self.on_msg,
args=(self._ngl_handle_msg,))
# # register to get data from JS side
self._handle_msg_thread.daemon = True
self._handle_msg_thread.start()
self._remote_call_thread = RemoteCallThread(self)
self._remote_call_thread.start()
self._trajlist = []
self._ngl_component_ids = []
self._init_structures = []
if parameters:
self.parameters = parameters
if isinstance(structure, Trajectory):
name = py_utils.get_name(structure, kwargs)
self.add_trajectory(structure, name=name)
elif isinstance(structure, (list, tuple)):
trajectories = structure
for trajectory in trajectories:
name = py_utils.get_name(trajectory, kwargs)
self.add_trajectory(trajectory, name=name)
else:
if structure is not None:
self.add_structure(structure, **kwargs)
# call before setting representations
self._set_initial_structure(self._init_structures)
if representations:
self._init_representations = representations
else:
self._init_representations = [
{"type": "cartoon", "params": {
"sele": "polymer"
}},
{"type": "ball+stick", "params": {
"sele": "hetero OR mol"
}},
{"type": "ball+stick", "params": {
"sele": "not protein and not nucleic"
}}
]
# keep track but making copy
if structure is not None:
self._representations = self._init_representations[:]
self._set_unsync_camera()
self.selector = str(uuid.uuid4()).replace('-', '')
self._remote_call('setSelector', target='Widget', args=[self.selector,])
self.selector = '.' + self.selector # for PlaceProxy
self._place_proxy = PlaceProxy(child=None, selector=self.selector)
self.player = TrajectoryPlayer(self)
self._already_constructed = True
class NGLWidget(DOMWidget):
_view_name = Unicode("NGLView").tag(sync=True)
_view_module = Unicode("nglview-js-widgets").tag(sync=True)
_image_data = Unicode().tag(sync=True)
selector = Unicode().tag(sync=True)
frame = Int().tag(sync=True)
count = Int(1).tag(sync=True)
background = Unicode('white').tag(sync=True)
loaded = Bool(False).tag(sync=False)
picked = Dict().tag(sync=True)
n_components = Int(0).tag(sync=True)
orientation = List().tag(sync=True)
_first_time_loaded = Bool(True).tag(sync=False)
# hack to always display movie
_n_dragged_files = Int().tag(sync=True)
_init_representations = List().tag(sync=True)
_init_structures_sync = List().tag(sync=True)
_parameters = Dict().tag(sync=True)
_full_stage_parameters = Dict().tag(sync=True)
_original_stage_parameters = Dict().tag(sync=True)
_coordinates_dict = Dict().tag(sync=False)
_camera_str = CaselessStrEnum(['perspective', 'orthographic'],
default_value='orthographic').tag(sync=True)
_repr_dict = Dict().tag(sync=False)
_ngl_component_ids = List().tag(sync=False)
_ngl_component_names = List().tag(sync=False)
_already_constructed = Bool(False).tag(sync=False)
_ngl_msg = None
_send_binary = Bool(True).tag(sync=False)
_init_gui = Bool(False).tag(sync=False)
_hold_image = Bool(False).tag(sync=False)
def __init__(self, structure=None, representations=None, parameters=None, **kwargs):
super(NGLWidget, self).__init__(**kwargs)
self._gui = None
self._init_gui = kwargs.pop('gui', False)
self._theme = kwargs.pop('theme', 'default')
self._widget_image = widget_image.Image()
self._widget_image.width = 900.
self._image_array = []
# do not use _displayed_callbacks since there is another Widget._display_callbacks
self._event = threading.Event()
self._ngl_displayed_callbacks_before_loaded = []
self._ngl_displayed_callbacks_after_loaded = []
_add_repr_method_shortcut(self, self)
self.shape = Shape(view=self)
self._handle_msg_thread = threading.Thread(target=self.on_msg,
args=(self._ngl_handle_msg,))
# # register to get data from JS side
self._handle_msg_thread.daemon = True
self._handle_msg_thread.start()
self._remote_call_thread = RemoteCallThread(self)
self._remote_call_thread.start()
self._trajlist = []
self._ngl_component_ids = []
self._init_structures = []
if parameters:
self.parameters = parameters
if isinstance(structure, Trajectory):
name = py_utils.get_name(structure, kwargs)
self.add_trajectory(structure, name=name)
elif isinstance(structure, (list, tuple)):
trajectories = structure
for trajectory in trajectories:
name = py_utils.get_name(trajectory, kwargs)
self.add_trajectory(trajectory, name=name)
else:
if structure is not None:
self.add_structure(structure, **kwargs)
# call before setting representations
self._set_initial_structure(self._init_structures)
if representations:
self._init_representations = representations
else:
self._init_representations = [
{"type": "cartoon", "params": {
"sele": "polymer"
}},
{"type": "ball+stick", "params": {
"sele": "hetero OR mol"
}},
{"type": "ball+stick", "params": {
"sele": "not protein and not nucleic"
}}
]
# keep track but making copy
if structure is not None:
self._representations = self._init_representations[:]
self._set_unsync_camera()
self.selector = str(uuid.uuid4()).replace('-', '')
self._remote_call('setSelector', target='Widget', args=[self.selector,])
self.selector = '.' + self.selector # for PlaceProxy
self._place_proxy = PlaceProxy(child=None, selector=self.selector)
self.player = TrajectoryPlayer(self)
self._already_constructed = True
@property
def parameters(self):
return self._parameters
@parameters.setter
def parameters(self, params):
params = _camelize_dict(params)
self._parameters = params
@property
def camera(self):
return self._camera_str
@camera.setter
def camera(self, value):
"""
Parameters
----------
value : str, {'perspective', 'orthographic'}
"""
self._camera_str = value
# use _remote_call so this function can be called right after
# self is displayed
self._remote_call("setParameters",
target='Stage',
kwargs=dict(cameraType=self._camera_str))
def _request_stage_parameters(self):
self._remote_call('requestUpdateStageParameters',
target='Widget')
@observe('picked')
def _on_picked(self, change):
picked = change['new']
if self.player.widget_picked is not None:
self.player.widget_picked.value = json.dumps(picked)
@observe('background')
def _update_background_color(self, change):
color = change['new']
self.parameters = dict(background_color=color)
@observe('_n_dragged_files')
def on_update_dragged_file(self, change):
if change['new'] - change['old'] == 1:
self._ngl_component_ids.append(uuid.uuid4())
@observe('n_components')
def _handle_n_components_changed(self, change):
if self.player.widget_repr is not None:
component_slider = widget_utils.get_widget_by_name(self.player.widget_repr, 'component_slider')
if change['new'] - 1 >= component_slider.min:
component_slider.max = change['new'] - 1
component_dropdown = widget_utils.get_widget_by_name(self.player.widget_repr, 'component_dropdown')
component_dropdown.options = tuple(self._ngl_component_names)
if change['new'] == 0:
component_dropdown.options = tuple([' '])
component_dropdown.value = ' '
component_slider.max = 0
reprlist_choices = widget_utils.get_widget_by_name(self.player.widget_repr, 'reprlist_choices')
reprlist_choices.options = tuple([' '])
repr_slider = widget_utils.get_widget_by_name(self.player.widget_repr, 'repr_slider')
repr_slider.max = 0
repr_name_text = widget_utils.get_widget_by_name(self.player.widget_repr, 'repr_name_text')
repr_selection = widget_utils.get_widget_by_name(self.player.widget_repr, 'repr_selection')
repr_name_text.value = ' '
repr_selection.value = ' '
@observe('_repr_dict')
def _handle_repr_dict_changed(self, change):
if self.player.widget_repr is not None:
repr_slider = widget_utils.get_widget_by_name(self.player.widget_repr, 'repr_slider')
component_slider = widget_utils.get_widget_by_name(self.player.widget_repr, 'component_slider')
repr_name_text = widget_utils.get_widget_by_name(self.player.widget_repr, 'repr_name_text')
repr_selection = widget_utils.get_widget_by_name(self.player.widget_repr, 'repr_selection')
reprlist_choices = widget_utils.get_widget_by_name(self.player.widget_repr, 'reprlist_choices')
repr_names = get_repr_names_from_dict(self._repr_dict, component_slider.value)
if change['new'] == {'c0': {}}:
repr_selection.value = ''
else:
reprlist_choices.options = tuple([str(i) + '-' + name for (i, name) in enumerate(repr_names)])
try:
reprlist_choices.value = reprlist_choices.options[repr_slider.value]
except IndexError:
if repr_slider.value == 0:
reprlist_choices.options = tuple(['',])
reprlist_choices.value = ''
else:
reprlist_choices.value = reprlist_choices.options[repr_slider.value-1]
# e.g: 0-cartoon
repr_name_text.value = reprlist_choices.value.split('-')[-1]
repr_slider.max = len(repr_names) - 1 if len(repr_names) >= 1 else len(repr_names)
def _update_count(self):
self.count = max(traj.n_frames for traj in self._trajlist if hasattr(traj,
'n_frames'))
def _wait_until_finished(self, timeout=0.0001):
# NGL need to send 'finished' signal to
# backend
self._event.clear()
while True:
# idle to make room for waiting for
# "finished" event sent from JS
time.sleep(timeout)
if self._event.is_set():
# if event is set from another thread
# break while True
break
def _run_on_another_thread(self, func, *args):
# use `event` to singal
# func(*args)
thread = threading.Thread(target=func, args=args,)
thread.daemon = True
thread.start()
return thread
@observe('loaded')
def on_loaded(self, change):
# trick for firefox on Linux
time.sleep(0.1)
if change['new']:
self._fire_callbacks(self._ngl_displayed_callbacks_before_loaded)
def _fire_callbacks(self, callbacks):
def _call(event):
for callback in callbacks:
callback(self)
if callback._method_name == 'loadFile':
self._wait_until_finished()
self._run_on_another_thread(_call, self._event)
def _refresh_render(self):
"""useful when you update coordinates for a single structure.
Notes
-----
If you are visualizing a trajectory with more than 1 frame, you can use the
player slider to trigger the refreshing.
"""
current_frame = self.frame
self.frame = int(1E6)
self.frame = current_frame
def sync_view(self):
"""call this if you want to sync multiple views of a single viewer
Note: unstable feature
"""
self._fire_callbacks(self._ngl_displayed_callbacks_after_loaded)
def _ipython_display_(self, **kwargs):
super(NGLWidget, self)._ipython_display_(**kwargs)
if self._first_time_loaded:
self._first_time_loaded = False
else:
self.sync_view()
if self._init_gui:
if self._gui is None:
self._gui = self.player._display()
display(self._gui)
if self._theme in ['dark', 'oceans16']:
from nglview import theme
display(theme.oceans16())
self._remote_call('cleanOutput',
target='Widget')
self._place_proxy._ipython_display_()
def display(self, gui=False, use_box=False):
if gui:
if use_box:
from nglview.widget_box import BoxNGL
box = BoxNGL([self, self.player._display()])
box._gui_style = 'row'
return box
else:
display(self)
display(self.player._display())
display(self._place_proxy)
return None
else:
return self
def _set_place_proxy(self, widget):
"""
Parameters
----------
widget : instance of ipywidgets.DOMWidget (or derived class)
Examples
--------
>>> from ipywidgets import IntSlider
>>> slider = IntSlider()
>>> import nglview
>>> view = nglview.demo()
>>> view
>>> view._set_place_proxy(slider)
>>> view._place_proxy
>>> # TODO: _place_proxy only has effect (adding widget to NGLWidget)
>>> # if it was displayed (should fix)
"""
self._place_proxy.child = widget
def _set_draggable(self, yes=True):
if yes:
self._remote_call('setDraggable',
target='Widget',
args=['',])
else:
self._remote_call('setDraggable',
target='Widget',
args=['destroy',])
def _set_sync_frame(self):
self._remote_call("setSyncFrame", target="Widget")
def _set_unsync_frame(self):
self._remote_call("setUnSyncFrame", target="Widget")
def _set_sync_camera(self):
self._remote_call("setSyncCamera", target="Widget")
def _set_unsync_camera(self):
self._remote_call("setUnSyncCamera", target="Widget")
def _set_delay(self, delay):
"""unit of millisecond
"""
self._remote_call("setDelay", target="Widget", args=[delay,])
def _set_spin(self, axis, angle):
self._remote_call('setSpin',
target='Stage',
args=[axis, angle])
def _set_selection(self, selection, component=0, repr_index=0):
self._remote_call("setSelection",
target='Representation',
args=[selection],
kwargs=dict(component_index=component,
repr_index=repr_index))
def _set_color_by_residue(self, colors, component_index=0, repr_index=0):
self._remote_call('setColorByResidue',
target='Widget',
args=[colors, component_index, repr_index])
def color_by(self, color_scheme, component=0):
'''update color for all representations of given component
Notes
-----
Unstable feature
Parameters
----------
color_scheme : str
component : int, default 0
component index
Examples
--------
>>> # component 0
>>> view.color_by('atomindex')
>>> # component 1
>>> view.color_by('atomindex', component=1)
'''
repr_names = get_repr_names_from_dict(self._repr_dict, component)
for index, _ in enumerate(repr_names):
self.update_representation(component=component,
repr_index=index, color_scheme=color_scheme)
@property
def representations(self):
return self._representations
@representations.setter
def representations(self, reps):
self._representations = reps[:]
for index in range(len(self._ngl_component_ids)):
self.set_representations(reps)
def update_representation(self, component=0, repr_index=0, **parameters):
"""
Parameters
----------
component : int, default 0
component index
repr_index : int, default 0
representation index for given component
parameters : dict
"""
parameters = _camelize_dict(parameters)
kwargs = dict(component_index=component,
repr_index=repr_index)
kwargs.update(parameters)
self._remote_call('setParameters',
target='Representation',
kwargs=kwargs)
self._remote_call('requestReprsInfo',
target='Widget')
def set_representations(self, representations, component=0):
"""
Parameters
----------
representations : list of dict
"""
self.clear_representations(component=component)
for params in representations:
assert isinstance(params, dict), 'params must be a dict'
kwargs = params['params']
kwargs.update({'component_index': component})
self._remote_call('addRepresentation',
target='compList',
args=[params['type'],],
kwargs=kwargs)
def _remove_representation(self, component=0, repr_index=0):
self._remote_call('removeRepresentation',
target='Widget',
args=[component, repr_index])
def _remove_representations_by_name(self, repr_name, component=0):
self._remote_call('removeRepresentationsByName',
target='Widget',
args=[repr_name, component])
def _update_representations_by_name(self, repr_name, component=0, **kwargs):
kwargs = _camelize_dict(kwargs)
self._remote_call('updateRepresentationsByName',
target='Widget',
args=[repr_name, component],
kwargs=kwargs)
def _display_repr(self, component=0, repr_index=0, name=None):
c = 'c' + str(component)
r = str(repr_index)
try:
name = self._repr_dict[c][r]['name']
except KeyError:
name = ''
return RepresentationControl(self, component, repr_index, name=name)
def _set_initial_structure(self, structures):
"""initialize structures for Widget
Parameters
----------
structures : list
list of Structure or Trajectory
"""
_init_structures_sync = structures if isinstance(structures, (list, tuple)) else [structures,]
if _init_structures_sync:
self._init_structures_sync = [
{"data": _structure.get_structure_string(),
"ext": _structure.ext,
"params": _structure.params,
"id": _structure.id}
for _structure in _init_structures_sync]
def _set_coordinates(self, index):
'''update coordinates for all trajectories at index-th frame
'''
if self._trajlist:
coordinates_dict = {}
for trajectory in self._trajlist:
traj_index = self._ngl_component_ids.index(trajectory.id)
try:
if trajectory.shown:
if self.player.interpolate:
t = self.player.iparams.get('t', 0.5)
step = self.player.iparams.get('step', 1)
coordinates_dict[traj_index] = interpolate.linear(index,
t=t, traj=trajectory, step=step)
else:
coordinates_dict[traj_index] = trajectory.get_coordinates(index)
else:
coordinates_dict[traj_index] = np.empty((0), dtype='f4')
except (IndexError, ValueError):
coordinates_dict[traj_index] = np.empty((0), dtype='f4')
self.coordinates_dict = coordinates_dict
else:
print("no trajectory available")
@property
def coordinates_dict(self):
"""
Returns
-------
out : dict of numpy 3D-array, dtype='f4'
coordinates of trajectories at current frame
"""
return self._coordinates_dict
@coordinates_dict.setter
def coordinates_dict(self, arr_dict):
self._coordinates_dict = arr_dict
if not self._send_binary:
# send base64
encoded_coordinates_dict = dict((k, encode_base64(v))
for (k, v) in self._coordinates_dict.items())
mytime = time.time() * 1000
self.send({'type': 'base64_single', 'data': encoded_coordinates_dict,
'mytime': mytime})
else:
# send binary
buffers = []
coordinates_meta = dict()
for index, arr in self._coordinates_dict.items():
buffers.append(arr.astype('f4').tobytes())
coordinates_meta[index] = index
mytime = time.time() * 1000
self.send({'type': 'binary_single', 'data': coordinates_meta,
'mytime': mytime}, buffers=buffers)
@observe('frame')
def on_frame_changed(self, change):
"""set and send coordinates at current frame
"""
self._set_coordinates(self.frame)
def clear(self, *args, **kwargs):
'''shortcut of `clear_representations`
'''
self.clear_representations(*args, **kwargs)
def clear_representations(self, component=0):
'''clear all representations for given component
Parameters
----------
component : int, default 0 (first model)
You need to keep track how many components you added.
'''
self._remote_call("clearRepresentations",
target='compList',
kwargs={'component_index': component})
@_update_url
def _add_shape(self, shapes, name='shape'):
"""add shape objects
TODO: update doc, caseless shape keyword
Parameters
----------
shapes : list of tuple
name : str, default 'shape'
name of given shape
Notes
-----
Supported shape: 'mesh', 'sphere', 'ellipsoid', 'cylinder', 'cone', 'arrow'.
See also
--------
{ngl_url}
Examples
--------
>>> sphere = ('sphere', [0, 0, 9], [1, 0, 0], 1.5)
>>> arrow = ('arrow', [1, 2, 7 ], [30, 3, 3], [1, 0, 1], 1.0)
>>> view._add_shape([sphere, arrow], name='my_shape')
"""
self._remote_call('addShape', target='Widget',
args=[name, shapes])
@_update_url
def add_representation(self, repr_type, selection='all', **kwargs):
'''Add structure representation (cartoon, licorice, ...) for given atom selection.
Parameters
----------
repr_type : str
type of representation. Please see {ngl_url} for further info.
selection : str or 1D array (atom indices) or any iterator that returns integer, default 'all'
atom selection
**kwargs: additional arguments for representation
Example
-------
>>> import nglview as nv
>>>
>>> t = (pt.datafiles.load_dpdp()[:].supej = pt.load(membrane_pdb)
trajrpose('@CA'))
>>> w = nv.show_pytraj(t)
>>> w.add_representation('cartoon', selection='protein', color='blue')
>>> w.add_representation('licorice', selection=[3, 8, 9, 11], color='red')
>>> w
Notes
-----
User can also use shortcut
>>> w.add_cartoon(selection) # w.add_representation('cartoon', selection)
'''
if repr_type == 'surface':
if 'useWorker' not in kwargs:
kwargs['useWorker'] = False
# avoid space sensitivity
repr_type = repr_type.strip()
# overwrite selection
selection = seq_to_string(selection).strip()
# make copy
kwargs2 = _camelize_dict(kwargs)
if 'component' in kwargs2:
component = kwargs2.pop('component')
else:
component = 0
for k, v in kwargs2.items():
try:
kwargs2[k] = v.strip()
except AttributeError:
# e.g.: opacity=0.4
kwargs2[k] = v
d = {'params': {'sele': selection}}
d['type'] = repr_type
d['params'].update(kwargs2)
params = d['params']
params.update({'component_index': component})
self._remote_call('addRepresentation',
target='compList',
args=[d['type'],],
kwargs=params)
def center(self, *args, **kwargs):
"""alias of `center_view`
"""
self.center_view(*args, **kwargs)
def center_view(self, zoom=True, selection='*', component=0):
"""center view for given atom selection
Examples
--------
view.center_view(selection='1-4')
"""
self._remote_call('centerView', target='compList',
args=[zoom, selection],
kwargs={'component_index': component})
@observe('_image_data')
def _on_render_image(self, change):
'''update image data to widget_image
Notes
-----
method name might be changed
'''
self._widget_image._b64value = change['new']
if self._hold_image:
self._image_array.append(change['new'])
def render_image(self, frame=None,
factor=4,
antialias=True,
trim=False,
transparent=False):
"""render and get image as ipywidgets.widget_image.Image
Parameters
----------
frame : int or None, default None
if None, use current frame
if specified, use this number.
factor : int, default 4
quality of the image, higher is better
antialias : bool, default True
trim : bool, default False
transparent : bool, default False
Examples
--------
# tell NGL to render send image data to notebook.
view.render_image()
# make sure to call `get_image` method
view.get_image()
Notes
-----
You need to call `render_image` and `get_image` in different notebook's Cells
"""
if frame is not None:
self.frame = frame
params = dict(factor=factor,
antialias=antialias,
trim=trim,
transparent=transparent)
self._remote_call('_exportImage',
target='Widget',
kwargs=params)
def download_image(self, filename='screenshot.png',
factor=4,
antialias=True,
trim=False,
transparent=False):
"""render and download scence at current frame
Parameters
----------
filename : str, default 'screenshot.png'
factor : int, default 4
quality of the image, higher is better
antialias : bool, default True
trim : bool, default False
transparent : bool, default False
"""
params = dict(factor=factor,
antialias=antialias,
trim=trim,
transparent=transparent)
self._remote_call('_downloadImage',
target='Widget',
args=[filename,],
kwargs=params)
def _ngl_handle_msg(self, widget, msg, buffers):
"""store message sent from Javascript.
How? use view.on_msg(get_msg)
"""
self._ngl_msg = msg
msg_type = self._ngl_msg.get('type')
if msg_type == 'request_frame':
self.frame += self.player.step
if self.frame >= self.count:
self.frame = 0
elif self.frame < 0:
self.frame = self.count - 1
elif msg_type == 'repr_parameters':
data_dict = self._ngl_msg.get('data')
name = data_dict.pop('name') + '\n'
selection = data_dict.get('sele', '') + '\n'
# json change True to true
data_dict_json = json.dumps(data_dict).replace('true', 'True').replace('false', 'False')
data_dict_json = data_dict_json.replace('null', '"null"')
if self.player.widget_repr is not None:
# TODO: refactor
repr_name_text = widget_utils.get_widget_by_name(self.player.widget_repr, 'repr_name_text')
repr_selection = widget_utils.get_widget_by_name(self.player.widget_repr, 'repr_selection')
repr_name_text.value = name
repr_selection.value = selection
elif msg_type == 'request_loaded':
if not self.loaded:
# trick to trigger observe loaded
# so two viewers can have the same representations
self.loaded = False
self.loaded = msg.get('data')
elif msg_type == 'all_reprs_info':
self._repr_dict = self._ngl_msg.get('data')
elif msg_type == 'stage_parameters':
self._full_stage_parameters = msg.get('data')
elif msg_type == 'async_message':
if msg.get('data') == 'ok':
self._event.set()
def _request_repr_parameters(self, component=0, repr_index=0):
self._remote_call('requestReprParameters',
target='Widget',
args=[component,
repr_index])
def add_structure(self, structure, **kwargs):
'''add structure to view
Parameters
----------
structure : nglview.Structure object
Examples
--------
>>> view.add_trajectory(traj0)
>>> view.add_trajectory(traj1)
>>> # then add Structure
>>> view.add_structure(...)
See Also
--------
nglview.NGLWidget.add_component
'''
if not isinstance(structure, Structure):
raise ValueError('{} is not an instance of Structure'.format(structure))
if self.loaded or self._already_constructed:
self._load_data(structure, **kwargs)
else:
# update via structure_list
self._init_structures.append(structure)
name = py_utils.get_name(structure, kwargs)
self._ngl_component_names.append(name)
self._ngl_component_ids.append(structure.id)
self.center_view(component=len(self._ngl_component_ids)-1)
self._update_component_auto_completion()
def add_trajectory(self, trajectory, **kwargs):
'''add new trajectory to `view`
Parameters
----------
trajectory: nglview.Trajectory or its derived class or
pytraj.Trajectory-like, mdtraj.Trajectory or MDAnalysis objects
See Also
--------
nglview.NGLWidget.add_component
Examples
--------
>>> import nglview as nv, pytraj as pt
>>> traj = pt.load(nv.datafiles.TRR, nv.datafiles.PDB)
>>> view = nv.show_pytraj(view)
>>> # show view first
>>> view
>>> # add new Trajectory
>>> traj2 = pt.datafiles.load_tz2()
>>> view.add_trajectory(traj2)
'''
backends = BACKENDS
package_name = trajectory.__module__.split('.')[0]
if package_name in backends:
trajectory = backends[package_name](trajectory)
else:
trajectory = trajectory
if self.loaded or self._already_constructed:
self._load_data(trajectory, **kwargs)
else:
# update via _init_structures_sync
self._init_structures.append(trajectory)
name = py_utils.get_name(trajectory, kwargs)
self._ngl_component_names.append(name)
setattr(trajectory, 'shown', True)
self._trajlist.append(trajectory)
self._update_count()
self._ngl_component_ids.append(trajectory.id)
self._update_component_auto_completion()
def add_pdbid(self, pdbid):
'''add new Structure view by fetching pdb id from rcsb
Examples
--------
>>> view = nglview.NGLWidget()
>>> view.add_pdbid('1tsu')
>>> # which is equal to
>>> # view.add_component('rcsb://1tsu.pdb')
'''
self.add_component('rcsb://{}.pdb'.format(pdbid))
def add_component(self, filename, **kwargs):
'''add component from file/trajectory/struture
Parameters
----------
filename : str or Trajectory or Structure or their derived class or url
**kwargs : additional arguments, optional
Examples
--------
>>> view = nglview.Widget()
>>> view
>>> view.add_component(filename)
Notes
-----
If you want to load binary file such as density data, mmtf format, it is
faster to load file from current or subfolder.
'''
self._load_data(filename, **kwargs)
# assign an ID
self._ngl_component_ids.append(str(uuid.uuid4()))
self._update_component_auto_completion()
def _load_data(self, obj, **kwargs):
'''
Parameters
----------
obj : nglview.Structure or any object having 'get_structure_string' method or
string buffer (open(fn).read())
'''
kwargs2 = _camelize_dict(kwargs)
try:
is_url = FileManager(obj).is_url
except NameError:
is_url = False
if 'defaultRepresentation' not in kwargs2:
kwargs2['defaultRepresentation'] = True
if not is_url:
if hasattr(obj, 'get_structure_string'):
blob = obj.get_structure_string()
kwargs2['ext'] = obj.ext
passing_buffer = True
binary = False
else:
fh = FileManager(obj,
ext=kwargs.get('ext'),
compressed=kwargs.get('compressed'))
# assume passing string
blob = fh.read()
passing_buffer = not fh.use_filename
if fh.ext is None and passing_buffer:
raise ValueError('must provide extension')
kwargs2['ext'] = fh.ext
binary = fh.is_binary
use_filename = fh.use_filename
if binary and not use_filename:
# send base64
blob = base64.b64encode(blob).decode('utf8')
blob_type = 'blob' if passing_buffer else 'path'
args=[{'type': blob_type, 'data': blob, 'binary': binary}]
else:
# is_url
blob_type = 'url'
url = obj
args=[{'type': blob_type, 'data': url, 'binary': False}]
name = py_utils.get_name(obj, kwargs2)
self._ngl_component_names.append(name)
self._remote_call("loadFile",
target='Stage',
args=args,
kwargs=kwargs2)
def remove_component(self, component_id):
"""remove component by its uuid
Examples
--------
>>> view.add_trajectory(traj0)
>>> view.add_trajectory(traj1)
>>> view.add_struture(structure)
>>> # remove last component
>>> view.remove_component(view._ngl_component_ids[-1])
"""
self._clear_component_auto_completion()
if self._trajlist:
for traj in self._trajlist:
if traj.id == component_id:
self._trajlist.remove(traj)
component_index = self._ngl_component_ids.index(component_id)
self._ngl_component_ids.remove(component_id)
self._ngl_component_names.pop(component_index)
self._remote_call('removeComponent',
target='Stage',
args=[component_index,])
self._update_component_auto_completion()
def _remote_call(self, method_name, target='Widget', args=None, kwargs=None):
"""call NGL's methods from Python.
Parameters
----------
method_name : str
target : str, {'Stage', 'Viewer', 'compList', 'StructureComponent'}
args : list
kwargs : dict
if target is 'compList', "component_index" could be passed
to specify which component will call the method.
Examples
--------
view._remote_call('loadFile', args=['1L2Y.pdb'],
target='Stage', kwargs={'defaultRepresentation': True})
# perform centerView for 1-th component
# component = Stage.compList[1];
# component.centerView(true, "1-12");
view._remote_call('centerView',
target='component',
args=[True, "1-12"],
kwargs={'component_index': 1})
"""
args = [] if args is None else args
kwargs = {} if kwargs is None else kwargs
msg = {}
if 'component_index' in kwargs:
msg['component_index'] = kwargs.pop('component_index')
if 'repr_index' in kwargs:
msg['repr_index'] = kwargs.pop('repr_index')
msg['target'] = target
msg['type'] = 'call_method'
msg['methodName'] = method_name
msg['args'] = args
msg['kwargs'] = kwargs
def callback(widget, msg=msg):
widget.send(msg)
callback._method_name = method_name
if self.loaded:
self._remote_call_thread.q.append(callback)
else:
# send later
# all callbacks will be called right after widget is loaded
self._ngl_displayed_callbacks_before_loaded.append(callback)
self._ngl_displayed_callbacks_after_loaded.append(callback)
def _get_traj_by_id(self, itsid):
"""return nglview.Trajectory or its derived class object
"""
for traj in self._trajlist:
if traj.id == itsid:
return traj
return None
def hide(self, indices):
"""set invisibility for given component/struture/trajectory (by their indices)
"""
traj_ids = set(traj.id for traj in self._trajlist)
for index in indices:
comp_id = self._ngl_component_ids[index]
if comp_id in traj_ids:
traj = self._get_traj_by_id(comp_id)
traj.shown = False
self._remote_call("setVisibility",
target='compList',
args=[False,],
kwargs={'component_index': index})
def show(self, **kwargs):
"""shortcut of `show_only`
"""
self.show_only(**kwargs)
def show_only(self, indices='all'):
"""set visibility for given components (by their indices)
Parameters
----------
indices : {'all', array-like}, component index, default 'all'
"""
traj_ids = set(traj.id for traj in self._trajlist)
if indices == 'all':
indices_ = set(range(self.n_components))
else:
indices_ = set(indices)
for index, comp_id in enumerate(self._ngl_component_ids):
if comp_id in traj_ids:
traj = self._get_traj_by_id(comp_id)
else:
traj = None
if index in indices_:
args = [True,]
if traj is not None:
traj.shown = True
else:
args = [False,]
if traj is not None:
traj.shown = False
self._remote_call("setVisibility",
target='compList',
args=args,
kwargs={'component_index': index})
def _js_console(self):
self.send(dict(type='get', data='any'))
def _get_full_params(self):
self.send(dict(type='get', data='parameters'))
def _display_image(self):
'''for testing
'''
from IPython import display
return display.Image(self._image_data)
def _clear_component_auto_completion(self):
for index, _ in enumerate(self._ngl_component_ids):
name = 'component_' + str(index)
delattr(self, name)
def _update_component_auto_completion(self):
trajids = [traj.id for traj in self._trajlist]
for index, cid in enumerate(self._ngl_component_ids):
comp = ComponentViewer(self, index)
name = 'component_' + str(index)
setattr(self, name, comp)
if cid in trajids:
traj_name = 'trajectory_' + str(trajids.index(cid))
setattr(self, traj_name, comp)
def __getitem__(self, index):
"""return ComponentViewer
"""
postive_index = py_utils.get_positive_index(index, len(self._ngl_component_ids))
return ComponentViewer(self, postive_index)
def __iter__(self):
"""return ComponentViewer
"""
for i, _ in enumerate(self._ngl_component_ids):
yield self[i]
def detach(self, split=False):
"""detach player from its original container.
Parameters
----------
split : bool, default False
if True, resize notebook then move it to the right of its container
"""
if not self.loaded:
raise RuntimeError("must display view first")
# resize notebook first
# width of the dialog will be calculated based on notebook container offset
if split:
# rename
js_utils._move_notebook_to_the_right()
self._remote_call('setDialog', target='Widget')