def __init__(self, mol):
super(ResidueSelector, self).__init__(mol)
self.selection_type = ipy.Dropdown(description='Clicks select:',
value=self.viewer.selection_type,
options=('Atom', 'Residue',
'Chain'))
traitlets.link((self.selection_type, 'value'),
(self.viewer, 'selection_type'))
self.residue_listname = ipy.HTML('<b>Selected residues:</b>')
self.residue_list = ipy.SelectMultiple(options=list(), height=150)
traitlets.directional_link((self.viewer, 'selected_atom_indices'),
(self.residue_list, 'options'),
self._atoms_to_residues)
self.residue_list.observe(self.remove_atomlist_highlight, 'value')
self.atom_list.observe(self.remove_reslist_highlight, 'value')
self.subtools.children = [
ipy.HBox([self.select_all_atoms_button, self.select_none])
]
self.toolpane.children = [
self.selection_type, self.atom_listname, self.atom_list,
self.residue_listname, self.residue_list
]
def append_msg(self, msg, section=False):
"""
Append a message in a new parragraph, with or without divider
Args:
msg (str): the message to display
section (bool, optional): add a Divider before the added message
Return:
self
"""
self.show()
if self.children[0]:
current_children = self.children[:]
if section:
# As the list is mutable, and the trait is only triggered when
# the children is changed, so have to create a copy.
divider = Divider(class_='my-4', style='opacity: 0.22')
# link Alert type with divider type
directional_link((self, 'type'), (divider, 'type_'))
current_children.extend(
[divider, v.Html(tag='p', children=[msg])])
self.children = current_children
else:
current_children.append(v.Html(tag='p', children=[msg]))
self.children = current_children
else:
self.add_msg(msg)
return self
def _make_ui_pane(self, hostheight):
layout = ipy.Layout(width='325px',
height=str(int(hostheight.rstrip('px')) - 50) + 'px')
#element_height = str(int(hostheight.rstrip('px')) - 125) + 'px'
element_height = None
# NOTE - element_height was used for the listbox-style orblist.
# HOWEVER ipywidgets 6.0 only displays those as a dropdown.
# This is therefore disabled until we can display listboxes again. -- AMV 7/16
# Orbital set selector
self.status_element = ipy.HTML(layout=ipy.Layout(width='inherit', height='20px'))
orbtype_label = ipy.Label("Orbital set:")
self.type_dropdown = ipy.Dropdown(options=list(self.wfn.orbitals.keys()))
initialtype = 'canonical'
if initialtype not in self.type_dropdown.options:
initialtype = next(iter(self.type_dropdown.options.keys()))
self.type_dropdown.value = initialtype
self.type_dropdown.observe(self.new_orb_type, 'value')
# List of orbitals in this set
orblist_label = ipy.Label("Orbital:")
self.orblist = ipy.Dropdown(options={None: None},
layout=ipy.Layout(width=layout.width, height=element_height))
traitlets.link((self.orblist, 'value'), (self, 'current_orbital'))
# Isovalue selector
isoval_label = ipy.Label('Isovalue:')
self.isoval_selector = ipy.FloatSlider(min=0.0, max=0.075,
value=0.01, step=0.00075,
readout_format='.4f',
layout=ipy.Layout(width=layout.width))
traitlets.link((self.isoval_selector, 'value'), (self, 'isoval'))
# Opacity selector
opacity_label = ipy.Label('Opacity:')
self.opacity_selector = ipy.FloatSlider(min=0.0, max=1.0,
value=0.8, step=0.01,
readout_format='.2f',
layout=ipy.Layout(width=layout.width))
traitlets.link((self.opacity_selector, 'value'), (self, 'orb_opacity'))
# Resolution selector
resolution_label = ipy.Label("Grid resolution:", layout=ipy.Layout(width=layout.width))
self.orb_resolution = ipy.Text(layout=ipy.Layout(width='75px',
positioning='bottom'))
self.orb_resolution.value = str(self.numpoints)
self.resolution_button = ipy.Button(description='Update resolution')
self.resolution_button.on_click(self.change_resolution)
traitlets.directional_link((self, 'numpoints'), (self.orb_resolution, 'value'),
transform=str)
self.uipane = ipy.VBox([self.status_element,
orbtype_label, self.type_dropdown,
orblist_label, self.orblist,
isoval_label, self.isoval_selector,
opacity_label, self.opacity_selector,
resolution_label, self.orb_resolution, self.resolution_button])
self.new_orb_type()
self.type_dropdown.observe(self.new_orb_type, 'value')
return self.uipane
def __init__(
self,
iterable_or_max,
title='',
format_str='%(current)d/%(max)d (%(percent)d%%) in %(elapsed).1f s, %(last_iter_time).2f s last iter; eta %(eta_avg).0f+-%(eta_stddev).0f s'
):
super(ProgressBarIPyNb, self).__init__(iterable_or_max, title)
self.format_str = format_str
self.progress_w = iw.FloatProgress(min=0,
max=100,
value=30,
width='100%')
self.title_w = iw.HTML(
'<h3 style="display: inline">%(title)s</h3> ' % self)
self.info_w = iw.HTML()
self.log_last_w = iw.HTML()
self.log_check_w = iw.Checkbox(value=False,
visible=False,
description='Show Log')
self.log_w = iw.HTML()
self.log_header_w = iw.HTML('<h2><small>Log messages</small></h2>')
directional_link((self.log_check_w, 'value'), (self.log_w, 'visible'))
directional_link((self.log_check_w, 'value'),
(self.log_header_w, 'visible'))
self.container_w = iw.VBox([
iw.HBox([self.title_w, self.info_w, self.log_last_w]),
iw.HBox([self.progress_w, self.log_check_w]), self.log_header_w,
self.log_w,
iw.HBox(height=20)
])
self.displayed = False
def __init__(self, mol):
super().__init__(mol)
self._atomset = collections.OrderedDict()
self.atom_listname = ipy.Label('Selected atoms:',
layout=ipy.Layout(width='100%'))
self.atom_list = ipy.SelectMultiple(options=list(
self.viewer.selected_atom_indices),
layout=ipy.Layout(height='150px'))
traitlets.directional_link((self.viewer, 'selected_atom_indices'),
(self.atom_list, 'options'),
self._atom_indices_to_atoms)
self.select_all_atoms_button = ipy.Button(
description='Select all atoms')
self.select_all_atoms_button.on_click(self.select_all_atoms)
self.select_none = ipy.Button(description='Clear all selections')
self.select_none.on_click(self.clear_selections)
self.representation_buttons = ipy.ToggleButtons(
options=['stick', 'ribbon', 'auto', 'vdw'], value='auto')
self.representation_buttons.observe(self._change_representation,
'value')
def construct_child(self):
if self.child_spawner is None:
self.child_spawner = self.child_class(
user = self.user,
db = self.db,
hub = self.hub,
authenticator = self.authenticator,
oauth_client_id = self.oauth_client_id,
server = self._server,
config = self.config,
**self.child_config
)
# initial state will always be wrong since it will see *our* state
self.child_spawner.clear_state()
if self.child_state:
self.child_spawner.load_state(self.child_state)
# link traits common between self and child
common_traits = (
set(self.trait_names()) &
set(self.child_spawner.trait_names()) -
set(self.child_config.keys())
)
for trait in common_traits:
directional_link((self, trait), (self.child_spawner, trait))
return self.child_spawner
def __init__(self, members, *args, **kwargs):
super(MultipleNetworks, self).__init__(*args, **kwargs)
self.members = members
self.member_list = []
self.holders = []
self.width_slider = s = widgets.IntSlider(value=self.svg_width, min=100, max=2000, step=10)
traitlets.directional_link((s, "value"), (self, "svg_width"))
self.boxes = b = self.make_boxes(self.members)
self.assembly = widgets.VBox(children=[s,b])
def make_text_displays(self):
self.row_text = widgets.Text(description="row", value="")
self.row_text.width = "100px"
self.col_text = widgets.Text(description="col", value="")
self.col_text.width = "100px"
sslider = self.size_slider = widgets.FloatSlider(value=550, min=550, max=3000,
step=10, readout=False, width="100px")
svg = self.svg
traitlets.directional_link((sslider, "value"), (svg, "width"))
traitlets.directional_link((sslider, "value"), (svg, "height"))
assembly = widgets.HBox(children=[self.row_text, self.col_text, sslider])
return assembly
def make_text_displays(self):
self.row_text = widgets.Text(description="row", value="")
self.row_text.layout.width = "200px"
self.col_text = widgets.Text(description="col", value="")
self.col_text.layout.width = "200px"
sslider = self.size_slider = widgets.FloatSlider(value=550, min=550, max=3000,
step=10, readout=False, width="100px")
sslider.layout.width = "150px"
svg = self.svg
traitlets.directional_link((sslider, "value"), (svg, "svg_width"))
traitlets.directional_link((sslider, "value"), (svg, "svg_height"))
assembly = widgets.HBox(children=[self.row_text, self.col_text, sslider])
return assembly
def debugging_display(self, tagline="debug message area for widget:", border='1px solid black'):
if border:
out = widgets.Output(layout={'border': border})
else:
out = widgets.Output()
if tagline:
with out:
print (tagline)
self.output = out
status_text = widgets.Text(description="status:", value="")
traitlets.directional_link((self, "status"), (status_text, "value"))
error_text = widgets.Text(description="error", value="")
traitlets.directional_link((self, "error_msg"), (error_text, "value"))
assembly = widgets.VBox(children=[self, status_text, error_text, out])
return assembly
def _link_dependent_props(self) -> None:
"""
Ensure that RemoteKernelManager, when used as part of an EnterpriseGatewayApp,
has certain necessary configuration stay in sync with the app's configuration.
When RemoteKernelManager is used independently, this function is a no-op, and
default values or configuration set on this class is used.
"""
try:
eg_instance = self.parent.parent
except AttributeError:
return
dependent_props = [
"authorized_users",
"unauthorized_users",
"port_range",
"impersonation_enabled",
"max_kernels_per_user",
"client_envs",
"inherited_envs",
"yarn_endpoint",
"alt_yarn_endpoint",
"yarn_endpoint_security_enabled",
"conductor_endpoint",
"remote_hosts",
"load_balancing_algorithm",
]
self._links = [
directional_link((eg_instance, prop), (self, prop))
for prop in dependent_props
]
def test_link_different(self):
"""Verify two traitlets of different types can be linked together using link."""
# Create two simple classes with Int traitlets.
class A(HasTraits):
value = Int()
class B(HasTraits):
count = Int()
a = A(value=9)
b = B(count=8)
# Conenct the two classes.
c = directional_link((a, 'value'), (b, 'count'))
# Make sure the values are the same at the point of linking.
self.assertEqual(a.value, b.count)
# Change one the value of the source and check that it synchronizes the target.
a.value = 5
self.assertEqual(b.count, 5)
# Change one the value of the target and check that it has no impact on the source
b.value = 6
self.assertEqual(a.value, 5)
def test_link_different(self):
"""Verify two traitlets of different types can be linked together using link."""
# Create two simple classes with Int traitlets.
class A(HasTraits):
value = Int()
class B(HasTraits):
count = Int()
a = A(value=9)
b = B(count=8)
# Conenct the two classes.
c = directional_link((a, "value"), (b, "count"))
# Make sure the values are the same at the point of linking.
self.assertEqual(a.value, b.count)
# Change one the value of the source and check that it synchronizes the target.
a.value = 5
self.assertEqual(b.count, 5)
# Change one the value of the target and check that it has no impact on the source
b.value = 6
self.assertEqual(a.value, 5)
def draw(self,
width=500,
height=500,
show_2dhydrogens=None,
display=False):
""" Visualize this molecule (Jupyter only).
Creates a 3D viewer, and, for small molecules, a 2D viewer).
Args:
width (int): width of the viewer in pixels
height (int): height of the viewer in pixels
show_2dhydrogens (bool): whether to show the hydrogens in 2d (default: True if there
are 10 or less heavy atoms, false otherwise)
display (bool): immediately display this viewer
Returns:
moldesign.ui.SelectionGroup
"""
viz2d = None
if self.num_atoms < 40:
viz2d = self.draw2d(width=width,
height=height,
display=False,
show_hydrogens=show_2dhydrogens)
viz3d = self.draw3d(width=width, height=height, display=False)
traitlets.link((viz3d, 'selected_atom_indices'),
(viz2d, 'selected_atom_indices'))
views = ipy.HBox([viz2d, viz3d])
else:
views = self.draw3d(display=False)
atom_inspector = uibase.components.AtomInspector()
traitlets.directional_link(
(viz2d or views, 'selected_atom_indices'),
(atom_inspector, 'value'),
lambda selected_atom_indices: atom_inspector.indices_to_value(
selected_atom_indices, self.atoms))
displayobj = uibase.SelectionGroup([views, atom_inspector])
if display:
IPython.display.display(displayobj)
return displayobj
def __init__(self, *args, **kwargs):
super(LinkedExpressionNetwork, self).__init__(*args, **kwargs)
self.network = dNetwork.NetworkDisplay()
self.expression = dExpression.ExpressionDisplay()
self.gene_button = self.make_button(u"\u21d3 Genes", self.gene_click)
self.condition_button = self.make_button(u"\u21d1 Condition",
self.condition_click)
self.cluster_button = self.make_button(u"\u21d1 Cluster",
self.cluster_click)
buttons = [self.gene_button, self.condition_button, self.cluster_button]
horizontal = widgets.HBox(children=buttons)
self.hideable = widgets.VBox(children=[horizontal, self.expression.assembly])
#traitlets.directional_link((self, "maximize"), (hideable, "visible"))
#traitlets.directional_link((self, "maximize"), (self.network, "maximize"))
self.on_trait_change(self.maximize_changed, "maximize")
traitlets.directional_link((self, "svg_width"), (self.network, "svg_width"))
self.assembly = widgets.VBox(children=[self.network.assembly, self.hideable])
def __init__(self, mol):
super(SelBase, self).__init__(mol)
self._atomset = collections.OrderedDict()
self.atom_listname = ipy.HTML('<b>Selected atoms:</b>')
self.atom_list = ipy.SelectMultiple(options=list(self.viewer.selected_atom_indices), height=150)
traitlets.directional_link(
(self.viewer, 'selected_atom_indices'),
(self.atom_list, 'options'),
self._atom_indices_to_atoms
)
self.select_all_atoms_button = ipy.Button(description='Select all atoms')
self.select_all_atoms_button.on_click(self.select_all_atoms)
self.select_none = ipy.Button(description='Clear all selections')
self.select_none.on_click(self.clear_selections)
def __init__(self, mol):
super(SelBase, self).__init__(mol)
self._atomset = collections.OrderedDict()
self.atom_listname = ipy.HTML('<b>Selected atoms:</b>')
self.atom_list = ipy.SelectMultiple(options=list(
self.viewer.selected_atom_indices),
height=150)
traitlets.directional_link((self.viewer, 'selected_atom_indices'),
(self.atom_list, 'options'),
self._atom_indices_to_atoms)
self.select_all_atoms_button = ipy.Button(
description='Select all atoms')
self.select_all_atoms_button.on_click(self.select_all_atoms)
self.select_none = ipy.Button(description='Clear all selections')
self.select_none.on_click(self.clear_selections)
def __init__(self, mol):
super(ResidueSelector, self).__init__(mol)
self.selection_type = ipy.Dropdown(description='Clicks select:',value=self.viewer.selection_type,
options=('Atom', 'Residue', 'Chain'))
traitlets.link((self.selection_type, 'value'), (self.viewer, 'selection_type'))
self.residue_listname = ipy.HTML('<b>Selected residues:</b>')
self.residue_list = ipy.SelectMultiple(options=list(), height=150)
traitlets.directional_link((self.viewer, 'selected_atom_indices'), (self.residue_list, 'options'), self._atoms_to_residues)
self.residue_list.observe(self.remove_atomlist_highlight, 'value')
self.atom_list.observe(self.remove_reslist_highlight, 'value')
self.subtools.children = [ipy.HBox([self.select_all_atoms_button, self.select_none])]
self.toolpane.children = [self.selection_type,
self.atom_listname,
self.atom_list,
self.residue_listname,
self.residue_list]
def __init__(self, *pargs, **kwargs):
self.drawing = True
self.last_draw_time = 0
self.draw_lock = threading.Lock()
super(Locations, self).__init__(*pargs, **kwargs)
self.diagram = D = cartesian_svg.doodle(-3, -6, 6, 2, html_width=700)
self.moving = None
a_slider = widgets.FloatSlider(value=3.0, min=0.2, max=10.0, step=0.2,
width="150px", description="Kim/Bob")
b_slider = widgets.FloatSlider(value=4.0, min=0.2, max=10.0, step=0.2,
width="150px", description="Jack/Janet")
traitlets.directional_link((a_slider, "value"), (self, "a"))
traitlets.directional_link((b_slider, "value"), (self, "b"))
self.on_trait_change(self.redraw, "a")
self.on_trait_change(self.redraw, "b")
assembly = widgets.VBox(children = [a_slider, b_slider, D.target])
display(assembly)
#D.show()
D.enable_events("click mousemove", self.event_callback)
self.redraw()
def __init__(self, mol):
super(BondSelector, self).__init__(mol)
self._bondset = collections.OrderedDict()
self._drawn_bond_state = set()
self.bond_listname = ipy.HTML('<b>Selected bonds:</b>')
self.bond_list = ipy.SelectMultiple(options=list(), height=150)
traitlets.directional_link((self.viewer, 'selected_atom_indices'),
(self.bond_list, 'options'),
self._atoms_to_bonds)
self.atom_list.observe(self.remove_bondlist_highlight, 'value')
self.subtools.children = [
ipy.HBox([self.select_all_atoms_button, self.select_none])
]
self.toolpane.children = (self.atom_listname, self.atom_list,
self.bond_listname, self.bond_list)
def draw(self, width=500, height=500, show_2dhydrogens=None, display=False):
""" Visualize this molecule (Jupyter only).
Creates a 3D viewer, and, for small molecules, a 2D viewer).
Args:
width (int): width of the viewer in pixels
height (int): height of the viewer in pixels
show_2dhydrogens (bool): whether to show the hydrogens in 2d (default: True if there
are 10 or less heavy atoms, false otherwise)
display (bool): immediately display this viewer
Returns:
moldesign.ui.SelectionGroup
"""
viz2d = None
if self.num_atoms < 40:
viz2d = self.draw2d(width=width, height=height,
display=False,
show_hydrogens=show_2dhydrogens)
viz3d = self.draw3d(width=width, height=height,
display=False)
traitlets.link((viz3d, 'selected_atom_indices'), (viz2d, 'selected_atom_indices'))
views = ipy.HBox([viz2d, viz3d])
else:
views = self.draw3d(display=False)
atom_inspector = uibase.components.AtomInspector()
traitlets.directional_link(
(viz2d or views, 'selected_atom_indices'),
(atom_inspector, 'value'),
lambda selected_atom_indices: atom_inspector.indices_to_value(selected_atom_indices, self.atoms)
)
displayobj = uibase.SelectionGroup([views, atom_inspector])
if display:
IPython.display.display(displayobj)
return displayobj
def __init__(self, cmap: str = "gray"):
"""Parameters
----------
cmap
Colormap to use for displaying images.
"""
if plt.isinteractive():
warnings.warn("Turning off matplotlib's interactive mode as it "
"is not compatible with this.")
plt.ioff()
# General options
self._algo_sel = ipywidgets.Dropdown(
options=[A.name for A in algorithms], description="algorithm")
self._loc_options = [A() for A in algorithms]
for lo in self._loc_options:
lo.observe(self._options_changed, "options")
# The figure
ax = plt.subplots()[1]
self.image_display = ImageDisplay(ax, cmap=cmap)
traitlets.directional_link((self, "input"),
(self.image_display, "input"))
# Display preview
self._show_loc_check = ipywidgets.Checkbox(
description="Show loc.", indent=False, value=True)
self._scatter_artist = None
left_box = ipywidgets.VBox([self._algo_sel, *self._loc_options,
self._show_loc_check])
super().__init__([left_box, self.image_display])
traitlets.link((self._algo_sel, "value"), (self, "algorithm"))
self.observe(self._update, "options")
self.observe(self._options_trait_changed, "options")
self._show_loc_check.observe(self._update, "value")
def __init__(self, mol):
super().__init__(mol)
self._atomset = collections.OrderedDict()
self.atom_listname = ipy.Label('Selected atoms:', layout=ipy.Layout(width='100%'))
self.atom_list = ipy.SelectMultiple(options=list(self.viewer.selected_atom_indices),
layout=ipy.Layout(height='150px'))
traitlets.directional_link(
(self.viewer, 'selected_atom_indices'),
(self.atom_list, 'options'),
self._atom_indices_to_atoms
)
self.select_all_atoms_button = ipy.Button(description='Select all atoms')
self.select_all_atoms_button.on_click(self.select_all_atoms)
self.select_none = ipy.Button(description='Clear all selections')
self.select_none.on_click(self.clear_selections)
self.representation_buttons = ipy.ToggleButtons(options=['stick','ribbon', 'auto', 'vdw'],
value='auto')
self.representation_buttons.observe(self._change_representation, 'value')
def __init__(self, mol):
super(BondSelector, self).__init__(mol)
self._bondset = collections.OrderedDict()
self._drawn_bond_state = set()
self.bond_listname = ipy.HTML('<b>Selected bonds:</b>')
self.bond_list = ipy.SelectMultiple(options=list(),
height=150)
traitlets.directional_link(
(self.viewer, 'selected_atom_indices'),
(self.bond_list, 'options'),
self._atoms_to_bonds
)
self.atom_list.observe(self.remove_bondlist_highlight, 'value')
self.subtools.children = [ipy.HBox([self.select_all_atoms_button,
self.select_none])]
self.toolpane.children = (self.atom_listname,
self.atom_list,
self.bond_listname,
self.bond_list)
def test_unlink(self):
"""Verify two linked traitlets can be unlinked."""
# Create two simple classes with Int traitlets.
class A(HasTraits):
value = Int()
a = A(value=9)
b = A(value=8)
# Connect the two classes.
c = directional_link((a, 'value'), (b, 'value'))
a.value = 4
c.unlink()
# Change one of the values to make sure they don't stay in sync.
a.value = 5
self.assertNotEqual(a.value, b.value)
def _src(self, proposal):
src = proposal['value']
# print(f'>> TransformTree {id(self)}: validate src = {src}')
link = None
if isinstance(src, Tree):
self.src_tree = src
elif isinstance(src, HasTraits) and src.has_trait('tree'):
link = directional_link((src, 'tree'), (self, 'src_tree'))
elif hasattr(src, 'tree'):
self.src_tree = getattr(src, 'tree')
elif src is None:
self.src_tree = None
else:
raise TraitError('must be a tree or an owner of a tree')
if self._link is not None:
self._link.unlink()
self._link = link
# print(f'<< TransformTree {id(self)}: validate src = {src}')
return src
def test_connect_same(self):
"""Verify two traitlets of the same type can be linked together using directional_link."""
# Create two simple classes with Int traitlets.
class A(HasTraits):
value = Int()
a = A(value=9)
b = A(value=8)
# Conenct the two classes.
c = directional_link((a, 'value'), (b, 'value'))
# Make sure the values are the same at the point of linking.
self.assertEqual(a.value, b.value)
# Change one the value of the source and check that it synchronizes the target.
a.value = 5
self.assertEqual(b.value, 5)
# Change one the value of the target and check that it has no impact on the source
b.value = 6
self.assertEqual(a.value, 5)
def controls(self):
from .layers import VALID_STRETCHES, UI_COLORMAPS
if self._controls is not None:
return self._controls
opacity = widgets.FloatSlider(
description='Opacity:',
value=self.opacity,
min=0,
max=1,
readout=False,
step=0.01,
layout={'width': '200px'}
)
link((self, 'opacity'), (opacity, 'value'))
stretch = widgets.Dropdown(
description='Stretch:',
options=VALID_STRETCHES,
value=self.stretch,
layout={'width': '200px'}
)
link((self, 'stretch'), (stretch, 'value'))
# NB, this will crash if `self.cmap` is not one of our allowed values
reverse_ui_colormaps = dict((kv[1], kv[0]) for kv in UI_COLORMAPS.items())
colormap = widgets.Dropdown(
description='Colormap:',
options=UI_COLORMAPS.keys(),
value=reverse_ui_colormaps[self.cmap.name],
layout={'width': '200px'}
)
directional_link((colormap, 'label'), (self, 'cmap'), lambda x: UI_COLORMAPS[x])
directional_link((self, 'cmap'), (colormap, 'label'), lambda x: reverse_ui_colormaps[x.name])
vrange = widgets.FloatRangeSlider(
description='Fine min/max:',
value=[self.vmin, self.vmax],
min=self._data_min,
max=self._data_max,
readout=True,
layout={'width': '600px'},
step=(self.vmax - self.vmin) / 100,
format='.3g'
)
# Linkage must be manual since vrange uses a pair of values whereas we
# have two separate traitlets.
vrange.observe(self._vrange_slider_updated, names=['value'])
def update_vrange(change):
# Note: when this function is called, these values are indeed updated.
vrange.value = (self.vmin, self.vmax)
self.observe(update_vrange, names=['vmin', 'vmax'])
def update_step(change):
vrange.step = (vrange.max - vrange.min) / 100
vrange.observe(update_step, names=['min', 'max'])
coarse_min = widgets.FloatText(
description='Coarse min:',
value=self._data_min,
layout={'width': '300px'}
)
link((coarse_min, 'value'), (vrange, 'min'))
coarse_max = widgets.FloatText(
description='Coarse max:',
value=self._data_max,
layout={'width': '300px'}
)
link((coarse_max, 'value'), (vrange, 'max'))
self._controls = widgets.VBox([
widgets.HBox([colormap, stretch, opacity]),
widgets.HBox([coarse_min, coarse_max]),
vrange,
])
return self._controls
def __init__(self, mol):
super().__init__(mol)
self._widgetshapes = {}
self._atom_labels = []
# All numbers here are assumed angstroms and radians for now ...
self._highlighted_bonds = []
self._highlighted_atoms = []
self.original_position = self.mol.positions.copy()
self.clear_button = ipy.Button(description='Clear selection')
self.clear_button.on_click(self.clear_selection)
self.label_box = ipy.Checkbox(description='Label atoms', value=False)
self.label_box.observe(self.label_atoms, 'value')
# Viewer
self.selection_description = ipy.HTML()
self.subtools.children = (HBox([self.clear_button, self.label_box]),
self.selection_description)
traitlets.directional_link(
(self.viewer, 'selected_atom_indices'),
(self.selection_description, 'value'),
self.get_first_atom
)
# Atom manipulation tools - self.{x,y,z}_slider
self.sliders = []
for dim, name in enumerate('xyz'):
slider = ReadoutFloatSlider(
min=-self.MAXDIST, max=self.MAXDIST,
description='<span style="color: {c}"><b>{n}</b><span>'.format(
n=name, c=self.viewer.AXISCOLORS[name]),
format=self.POSFMT)
slider.dim = dim
setattr(self, name + '_slider', slider)
self.sliders.append(slider)
slider.observe(self.set_atom_pos, 'value')
# Bond manipulation tools
self.rigid_mol_selector = ipy.ToggleButtons(description='Position adjustment',
options={'selected atoms only':False,
'rigid molecule':True},
value=True)
self.length_slider = ReadoutFloatSlider(min=0.1, max=self.MAXDIST, format=self.POSFMT)
self.length_slider.observe(self.set_distance, 'value')
self.angle_slider = ReadoutFloatSlider(min=1.0, max=179.0, step=2.0, format=self.DEGFMT)
self.angle_slider.observe(self.set_angle, 'value')
self.dihedral_slider = ReadoutFloatSlider(min=-90.0, max=360.0, step=4.0,
format=self.DEGFMT)
self.dihedral_slider.observe(self.set_dihedral, 'value')
self.bond_tools = VBox((self.rigid_mol_selector,
self.length_slider,
self.angle_slider,
self.dihedral_slider))
self.movement_selector = ipy.ToggleButtons(description='Move:',
value='atom',
options=['atom', 'residue', 'chain'])
self.atom_tools = VBox((self.movement_selector,
self.x_slider,
self.y_slider,
self.z_slider))
self.reset_button = ipy.Button(description='Reset geometry')
self.reset_button.on_click(self.reset_geometry)
self.tool_holder = VBox()
self.toolpane.children = (self.tool_holder,
self.reset_button)
self.viewer.observe(self._set_tool_state,
names='selected_atom_indices')
def __init__(self, mol):
super(GeometryBuilder, self).__init__(mol)
# All numbers here are assumed angstroms and radians for now ...
self._highlighted_bonds = []
self._highlighted_atoms = []
self.original_position = self.mol.positions.copy()
self.clear_button = ipy.Button(description='Clear selection')
self.clear_button.on_click(self.clear_selection)
self.label_box = ipy.Checkbox(description='Label atoms', value=False)
self.label_box.observe(self.label_atoms, 'value')
# Viewer
self.selection_description = ipy.HTML()
self.subtools.children = (ipy.HBox([self.clear_button, self.label_box
]), self.selection_description)
traitlets.directional_link((self.viewer, 'selected_atom_indices'),
(self.selection_description, 'value'),
self.get_first_atom)
# Atom manipulation tools
self.x_slider = ReadoutFloatSlider(min=-self.MAXDIST,
max=self.MAXDIST,
description='<b>x</b>',
format=self.POSFMT)
self.x_slider.observe(self.set_atom_x, 'value')
self.y_slider = ReadoutFloatSlider(min=-self.MAXDIST,
max=self.MAXDIST,
description='<b>y</b>',
format=self.POSFMT)
self.y_slider.observe(self.set_atom_y, 'value')
self.z_slider = ReadoutFloatSlider(min=-self.MAXDIST,
max=self.MAXDIST,
description='<b>z</b>',
format=self.POSFMT)
self.z_slider.observe(self.set_atom_z, 'value')
# Bond manipulation tools
self.adjust_button = ipy.Checkbox(description='Adjust entire molecule',
align='end',
value=True)
self.length_slider = ReadoutFloatSlider(min=0.1,
max=self.MAXDIST,
format=self.POSFMT)
self.length_slider.observe(self.set_distance, 'value')
self.angle_slider = ReadoutFloatSlider(min=1.0,
max=179.0,
step=2.0,
format=self.DEGFMT)
self.angle_slider.observe(self.set_angle, 'value')
self.dihedral_slider = ReadoutFloatSlider(min=-90.0,
max=360.0,
step=4.0,
format=self.DEGFMT)
self.dihedral_slider.observe(self.set_dihedral, 'value')
self.bond_tools = ipy.VBox((self.adjust_button, self.length_slider,
self.angle_slider, self.dihedral_slider))
self.atom_tools = ipy.VBox(
(self.adjust_button, self.x_slider, self.y_slider, self.z_slider))
self.reset_button = ipy.Button(description='Reset geometry')
self.reset_button.on_click(self.reset_geometry)
self.tool_holder = ipy.VBox()
self.toolpane.children = (self.tool_holder, self.reset_button)
traitlets.directional_link((self.viewer, 'selected_atom_indices'),
(self.tool_holder, 'children'),
self._get_tool_state)
def make_linkages(self):
traitlets.link((self.width_slider, "value"), (self.network, "svg_width"))
traitlets.directional_link((self.parent, "svg_width"), (self.network, "svg_width"))
traitlets.directional_link((self.maximize_cb, "value"), (self.network, "maximize"))
def __init__(self, mol):
super(GeometryBuilder, self).__init__(mol)
# All numbers here are assumed angstroms and radians for now ...
self._highlighted_bonds = []
self._highlighted_atoms = []
self.original_position = self.mol.positions.copy()
self.clear_button = ipy.Button(description='Clear selection')
self.clear_button.on_click(self.clear_selection)
self.label_box = ipy.Checkbox(description='Label atoms', value=False)
self.label_box.observe(self.label_atoms, 'value')
# Viewer
self.selection_description = ipy.HTML()
self.subtools.children = (ipy.HBox([self.clear_button, self.label_box]),
self.selection_description)
traitlets.directional_link(
(self.viewer, 'selected_atom_indices'),
(self.selection_description, 'value'),
self.get_first_atom
)
# Atom manipulation tools
self.x_slider = ReadoutFloatSlider(min=-self.MAXDIST, max=self.MAXDIST,
description='<b>x</b>', format=self.POSFMT)
self.x_slider.observe(self.set_atom_x, 'value')
self.y_slider = ReadoutFloatSlider(min=-self.MAXDIST, max=self.MAXDIST,
description='<b>y</b>', format=self.POSFMT)
self.y_slider.observe(self.set_atom_y, 'value')
self.z_slider = ReadoutFloatSlider(min=-self.MAXDIST, max=self.MAXDIST,
description='<b>z</b>', format=self.POSFMT)
self.z_slider.observe(self.set_atom_z, 'value')
# Bond manipulation tools
self.adjust_button = ipy.Checkbox(description='Adjust entire molecule', align='end', value=True)
self.length_slider = ReadoutFloatSlider(min=0.1, max=self.MAXDIST, format=self.POSFMT)
self.length_slider.observe(self.set_distance, 'value')
self.angle_slider = ReadoutFloatSlider(min=1.0, max=179.0, step=2.0, format=self.DEGFMT)
self.angle_slider.observe(self.set_angle, 'value')
self.dihedral_slider = ReadoutFloatSlider(min=-90.0, max=360.0, step=4.0, format=self.DEGFMT)
self.dihedral_slider.observe(self.set_dihedral, 'value')
self.bond_tools = ipy.VBox((self.adjust_button,
self.length_slider,
self.angle_slider,
self.dihedral_slider))
self.atom_tools = ipy.VBox((self.adjust_button,
self.x_slider,
self.y_slider,
self.z_slider))
self.reset_button = ipy.Button(description='Reset geometry')
self.reset_button.on_click(self.reset_geometry)
self.tool_holder = ipy.VBox()
self.toolpane.children = (self.tool_holder,
self.reset_button)
traitlets.directional_link(
(self.viewer, 'selected_atom_indices'),
(self.tool_holder, 'children'),
self._get_tool_state
)
def __init__(self):
self.title_html = widgets.HTML("Gene network")
self.zoom_button = self.make_button("zoom", self.zoom_click, True)
self.trim_button = self.make_button("trim", self.trim_click)
self.layout_button = self.make_button("layout", self.layout_click)
self.expand_button = self.make_button("expand", self.expand_click)
self.regulates_button = self.make_button("regulates", self.regulates_click)
self.targeted_button = self.make_button("targeted by", self.targeted_click)
self.focus_button = self.make_button("focus", self.focus_click)
self.restore_button = self.make_button("restore", self.restore_click)
self.ignore_button = self.make_button("ignore", self.ignore_click)
self.nodes_button = self.make_button("list nodes", self.nodes_click)
self.edges_button = self.make_button("list edges", self.edges_click)
self.layout_dropdown = self.make_layout_dropdown()
self.labels_button = self.make_checkbox("labels", self.labels_click)
self.colors_button = self.make_checkbox("colors", self.colors_click)
self.draw_button = self.make_button("draw", self.draw_click)
# Assemble the layout
self.threshhold_assembly = self.make_threshhold_assembly()
self.pattern_assembly = self.make_pattern_assembly()
self.info_area = widgets.Textarea(description="status")
self.colors_assembly = self.make_colors_assembly()
self.dialog = self.make_dialog()
self.colors_assembly.visible = False
svg = self.svg = canvas.SVGCanvasWidget()
sslider = self.size_slider = widgets.FloatSlider(value=500, min=500, max=2000, step=10,
readout=False, width="150px")
self.depth_slider = widgets.IntSlider(
description="depth", value=0, min=0, max=5, width="50px")
traitlets.directional_link((sslider, "value"), (svg, "width"))
traitlets.directional_link((sslider, "value"), (svg, "height"))
#self.svg = widgets.Button(description="dummy button")
svg.add_style("background-color", "white")
svg.watch_event = "click mousedown mouseup mousemove mouseover"
svg.default_event_callback = self.svg_callback
left_panel = [self.title_html,
self.svg,
self.threshhold_assembly,
self.pattern_assembly,
self.info_area]
self.vertical = widgets.VBox(children=left_panel)
buttons = [self.zoom_button,
self.focus_button,
self.ignore_button,
self.trim_button,
self.expand_button,
self.regulates_button,
self.targeted_button,
self.layout_dropdown,
self.layout_button,
self.nodes_button,
self.edges_button,
self.labels_button,
self.restore_button,
self.size_slider,
self.draw_button,
self.depth_slider,
self.colors_button,
self.colors_assembly,
self.dialog]
self.inputs = widgets.VBox(children=buttons)
self.assembly = widgets.HBox(children=[self.inputs, self.vertical])
self.select_start = None
self.select_end = None
self.selection_id = None
self.selecting = False
self.data_graph = None
self.data_positions = None
self.display_positions = None
self.display_graph = None
self.selected_nodes = None
self.svg_origin = dGraph.pos(0, 0)
self.moving_node = None
def __init__(self, mol):
super().__init__(mol)
self._widgetshapes = {}
self._atom_labels = []
# All numbers here are assumed angstroms and radians for now ...
self._highlighted_bonds = []
self._highlighted_atoms = []
self.original_position = self.mol.positions.copy()
self.clear_button = ipy.Button(description='Clear selection')
self.clear_button.on_click(self.clear_selection)
self.label_box = ipy.Checkbox(description='Label atoms', value=False)
self.label_box.observe(self.label_atoms, 'value')
# Viewer
self.selection_description = ipy.HTML()
self.subtools.children = (HBox([self.clear_button, self.label_box]),
self.selection_description)
traitlets.directional_link((self.viewer, 'selected_atom_indices'),
(self.selection_description, 'value'),
self.get_first_atom)
# Atom manipulation tools - self.{x,y,z}_slider
self.sliders = []
for dim, name in enumerate('xyz'):
slider = ReadoutFloatSlider(
min=-self.MAXDIST,
max=self.MAXDIST,
description='<span style="color: {c}"><b>{n}</b><span>'.format(
n=name, c=self.viewer.AXISCOLORS[name]),
format=self.POSFMT)
slider.dim = dim
setattr(self, name + '_slider', slider)
self.sliders.append(slider)
slider.observe(self.set_atom_pos, 'value')
# Bond manipulation tools
self.rigid_mol_selector = ipy.ToggleButtons(
description='Position adjustment',
options={
'selected atoms only': False,
'rigid molecule': True
},
value=True)
self.length_slider = ReadoutFloatSlider(min=0.1,
max=self.MAXDIST,
format=self.POSFMT)
self.length_slider.observe(self.set_distance, 'value')
self.angle_slider = ReadoutFloatSlider(min=1.0,
max=179.0,
step=2.0,
format=self.DEGFMT)
self.angle_slider.observe(self.set_angle, 'value')
self.dihedral_slider = ReadoutFloatSlider(min=-90.0,
max=360.0,
step=4.0,
format=self.DEGFMT)
self.dihedral_slider.observe(self.set_dihedral, 'value')
self.bond_tools = VBox((self.rigid_mol_selector, self.length_slider,
self.angle_slider, self.dihedral_slider))
self.movement_selector = ipy.ToggleButtons(
description='Move:',
value='atom',
options=['atom', 'residue', 'chain'])
self.atom_tools = VBox((self.movement_selector, self.x_slider,
self.y_slider, self.z_slider))
self.reset_button = ipy.Button(description='Reset geometry')
self.reset_button.on_click(self.reset_geometry)
self.tool_holder = VBox()
self.toolpane.children = (self.tool_holder, self.reset_button)
self.viewer.observe(self._set_tool_state,
names='selected_atom_indices')
def __init__(self, dataset, *args, **kwargs):
super(Nearest, self).__init__(*args, **kwargs)
self.dataset = dataset
feature_names = list(dataset.feature_names)
self.x_name = feature_names[0]
self.y_name = feature_names[1]
sc = self.scatter_plot = js_proxy.ProxyWidget()
xd = self.x_dropdown = widgets.Dropdown(
options=list(feature_names), value=self.x_name)
yd = self.y_dropdown = widgets.Dropdown(
options=list(feature_names), value=self.y_name)
bc = self.border_checkbox = widgets.Checkbox(description="border", value=True)
ic = self.interior_checkbox = widgets.Checkbox(description="interior", value=True)
tc = self.training_checkbox = widgets.Checkbox(description="training", value=True)
tstc = self.test_checkbox = widgets.Checkbox(description="test", value=True)
ns = self.n_slider = widgets.IntSlider(value=self.n_neighbors, min=1, max=20,
description="neighbors", width="50px")
ss = self.n_slider = widgets.FloatSlider(value=self.n_neighbors, min=0.2, max=0.5,
description="test size", width="50px", step=0.1)
traitlets.directional_link((ss, "value"), (self, "test_size"))
traitlets.directional_link((xd, "value"), (self, "x_name"))
traitlets.directional_link((yd, "value"), (self, "y_name"))
traitlets.directional_link((bc, "value"), (self, "show_borders"))
traitlets.directional_link((ic, "value"), (self, "prediction_grid"))
traitlets.directional_link((ns, "value"), (self, "n_neighbors"))
traitlets.directional_link((tc, "value"), (self, "show_training"))
traitlets.directional_link((tstc, "value"), (self, "show_test"))
xd.on_trait_change(self.redraw, "value")
ss.on_trait_change(self.redraw, "value")
yd.on_trait_change(self.redraw, "value")
bc.on_trait_change(self.redraw, "value")
tc.on_trait_change(self.redraw, "value")
ic.on_trait_change(self.redraw, "value")
tstc.on_trait_change(self.redraw, "value")
ns.on_trait_change(self.redraw, "value")
controls = widgets.VBox(children=[xd, yd, bc, ic, tc, tstc, ns, ss])
self.assembly = widgets.HBox(children=[controls, sc])
