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row25 = [param_name25, self.attachment_receptor_threshold, units_button25, desc_button25]
row26 = [param_name26, self.max_attachment_distance, units_button26, desc_button26]
row27 = [param_name27, self.min_attachment_distance, units_button27, desc_button27]
row28 = [param_name28, self.motility_shutdown_detection_threshold, units_button28, desc_button28]
row29 = [param_name29, self.attached_worker_migration_bias, units_button29, desc_button29]
row30 = [param_name30, self.unattached_worker_migration_bias, units_button30, desc_button30]
box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
box20 = Box(children=row20, layout=box_layout)
box21 = Box(children=row21, layout=box_layout)
box22 = Box(children=row22, layout=box_layout)
box23 = Box(children=row23, layout=box_layout)
box24 = Box(children=row24, layout=box_layout)
row27 = [param_name27, self.min_attachment_distance, units_button27, desc_button27]
row28 = [param_name28, self.motility_shutdown_detection_threshold, units_button28, desc_button28]
row29 = [param_name29, self.attached_worker_migration_bias, units_button29, desc_button29]
row30 = [param_name30, self.unattached_worker_migration_bias, units_button30, desc_button30]
box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
box20 = Box(children=row20, layout=box_layout)
box21 = Box(children=row21, layout=box_layout)
box22 = Box(children=row22, layout=box_layout)
box23 = Box(children=row23, layout=box_layout)
box24 = Box(children=row24, layout=box_layout)
box25 = Box(children=row25, layout=box_layout)
box26 = Box(children=row26, layout=box_layout)
row20 = [param_name20, self.tumor_immunogenicity_standard_deviation, units_button20, desc_button20]
row21 = [param_name21, self.oncoprotein_saturation, units_button21, desc_button21]
row22 = [param_name22, self.oncoprotein_threshold, units_button22, desc_button22]
row23 = [param_name23, self.max_attachment_distance, units_button23, desc_button23]
row24 = [param_name24, self.min_attachment_distance, units_button24, desc_button24]
box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
box20 = Box(children=row20, layout=box_layout)
box21 = Box(children=row21, layout=box_layout)
box22 = Box(children=row22, layout=box_layout)
box23 = Box(children=row23, layout=box_layout)
box24 = Box(children=row24, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
box20 = Box(children=row20, layout=box_layout)
box21 = Box(children=row21, layout=box_layout)
box22 = Box(children=row22, layout=box_layout)
box23 = Box(children=row23, layout=box_layout)
box24 = Box(children=row24, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
box6,
box7,
box8,
box9,
box10,
box11,
box12,
box13,
box14,
zoom=2.5,
mac_scrollbar=True,
timeit=False):
if platform.system() != "Darwin":
mac_scrollbar = False
# Output widget
output_height = height * 0.4 - 20 + 2
self.info = Info(tree_width, output_height - 6)
self.info.html.add_class("scroll-area")
if mac_scrollbar:
self.info.html.add_class("mac-scrollbar")
self.output = Box([self.info.html])
self.output.layout = Layout(
height="%dpx" % output_height, width="%dpx" % tree_width, overflow_y="scroll", overflow_x="scroll")
self.output.add_class("view_output")
## Threejs rendering of Cadquery objects
self.cq_view = CadqueryView(
width=cad_width,
height=height,
quality=quality,
edge_accuracy=edge_accuracy,
default_mesh_color=self.default_mesh_color,
default_edge_color=self.default_edge_color,
info=self.info,
timeit=timeit)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
box20 = Box(children=row20, layout=box_layout)
box21 = Box(children=row21, layout=box_layout)
box22 = Box(children=row22, layout=box_layout)
box23 = Box(children=row23, layout=box_layout)
box24 = Box(children=row24, layout=box_layout)
box25 = Box(children=row25, layout=box_layout)
box26 = Box(children=row26, layout=box_layout)
box27 = Box(children=row27, layout=box_layout)
box28 = Box(children=row28, layout=box_layout)
box29 = Box(children=row29, layout=box_layout)
self.tab = VBox([
box1,
box2,
Subclass of the standard geometry viewer with added UI for rendering orbitals
Args:
mol (mdt.Molecule): a molecule with A) orbitals, and
B) an energy model with calculate_orbital_grid
**kwargs (dict): kwargs for the viewer
"""
def __init__(self, mol, **kwargs):
self.viewer = GeometryViewer(mol=mol, **process_widget_kwargs(kwargs))
self.viewer.wfns = [mol.wfn]
self.uipane = OrbitalUIPane(self, hostheight=self.viewer.layout.height)
hb = HBox([self.viewer, self.uipane])
super(OrbitalViewer, self).__init__([hb])
class OrbitalUIPane(Selector, ipy.Box):
# TODO: deal with orbitals not present in all frames of a trajectory
# TODO: deal with orbital properties (occupation and energy) changing over a trajectory
def __init__(self, viz, hostheight, **kwargs):
self.viz = viz
kwargs.setdefault('width', '325px')
self.type_dropdown = ipy.Dropdown(options=list(self.viz.viewer.wfn.orbitals.keys()))
initial_orb = 'canonical'
if initial_orb not in self.type_dropdown.options:
initial_orb = next(iter(self.type_dropdown.options.keys()))
self.type_dropdown.value = initial_orb
self.type_dropdown.observe(self.new_orb_type, 'value')
kwargs['height'] = str(int(hostheight.rstrip('px')) - 50) + 'px'
height = str(int(hostheight.rstrip('px')) - 125) + 'px'
def __init__(self):
from .docker import DockerConfig
from .interfaces import InterfaceStatus
from .visualization import MdtExtensionConfig
self.interface_status = InterfaceStatus()
self.compute_config = DockerConfig()
self.nbextension_config = MdtExtensionConfig()
self.changelog = ChangeLog()
self.tab_list = StyledTab([ipy.Box(),
self.nbextension_config,
self.interface_status,
self.compute_config,
self.changelog])
self.tab_list.set_title(0, '^')
self.tab_list.set_title(1, 'Notebook config')
self.tab_list.set_title(2, "Interfaces")
self.tab_list.set_title(3, 'Docker config')
self.tab_list.set_title(4, "What's new")
self.children = [self.make_header(), self.tab_list]
super().__init__(children=self.children)
toggle_types = {'checkbox': CheckboxPlus,
'button': widgets.ToggleButton}
toggle_type = kwd.pop('toggle_type', 'checkbox')
if toggle_type not in toggle_types:
raise ValueError('toggle_type must be one of '
'{}'.format(toggle_type.keys()))
super(ToggleContainer, self).__init__(*args, **kwd)
self._toggle_container = widgets.Box()
# Boxes no longer have a description in ipywidgets 7 so add one here
self._toggle_container.description = 'toggle holder'
self._checkbox = toggle_types[toggle_type](description=self.description)
self._toggle_container.children = [self._checkbox]
self._container = widgets.VBox()
# Boxes no longer have a description in ipywidgets 7 so add one here
self._container.description = "Toggle-able container"
self._state_monitor_container = widgets.Box(visibility='hidden')
# Boxes no longer have a description in ipywidgets 7 so add one here
self._state_monitor_container.description = "For internal use only"
self._state_monitor_container.layout.visibility = 'hidden'
self._state_monitor_container.display = 'none'
self._state_monitor = widgets.Checkbox(visibility='hidden')
self._state_monitor.layout.visibility = 'hidden'
self._state_monitor.layout.display = 'none'
self._state_monitor_container.children = [self._state_monitor]
self.children = [
self._toggle_container,
self._container,
self._state_monitor,
]
self._link_children()
'initial_real_power',
'initial_reactive_power',
)
def _less_than_maximum_real_power_check(self, proposal):
if not proposal['value'] <= self.maximum_real_power:
raise t.TraitError(
'{class_name}().{trait_name} must be a less than or equal to {class_name}().maximum_real_power.'.format(
class_name=proposal['owner'].__class__.__name__,
trait_name=proposal['trait'].name
)
)
else:
return proposal['value']
class GeneratorView(ipyw.Box):
model = t.Instance(Generator)
def __init__(self, model=None, *args, **kwargs):
if model is not None:
self.model = model
else:
self.model = Generator()
super(GeneratorView, self).__init__(*args, **kwargs)
self._title = ipyw.HTML('Generator:')
self._name = ipyw.Text(
value='GenCo0',