def carousel(children=(), **layout):
"A horizontally scrolling carousel"
def_layout = dict(overflow='scroll hidden', flex_flow='row', display='flex')
res = Box([], layout=merge(def_layout, layout))
res.observe(_update_children, names='children')
res.children = children
return res
def make_box_for_grid(image_widget, title, size=(250, 250)):
"""
Make a VBox to hold caption/image for demonstrating
option_fit values.
"""
modes = ['oblique', 'X', 'Y', 'Z']
# make layout
box_layout = Layout()
box_layout.width = f'{size[0]}px'
box_layout.height = f'{size[1]}px'
box_layout.border = '0px'
# Make the caption
if title is not None:
title_str = "'{}'".format(title)
else:
title_str = str(title)
h = HTML(value='' + str(title_str) + '')
# Make the box with the image widget inside it
boxb = Box()
boxb.layout = box_layout
boxb.children = [image_widget]
# Compose into a vertical box
vb = VBox()
vb.layout.align_items = 'center'
vb.children = [h, boxb]
return vb
def carousel(
children: (tuple, list) = (), # `Box` objects to display in a carousel
**layout
) -> Box: # An `ipywidget`'s carousel
"A horizontally scrolling carousel"
def_layout = dict(overflow='scroll hidden',
flex_flow='row',
display='flex')
res = Box([], layout=merge(def_layout, layout))
res.observe(_update_children, names='children')
res.children = children
return res
def on_use_button_clicked(current: widgets.Button, results: List[Dict[str,
str]],
layout: widgets.Box) -> None:
molecule_sheet = layout.children[LayoutPosition.SEARCH_OUTPUT.value]
for i, button in enumerate(molecule_sheet.cells[0].value):
if button == current:
clear_search_output(layout)
add_row_with_inchi(results[i]["name"], results[i]["inchi"])
return
row_display = widgets.HTML(value="Could not located clicked button!")
layout.children = swap_layout(layout.children,
LayoutPosition.SEARCH_OUTPUT.value,
row_display)
def extract_all(layout: widgets.Box) -> None:
"""launch msms refs extraction and export"""
with get_new_log_box(layout):
if is_valid_input_sheet():
logger.info("Extracting MSMS reference spectrums....")
input_sheet = ipysheet.sheet("input")
new_refs_df = generate_msms_refs_df(input_sheet)
if new_refs_df.empty:
return
sheet = create_refs_sheet(new_refs_df)
layout.children = swap_layout(layout.children,
LayoutPosition.SHEET_OUTPUT.value,
sheet)
def is_valid_num_results(num: int,
input_value: str,
layout: widgets.Box,
max_valid: int = 100) -> bool:
if 0 < num <= max_valid:
return True
if num == 0:
message = f"""<b>No molecule names containing '{input_value}' and with a MW within
the search range were found in the database.</b>"""
else:
message = f"""<b>Too many matches (>{max_valid}).
{num} matches of '{input_value}' within the MW range were found in the database.</b>"""
message_widget = widgets.HTML(value=message)
layout.children = swap_layout(layout.children,
LayoutPosition.SEARCH_OUTPUT.value,
message_widget)
return False
def _interactive(interact_f, kwargs_widgets):
# this is a modified version of interactive() in ipywidget.widgets.interaction
container = Box(_dom_classes=['widget-interact'])
container.children = [w for w in kwargs_widgets if isinstance(w, DOMWidget)]
def call_f(name=None, old=None, new=None):
kwargs = dict((widget._kwarg, widget.value) for widget in kwargs_widgets)
try:
interact_f(**kwargs)
except Exception as e:
container.log.warn("Exception in interact callback: %s", e, exc_info=True)
for widget in kwargs_widgets:
widget.on_trait_change(call_f, 'value')
container.on_displayed(lambda _: call_f(None, None, None))
return container
def _interactive(interact_f, kwargs_widgets):
# this is a modified version of interactive() in ipywidget.widgets.interaction
container = Box(_dom_classes=['widget-interact'])
container.children = [w for w in kwargs_widgets if isinstance(w, DOMWidget)]
def call_f(name=None, old=None, new=None):
kwargs = dict((widget._kwarg, widget.value) for widget in kwargs_widgets)
try:
interact_f(**kwargs)
except Exception as e:
container.log.warn("Exception in interact callback: %s", e, exc_info=True)
for widget in kwargs_widgets:
widget.on_trait_change(call_f, 'value')
container.on_displayed(lambda _: call_f(None, None, None))
return container
def search(query: str, min_mw: float, max_mw: float,
layout: widgets.Box) -> None:
with get_new_log_box(layout):
clear_search_output(layout)
results = get_synonym_matches(query)
for cur in results:
RDLogger.DisableLog("rdApp.*") # hide rdkit warnings
cur["mol"] = cheminfo.normalize_molecule(
Chem.inchi.MolFromInchi(cur["inchi"]))
cur["norm_inchi"] = Chem.inchi.MolToInchi(cur["mol"])
RDLogger.EnableLog("rdApp.*")
cur["MW"] = ExactMolWt(cur["mol"])
filtered = filter_by_mw(filter_to_norm_inchi_in_db(results), min_mw,
max_mw)
logger.debug("Found %d matches to %s.", len(filtered), query)
if not is_valid_num_results(len(filtered), query, layout):
return
final = sorted(filtered, key=lambda x: x["MW"])
logger.debug("Num mols: %d", len(final))
column_names = ["", "Name", "MW", "Structure"]
sheet = ipysheet.sheet(
rows=len(final),
columns=len(column_names),
column_headers=column_names,
column_resizing=False,
column_width=[1, 4, 2, 10],
)
buttons = [
widgets.Button(description="use",
layout=widgets.Layout(width="100%")) for x in final
]
for button in buttons:
button.on_click(
lambda current: on_use_button_clicked(current, final, layout))
ipysheet.column(0, buttons)
ipysheet.column(1, [x["name"] for x in final])
ipysheet.column(2, [ExactMolWt(x["mol"]) for x in final])
ipysheet.column(3, [cheminfo.mol_to_image(x["mol"]) for x in final])
layout.children = swap_layout(layout.children,
LayoutPosition.SEARCH_OUTPUT.value,
sheet)
def clear_search_output(layout: widgets.Box) -> None:
blank = widgets.HTML(value="")
layout.children = swap_layout(layout.children,
LayoutPosition.SEARCH_OUTPUT.value, blank)
