def get_context_data(self, **kwargs):
context = super(BioactiveCoreListView, self).get_context_data(**kwargs)
medicinals = BioactiveCore.objects.medicinal().prefetch_related('bioactives').order_by('name')
context.update({
'body_systems': Activity.classified_actions_mechs(),
'substructure_sets': [
{'subset': medicinals,
'label': 'Medicinal'},
{'subset': BioactiveCore.objects.food().exclude(name='Oligosaccharides').order_by('name'),
'label': 'Nutraceutical'},
],
'choice_form': ChemDataChoiceSubmitForm,
})
if self.request.GET.get('stats_data'):
averages, stats_arrays = BioactiveCore.compound_sets_stats(core_set=medicinals)
for chem_prop, val in averages.items():
plot = self.make_plot(val, chem_prop, 'mean')
if plot:
script, div = components(plot, CDN)
context['plot_script' + '_' + chem_prop] = script
context['plot_div' + '_' + chem_prop] = div
sds = {}
for cp in chemical_properties_label_map.keys():
sds[cp] = [(a[0], a[1][cp].std()) for a in stats_arrays]
for chem_prop, val in sds.items():
plot = self.make_plot(val, chem_prop, 'std dev in')
if plot:
script, div = components(plot, CDN)
context['sd_plot_script' + '_' + chem_prop] = script
context['sd_plot_div' + '_' + chem_prop] = div
context['data_display'] = 'true'
return context
def get_context_data(self, **kwargs):
context = super(MechanismListView, self).get_context_data(**kwargs)
context.update({
'filter_form': ClassficationChoiceForm,
'is_filtered': self.is_filtered,
'compound_search': BioactiveSearchForm(),
'protein_search': ProteinSearchForm(),
})
selected_mechanisms = self.request.GET.getlist('selected_mechanisms')
if selected_mechanisms:
context.update({
'choice_form': ChemDataChoiceSubmitForm,
'data_display': 'true',
})
id_list = [int(a) for a in selected_mechanisms if a]
if self.request.GET.get('mean_data'):
averages = Activity.bioactives_data_stats(id_list)
for chem_prop, val in averages.items():
plot = self.make_plot(val, chem_prop, 'mean')
if plot:
script, div = components(plot, CDN)
context['plot_script' + '_' + chem_prop] = script
context['plot_div' + '_' + chem_prop] = div
stats_arrays = Activity.bioactives_data_stats(id_list,
std_dev=True)
sds = {}
for cp in chemical_properties_label_map.keys():
sds[cp] = [(a[0], a[1][cp].std()) for a in stats_arrays]
for chem_prop, val in sds.items():
plot = self.make_plot(val, chem_prop, 'std dev in')
if plot:
script, div = components(plot, CDN)
context['sd_plot_script' + '_' + chem_prop] = script
context['sd_plot_div' + '_' + chem_prop] = div
return context
def get_context_data(self, **kwargs):
context = super(SubstructureListView, self).get_context_data(**kwargs)
context.update({
'substructure_sets': [
{
'subset': Substructure.objects.acyclic_terpenoids(),
'label': 'Acyclic Terpenoids'
},
{
'subset': Substructure.objects.cyclic_terpenoids(),
'label': 'Cyclic Terpenoids'
},
{
'subset': Substructure.objects.cycloaliphatics(),
'label': 'Cycloaliphatics'
},
{
'subset': Substructure.objects.aromatic_compounds(),
'label': 'Aromatics'
},
],
'choice_form':
ChemDataChoiceSubmitForm,
'odor_types':
OdorType.objects.values('term'),
})
if self.request.GET.get('stats_data'):
for cp in chemical_properties_label_map.keys():
plot = self.make_plot(cp)
if plot:
script, div = components(plot, CDN)
context['plot_script' + '_' + cp] = script
context['plot_div' + '_' + cp] = div
context['data_display'] = 'true'
return context
def bioactive_set_properties(self):
chem_props = {
k:
np.array([a.chemical_properties[k] for a in self.bioactives.all()])
for k in chemical_properties_label_map.keys()
}
cleaned_arrays = {
k: v[v != np.array(None)]
for k, v in chem_props.items()
}
return cleaned_arrays
def compound_sets_stats(cls, core_set):
chem_properties = chemical_properties_label_map.keys()
avg_data = {chem_prop: [] for chem_prop in chem_properties}
bioactive_properties = []
for core in core_set:
bioactive_properties.append(
(core.name, core.bioactive_set_properties))
for chem_prop in chem_properties:
avg_data[chem_prop].append(
(core.name, core.bioactives.all().chemical_property_avg(
chem_prop).get('as_float__avg')))
return avg_data, bioactive_properties
def bioactives_data_stats(cls, id_list, std_dev=False):
properties = chemical_properties_label_map.keys()
activities = cls.objects.filter(
id__in=id_list).prefetch_related('bioactives')
if std_dev:
return [(a.name, a.mechanism_bioactives_properties)
for a in activities]
data = {}
for chem_prop in properties:
average_data = [(a.name, a.bioactives.all().chemical_property_avg(
chem_prop).get('as_float__avg')) for a in activities]
data[chem_prop] = [ad for ad in average_data if ad[1]]
return data
def get_context_data(self, **kwargs):
context = super(BioactiveCoreMatchList, self).get_context_data(**kwargs)
context['page_header'] = self.bioactive_core.name
if self.bioactive_vals:
context.update({
'choice_form': ChemDataChoiceSubmitForm,
'page_title': self.bioactive_core.name,
'data_display': 'true',
'cid_numbers': [{'number': b['cid_number_2'] or b['cid_number'],
'name': b['chemical_name'][:23] + '...' if len(b['chemical_name']) > 25
else b['chemical_name'][:23] or b['iupac_name'][:32]}
for b in self.bioactive_vals],
})
properties = chemical_properties_label_map.keys()
for cp in properties:
plot = self.make_plot(cp)
script, div = components(plot, CDN)
context['plot_script' + '_' + cp] = script
context['plot_div' + '_' + cp] = div
return context