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Commit 19aa824d authored by Hervé MENAGER's avatar Hervé MENAGER
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refactor annotations to compound queryset to the model level 

this is mainly to be used in compounds list, but will ultimately be
useful everywhere


Former-commit-id: 720068133a0e7c7f5d9bd562d77467ab70d0c477
parent 74a9218e
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ippisite/ippidb/models.py
+ 19
− 21
View file @ 19aa824d
......@@ -6,8 +6,11 @@ from __future__ import unicode_literals
import operator
from django.db import models
from django.db.models import Max
from django.conf import settings
from django.db.models import Max, Min, Count, F, Q
from django.db.models.functions import Cast
from django.db.models import FloatField
from .utils import FingerPrinter, smi2inchi, smi2inchikey
from .ws import get_pubmed_info, get_google_patent_info, get_uniprot_info, get_taxonomy_info, get_go_info, get_pfam_info
......@@ -268,7 +271,22 @@ class PpiComplex(models.Model):
return 'PPI {}, Complex {} ({})'.format(self.ppi, self.complex, self.cc_nb)
class CompoundManager(models.Manager):
def get_queryset(self):
qs = super().get_queryset()
# with number of publications
qs = qs.annotate(pubs=Count('refcompoundbiblio', distinct=True))
# with best activity
qs = qs.annotate(best_activity=Max('compoundactivityresult__activity'))
# with LE
qs = qs.annotate(le=Cast(1.37 * Max('compoundactivityresult__activity') / F('nb_atom_non_h'),FloatField()))
# with LLE
qs = qs.annotate(lle=Cast(Max('compoundactivityresult__activity') - F('a_log_p'),FloatField()))
return qs
class Compound(AutoFillableModel):
objects = CompoundManager()
canonical_smile = models.TextField(
'Canonical Smile', unique=True)
is_macrocycle = models.BooleanField('Contains one or more macrocycles')
......@@ -454,26 +472,6 @@ class Compound(AutoFillableModel):
return None
return self.compoundactivityresult_set.filter(activity=best_pXC50_activity)[0]
@property
def le(self):
"""
LE: Ligand Efficiency
"""
best_pXC50_activity = self.best_pXC50_activity
if best_pXC50_activity is None:
return None
return (1.37 * float(best_pXC50_activity))/self.nb_atom_non_h
@property
def lle(self):
"""
LLE: Lipophilic Efficiency
"""
best_pXC50_activity = self.best_pXC50_activity
if best_pXC50_activity is None:
return None
return float(best_pXC50_activity - self.a_log_p)
@property
def best_pXC50_activity_ppi_name(self):
"""
......
ippisite/ippidb/templates/compound_list.html
+ 13
− 13
View file @ 19aa824d
......@@ -63,9 +63,9 @@
Activity and Efficiencies
</button>
<div class="dropdown-menu" aria-labelledby="aeMenuButton">
{% include "modal_open_button.html" with label="Best Activity" param_name="qs_ba" %}
{% include "modal_open_button.html" with label="LE" param_name="qs_le" %}
{% include "modal_open_button.html" with label="LLE" param_name="qs_lle" %}
{% include "modal_open_button.html" with label="Best Activity" param_name="best_activity" %}
{% include "modal_open_button.html" with label="LE" param_name="le" %}
{% include "modal_open_button.html" with label="LLE" param_name="lle" %}
</div>
</div>
<div class="dropdown btn-group" style="display: inline-flex;">
......@@ -125,7 +125,7 @@
<div class="m-2 d-flex justify-content-between">
<span>{{ paginator.count }} compounds</span>
{% if selected_family or selected_ppi or selected_disease or selected_taxonomy or selected_boundcomplex or molecular_weight or a_log_p or nb_donor_h or nb_acceptor_h or tpsa or nb_rotatable_bonds or nb_aromatic_sssr or nb_chiral_centers or fsp3 or pubs or similar_to or qs_ba or qs_le or qs_lle %}
{% if selected_family or selected_ppi or selected_disease or selected_taxonomy or selected_boundcomplex or molecular_weight or a_log_p or nb_donor_h or nb_acceptor_h or tpsa or nb_rotatable_bonds or nb_aromatic_sssr or nb_chiral_centers or fsp3 or pubs or similar_to or best_activity or le or lle %}
<span>
&nbsp;-&nbsp;filters:&nbsp;
{% if selected_family %}
......@@ -183,14 +183,14 @@
{% if similar_to %}
{% include "similarity_badge.html" with param_name="similar_to" param_value=similar_to_query param_label="Similar to " %}
{% endif %}
{% if qs_ba %}
{% include "slider_badge.html" with param_name="qs_ba" param_value_min=qs_ba_value_min param_value_max=qs_ba_value_max param_label="Best Act." %}
{% if best_activity %}
{% include "slider_badge.html" with param_name="best_activity" param_value_min=best_activity_value_min param_value_max=best_activity_value_max param_label="Best Act." %}
{% endif %}
{% if qs_le %}
{% include "slider_badge.html" with param_name="qs_le" param_value_min=qs_le_value_min param_value_max=qs_le_value_max param_label="LE" %}
{% if le %}
{% include "slider_badge.html" with param_name="le" param_value_min=le_value_min param_value_max=le_value_max param_label="LE" %}
{% endif %}
{% if qs_lle %}
{% include "slider_badge.html" with param_name="qs_lle" param_value_min=qs_lle_value_min param_value_max=qs_lle_value_max param_label="LLE" %}
{% if lle %}
{% include "slider_badge.html" with param_name="lle" param_value_min=lle_value_min param_value_max=lle_value_max param_label="LLE" %}
{% endif %}
</span>
{% endif %}
......@@ -261,8 +261,8 @@
{% include "slider_modal.html" with label="FSP3" param_name="fsp3" param_min=fsp3_min param_max=fsp3_max param_value=fsp3 param_value_min=fsp3_value_min param_value_max=fsp3_value_max step='0.1' param_label='Select a cutoff value for the FSP3 of the compounds to be selected'%}
{% include "slider_modal.html" with label="Publications" param_name="pubs" param_min=pubs_min param_max=pubs_max param_value=pubs param_value_min=pubs_value_min param_value_max=pubs_value_max step='1' param_label='Select a cutoff value for the number of publications mentioning the compounds to be selected'%}
{% include "marvinjs_modal.html" with smiles=similar_to_query fingerprint=similar_to_fingerprint %}
{% include "slider_modal.html" with label="Best Activiry" param_name="qs_ba" param_min=qs_ba_min param_max=qs_ba_max param_value=qs_ba param_value_min=qs_ba_value_min param_value_max=qs_ba_value_max step='1' param_label='Select a cutoff value for the best activity of the compounds to be selected'%}
{% include "slider_modal.html" with label="LE" param_name="qs_le" param_min=qs_le_min param_max=qs_le_max param_value=qs_le param_value_min=qs_le_value_min param_value_max=qs_le_value_max step='0.1' param_label='Select a cutoff value for the LE of the compounds to be selected'%}
{% include "slider_modal.html" with label="LLE" param_name="qs_lle" param_min=qs_lle_min param_max=qs_lle_max param_value=qs_lle param_value_min=qs_lle_value_min param_value_max=qs_lle_value_max step='1' param_label='Select a cutoff value for the LLE of the compounds to be selected'%}
{% include "slider_modal.html" with label="Best Activiry" param_name="best_activity" param_min=best_activity_min param_max=best_activity_max param_value=best_activity param_value_min=best_activity_value_min param_value_max=best_activity_value_max step='1' param_label='Select a cutoff value for the best activity of the compounds to be selected'%}
{% include "slider_modal.html" with label="LE" param_name="le" param_min=le_min param_max=le_max param_value=le param_value_min=le_value_min param_value_max=le_value_max step='0.1' param_label='Select a cutoff value for the LE of the compounds to be selected'%}
{% include "slider_modal.html" with label="LLE" param_name="lle" param_min=lle_min param_max=lle_max param_value=lle param_value_min=lle_value_min param_value_max=lle_value_max step='1' param_label='Select a cutoff value for the LLE of the compounds to be selected'%}
{% endblock %}
ippisite/ippidb/templates/compound_t_list.html
+ 4
− 4
View file @ 19aa824d
......@@ -20,7 +20,7 @@
{% include "compound_t_colhead.html" with col_id="nb_chiral_centers" col_name="R/S" col_title="Number of chiral centers" %}
{% include "compound_t_colhead.html" with col_id="le" col_name="LE" col_title="Ligand Efficiency" %}
{% include "compound_t_colhead.html" with col_id="lle" col_name="LLE" col_title="Lipophilic Efficiency" %}
{% include "compound_t_colhead.html" with col_id="qs_ba" col_name="Best Activity" col_title="Best pXC50 Activity" %}
{% include "compound_t_colhead.html" with col_id="best_activity" col_name="Best Activity" col_title="Best pXC50 Activity" %}
<button type="button" class="btn btn-primary float-right" style="width: inherit!important" data-toggle="modal" data-target="#selectColumns">
<i class="fa fa-columns" title="customize columns"></i>
</button>
......@@ -84,8 +84,8 @@
{% if "lle" in fields %}
<td scope="col">{{ compound.lle|floatformat:2 }}</td>
{% endif %}
{% if "qs_ba" in fields %}
<td scope="col">{{ compound.qs_ba|floatformat:2 }}</td>
{% if "best_activity" in fields %}
<td scope="col">{{ compound.best_activity|floatformat:2 }}</td>
{% endif %}
</tr>
{% endfor %}
......@@ -155,7 +155,7 @@
<label><input type="checkbox" name="field" value="lle" class="mr-1" {% if 'lle' in fields %}checked="checked"{% endif %} />Lipophilic Efficiency</label>
</div>
<div class="row">
<label><input type="checkbox" name="field" value="qs_ba" class="mr-1" {% if 'qs_ba' in fields %}checked="checked"{% endif %} />Best pXC50 Activity</label>
<label><input type="checkbox" name="field" value="best_activity" class="mr-1" {% if 'best_activity' in fields %}checked="checked"{% endif %} />Best pXC50 Activity</label>
</div>
</div>
<div class="modal-footer">
......
ippisite/ippidb/views.py
+ 7
− 29
View file @ 19aa824d
......@@ -279,19 +279,6 @@ class CompoundRangeFilterHandler(object):
queryset = queryset.filter(**filter_dict)
# max and min value are the max and min for
qs = Compound.objects
# annotate
# with number of publications
if self.parameter_name == 'pubs':
qs = qs.annotate(pubs=Count('refcompoundbiblio', distinct=True))
# with best activity
elif self.parameter_name == 'qs_ba':
qs = qs.annotate(qs_ba=Max('compoundactivityresult__activity'))
# with LE
elif self.parameter_name == 'qs_le':
qs = qs.annotate(qs_le=Cast(1.37 * Max('compoundactivityresult__activity') / F('nb_atom_non_h'),FloatField()))
# with LLE
elif self.parameter_name == 'qs_lle':
qs = qs.annotate(qs_lle=Cast(Max('compoundactivityresult__activity') - F('a_log_p'),FloatField()))
self.filter_context[self.parameter_name+'_max'] = self.get_max(qs)
self.filter_context[self.parameter_name+'_min'] = self.get_min(qs)
return queryset
......@@ -344,7 +331,7 @@ class CompoundListView(ListView):
table_view_default_fields = ['id', 'canonical_smiles', 'common_name', 'molecular_weight', 'a_log_p', 'compound_action_ligand_ids', 'pubs']
sort_by_option_ids = ['id', 'molecular_weight', 'a_log_p', 'nb_aromatic_sssr', 'nb_chiral_centers', 'pubs', 'qs_le', 'qs_lle', 'qs_ba']
sort_by_option_ids = ['id', 'molecular_weight', 'a_log_p', 'nb_aromatic_sssr', 'nb_chiral_centers', 'pubs', 'le', 'lle', 'best_activity']
def get_ordering(self):
# sort by options
......@@ -353,11 +340,11 @@ class CompoundListView(ListView):
for sort_by_option_id in self.sort_by_option_ids:
if sort_by_option_id == 'pubs':
name = 'Number of publications'
elif sort_by_option_id == 'qs_le':
elif sort_by_option_id == 'le':
name = 'Ligand Efficiency'
elif sort_by_option_id == 'qs_lle':
elif sort_by_option_id == 'lle':
name = 'Lipophilic Efficiency'
elif sort_by_option_id == 'qs_ba':
elif sort_by_option_id == 'best_activity':
name = 'Best Activity'
else:
name = compound_fields.get(sort_by_option_id)
......@@ -397,15 +384,6 @@ class CompoundListView(ListView):
self.filter_context = {}
# get queryset
qs = super().get_queryset()
# annotate
# with number of publications
qs = qs.annotate(pubs=Count('refcompoundbiblio', distinct=True))
# with best activity
qs = qs.annotate(qs_ba=Max('compoundactivityresult__activity'))
# with LE
qs = qs.annotate(qs_le=Cast(1.37 * Max('compoundactivityresult__activity') / F('nb_atom_non_h'),FloatField()))
# with LLE
qs = qs.annotate(qs_lle=Cast(Max('compoundactivityresult__activity') - F('a_log_p'),FloatField()))
# add filters
cfhs = [\
CompoundListFilterHandler(PpiFamily, 'compoundaction__ppi__family', 'ppi__compoundaction__compound', 'family', self.filter_context, self.request.GET),
......@@ -423,9 +401,9 @@ class CompoundListView(ListView):
CompoundRangeFilterHandler('nb_chiral_centers', self.filter_context, self.request.GET),
CompoundRangeFilterHandler('fsp3', self.filter_context, self.request.GET, 0.1),
CompoundRangeFilterHandler('pubs', self.filter_context, self.request.GET),
CompoundRangeFilterHandler('qs_ba', self.filter_context, self.request.GET),
CompoundRangeFilterHandler('qs_le', self.filter_context, self.request.GET, 0.1),
CompoundRangeFilterHandler('qs_lle', self.filter_context, self.request.GET),
CompoundRangeFilterHandler('best_activity', self.filter_context, self.request.GET),
CompoundRangeFilterHandler('le', self.filter_context, self.request.GET, 0.1),
CompoundRangeFilterHandler('lle', self.filter_context, self.request.GET),
ExistsFilterHandler('pubchem_id', self.filter_context, self.request.GET),
ExistsFilterHandler('chemspider_id', self.filter_context, self.request.GET),
ExistsFilterHandler('chembl_id', self.filter_context, self.request.GET),
......
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