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Commit 2b89ddbf authored by Rachel TORCHET's avatar Rachel TORCHET
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Merge branch 'master' of https://gitlab.pasteur.fr/hub/iPPIDB 

Former-commit-id: 3314235576b8b3cfa09dbc512c54e0bc6b65e8c1
parents 75776fb6 a663f6d5
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ippisite/ippidb/management/commands/lle_le.py 0 → 100644
+ 17
− 0
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import glob
from django.utils import timezone
from django.core.management import BaseCommand, CommandError
from ippidb.models import Compound
class Command(BaseCommand):
help = "Generate the data for the compound LE vs LLE biplot"
def handle(self, *args, **options):
self.stdout.write(self.style.SUCCESS('Generating the LE vs. LLE biplot...'))
df = Compound.objects.all().to_dataframe()
df['le']=df[
print(df.to_csv())
print(df.columns)
ippisite/ippidb/models.py
+ 56
− 0
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from __future__ import unicode_literals
from django.db import models
from django_pandas.managers import DataFrameManager
from .ws import get_pubmed_info, get_epo_info, get_uniprot_info, get_taxonomy_info, get_go_info, get_pfam_info
......@@ -321,6 +322,8 @@ class Compound(models.Model):
mddr_compound = models.ForeignKey(
'MDDRCompoundImport', models.CASCADE, blank=True, null=True)
objects = DataFrameManager()
@property
def biblio_refs(self):
"""
......@@ -351,6 +354,59 @@ class Compound(models.Model):
pdb_ids.add(ca.pdb_id)
return pdb_ids
@property
def hba_hbd(self):
return self.nb_acceptor_h + self.nb_donor_h
@property
def lipinsky_mw(self):
return self.molecular_weight <= 500
@property
def lipinsky_hba(self):
return self.nb_acceptor_h <= 10
@property
def lipinsky_hbd(self):
return self.nb_donor_h <= 5
@property
def lipinsky_a_log_p(self):
return self.a_log_p <= 5
@property
def lipinsky_global(self):
return int(self.lipinsky_mw) + int(self.lipinsky_hba) + \
int(self.lipinsky_hbd) + int(self.lipinsky_a_log_p) >= 3
@property
def veber_hba_hbd(self):
return self.nb_acceptor_h + self.nb_donor_h <= 12
@property
def veber_tpsa(self):
return self.tpsa <= 140
@property
def veber_rb(self):
return self.nb_rotatable_bonds <= 10
@property
def veber_global(self):
return self.veber_rb and (self.veber_hba_hbd or self.veber_tpsa)
@property
def pfizer_a_log_p(self):
return self.a_log_p <= 3
@property
def pfizer_tpsa(self):
return self.tpsa >= 75
@property
def pfizer_global(self):
return self.pfizer_a_log_p and self.pfizer_tpsa
class MDDRActivityClass(models.Model):
name = models.CharField('Activity Class', max_length=100, unique=True)
......
ippisite/ippidb/static/chartjs/Chart.bundle.js 0 → 100644
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ippisite/ippidb/templates/base.html
+ 31
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......@@ -10,9 +10,10 @@
<link rel="stylesheet" href="/static/css/ippidb-typeahead.css">
<script src="/static/jquery/jquery-3.3.1.min.js"></script>
<script src="/static/bootstrap/js/bootstrap.min.js"></script>
<script src="/static/bootstrap/js/bootstrap.bundle.min.js"></script>
<script src="/static/typeahead/typeahead.bundle.min.js"></script>
<script defer src="/static/font-awesome/js/fontawesome-all.min.js"></script>
<script src="/static/chartjs/Chart.bundle.js"></script>
<script src="/static/js/ippidb.js" type="text/javascript"></script>
......@@ -63,6 +64,35 @@
});
$('#'+idSearch).on('typeahead:select', onSelect);
};
var drawCompoundDescriptorRadarChart = function(canvasId, mw, alogP, hbd, hba, tpsa, rb, ar, fsp3, rs){
var radarChartData = {
"labels":["MW","ALogP","HBD","HBA","TPSA","RB","Ar","Fsp3","R/S"],
"datasets":[
{"label":"Descriptor's threshold",
"data":[500/1200,(5+3)/15,5/15,10/15,140/250,10/20,4/10,1-(0.4/1),1-(1/10)],
"fill":true,
"backgroundColor":"rgba(54, 162, 235, 0.2)",
"borderColor":"rgb(54, 162, 235)",
"pointBackgroundColor":"rgb(54, 162, 235)",
"pointBorderColor":"#fff",
"pointHoverBackgroundColor":"#fff",
"pointHoverBorderColor":"rgb(54, 162, 235)"},
{"label":"Descriptor's value for the compound",
"data":[mw/1200,(alogP+3)/15,hbd/15,hba/15,tpsa/250,rb/20,ar/10,1-(fsp3/1),1-(rs/10)],
"fill":true,
"backgroundColor":"rgba(255, 99, 132, 0.2)",
"borderColor":"rgb(255, 99, 132)",
"pointBackgroundColor":"rgb(255, 99, 132)",
"pointBorderColor":"#fff",
"pointHoverBackgroundColor":"#fff",
"pointHoverBorderColor":"rgb(255, 99, 132)"}],
"options":{"elements":{"line":{"tension":0,"borderWidth":3}}}
};
var myRadar = new Chart(document.getElementById(canvasId).getContext("2d"),
{type: 'radar',
data: radarChartData,
options: { scaleLineWidth : 1, pointLabelFontFamily : "'Helvetica Neue'", pointLabelFontSize : 12, scaleOverride : true, scaleSteps : 5, scaleStepWidth : 0.2}});
};
</script>
</head>
......
ippisite/ippidb/templates/compound_card.html
+ 86
− 26
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......@@ -5,19 +5,15 @@
{% block content %}
{% include "kekule_display.html" %}
<div id="mainnav">
</div>
<div class="inner-wrap">
<div id="main-wrapper" class="page">
<div id="main">
<div id="content" class="main-content">
<main role="main">
<div class="row">
<div class="container-fluid">
<div class="row flex-xl-nowrap">
<div class="col-3">
<div class="nav flex-column nav-pills" id="v-pills-tab" role="tablist">
<a class="nav-link active" id="v-pills-compound-tab" data-toggle="pill" href="#v-pills-compound" role="tab" aria-controls="v-pills-compound" aria-expanded="true">Compound</a>
<a class="nav-link" id="v-pills-physicochemistry-tab" data-toggle="pill" href="#v-pills-physicochemistry" role="tab" aria-controls="v-pills-physicochemistry" aria-expanded="true">Physicochemistry</a>
<a class="nav-link" id="v-pills-pharmacology-tab" data-toggle="pill" href="#v-pills-pharmacology" role="tab" aria-controls="v-pills-pharmacology" aria-expanded="true">Pharmocology</a>
<a class="nav-link" id="v-pills-pharmacokinetics-tab" data-toggle="pill" href="#v-pills-pharmacokinetics" role="tab" aria-controls="v-pills-pharmacokinetics" aria-expanded="true">Pharmacokinetics</a>
<a class="nav-link" id="v-pills-drugsimilarity-tab" data-toggle="pill" href="#v-pills-drugsimilarity" role="tab" aria-controls="v-pills-drugsimilarity" aria-expanded="true">Drug similarity</a>
</div>
</div>
<div class="col-9">
......@@ -26,18 +22,6 @@
<div class="card">
<div class="card-body">
{% include "pubchem_img.html" %}
<!--
<div id="{{ compound.id }}_smilesdisplay"
data-widget="Kekule.ChemWidget.Viewer2D" data-auto-size="true" data-padding="20"
data-toolbar-evoke-modes="[0]">
</div>
<textarea rows="10" cols="50" id="{{ compound.id }}_smilesvalue" style="display:none;">{{ compound.canonical_smile }}</textarea>
<script>
$(window).on('load', function(){
kekule_display('{{ compound.id }}_smilesvalue','{{ compound.id }}_smilesdisplay')
});
</script>
-->
<ul class="list-group">
<li class="list-group-item">Common name: {{ compound.common_name }}</li>
<li class="list-group-item">Canonical SMILES: {{ compound.canonical_smile }}</li>
......@@ -89,16 +73,92 @@
</div>
</div>
</div>
<div class="tab-pane fade" id="v-pills-physicochemistry" role="tabpanel" aria-labelledby="v-pills-physicochemistry-tab">
<div class="row">
<div class="card col-sm-12 col-md-6">
<h5 class="card-header">Physicochemical filters</h5>
<div class="card-body">
<table class="table table-sm col-sm-12 col-md-6">
<thead>
<tr>
<th class="col-sm-3" scope="col">Descriptor</th>
<th class="col-sm-3" scope="col">Lipinski's RO5</th>
<th class="col-sm-3" scope="col">Veber</th>
<th class="col-sm-3" scope="col">Pfizer's 3/75</th>
</tr>
</thead>
<tbody>
<tr>
<th scope="row">Global</th>
<td class="{% if compound.lipinsky_global %}bg-success{% else %}bg-danger{% endif %}"></td>
<td class="{% if compound.veber_global %}bg-success{% else %}bg-danger{% endif %}"></td>
<td class="{% if compound.pfizer_global %}bg-success{% else %}bg-danger{% endif %}"></td>
</tr>
<tr>
<th scope="row">MW</th>
<td class="{% if compound.lipinsky_mw %}bg-success{% else %}bg-danger{% endif %}" title="Molecular weight <= 500g/mol">{{ compound.molecular_weight }}g/mol</td>
<td class="bg-light"></td>
<td class="bg-light"></td>
</tr>
<tr>
<th scope="row">HBA</th>
<td class="{% if compound.lipinsky_hba %}bg-success{% else %}bg-danger{% endif %}" title="HBA <= 10">{{ compound.nb_acceptor_h }}</td>
<td class="bg-light"></td>
<td class="bg-light"></td>
</tr>
<tr>
<th scope="row">HBD</th>
<td class="{% if compound.lipinsky_hbd %}bg-success{% else %}bg-danger{% endif %}" title="HBD <= 5">{{ compound.nb_donor_h }}</td>
<td class="bg-light"></td>
<td class="bg-light"></td>
</tr>
<tr>
<th scope="row">HBA + HBD</th>
<td class="bg-light"></td>
<td class="{% if compound.veber_hba_hbd %}bg-success{% else %}bg-danger{% endif %}" title="HBD + HBA <= 12">{{ compound.hba_hbd }}</td>
<td class="bg-light"></td>
</tr>
<tr>
<th scope="row">AlogP</th>
<td class="{% if compound.lipinsky_a_log_p %}bg-success{% else %}bg-danger{% endif %}" title="AlogP <= 5">{{ compound.a_log_p }}</td>
<td class="bg-light"></td>
<td class="{% if compound.pfizer_a_log_p %}bg-success{% else %}bg-danger{% endif %}" title="AlogP <= 3">{{ compound.a_log_p }}</td>
</tr>
<tr>
<th scope="row">TPSA</th>
<td class="bg-light"></td>
<td class="{% if compound.veber_tpsa %}bg-success{% else %}bg-danger{% endif %}" title="TPSA <= 140">{{ compound.tpsa }}</td>
<td class="{% if compound.pfizer_tpsa %}bg-success{% else %}bg-danger{% endif %}" title="TPSA <= 75">{{ compound.tpsa }}</td>
</tr>
<tr>
<th scope="row">RB</th>
<td class="bg-light"></td>
<td class="{% if compound.veber_rb %}bg-success{% else %}bg-danger{% endif %}" title="RB <= 10">{{ compound.nb_rotatable_bonds }}</td>
<td class="bg-light"></td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="card col-sm-12 col-md-6">
<h5 class="card-header">Radar chart</h5>
<div class="card-body">
<canvas id="radar"></canvas>
<script>
drawCompoundDescriptorRadarChart('radar', {{ compound.molecular_weight }}, {{ compound.a_log_p }}, {{ compound.nb_donor_h }}, {{ compound.nb_acceptor_h }}, {{ compound.tpsa }}, {{ compound.nb_rotatable_bonds }}, {{ compound.nb_benzene_like_rings }}, {{ compound.fsp3 }}, {{ compound.nb_chiral_centers }});
</script>
</div>
</div>
</div>
</div>
<div class="tab-pane fade" id="v-pills-pharmacology" role="tabpanel" aria-labelledby="v-pills-pharmacology-tab">
</div>
<div class="tab-pane fade" id="v-pills-pharmacokinetics" role="tabpanel" aria-labelledby="v-pills-pharmacokinetics-tab">
<div class="tab-pane fade" id="v-pills-drugsimilarity" role="tabpanel" aria-labelledby="v-pills-drugsimilarity-tab">
</div>
</div>
</div>
</div>
</main><!-- .site-main -->
</div>
</div><!-- div main -->
</div>
</div>
{% endblock %}
ippisite/requirements.txt
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Django==1.11
django-bootstrap3
django-pandas
bioservices
#typing
django-extensions>=2.0.5
......
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