diff --git a/ippisite/ippidb/templates/compound_abstract.html b/ippisite/ippidb/templates/compound_abstract.html
index 82110001a00658878fafadbe3f30d18222c1425d..f089776fc0f4de43be590f7ad15e73614f710702 100644
--- a/ippisite/ippidb/templates/compound_abstract.html
+++ b/ippisite/ippidb/templates/compound_abstract.html
@@ -1,6 +1,6 @@
<div class="row m-2 border border-info bg-light">
<div class="col-sm-3 border-info d-flex justify-content-center align-content-center">
- <img src="https://pubchem.ncbi.nlm.nih.gov/image/imagefly.cgi?cid={{ compound.pubchem_id }}&width=300&height=300" style="width:300px;height:300px;"/>
+ <a href="/compound/{{ compound.id }}">{% include "pubchem_img.html" %}</a>
</div>
<div class="col-sm-9">
<ul class="list-group">
@@ -20,19 +20,6 @@
<li class="list-group-item">Mentionned in {% include "biblio_citation.html" with bibliography=biblio_ref.bibliography%} as <i>{{ biblio_ref.compound_name }}</i></li>
{% endfor %}
</ul>
- {%if compound.pubchem_id or compound.chembl_id or compound.chemspider_id %}
- <p>in other databases</p>
- <ul class="list-group">
- {% if compound.pubchem_id %}
- <li class="list-group-item">PubChem: <a href="https://pubchem.ncbi.nlm.nih.gov/compound/{{ compound.pubchem_id }}" target="_blank">{{ compound.pubchem_id }}</a></li>
- {% endif %}
- {% if compound.chembl_id %}
- <li class="list-group-item">ChEMBL: <a href="https://www.ebi.ac.uk/chembldb/compound/inspect/{{ compound.chembl_id}}" target="_blank">{{ compound.chembl_id}}</a></li>
- {% endif %}
- {% if compound.chemspider_id %}
- <li class="list-group-item">ChemSpider: <a href="http://www.chemspider.com/Chemical-Structure.{{ compound.chemspider_id}}.html" target="_blank">{{ compound.chemspider_id}}</a></li>
- {% endif %}
- </ul>
- {% endif %}
+ {% include "compound_db_links.html" %}
</div>
</div>
diff --git a/ippisite/ippidb/templates/compound_card.html b/ippisite/ippidb/templates/compound_card.html
new file mode 100644
index 0000000000000000000000000000000000000000..6b0927267ded840994071464337e93c3343e353c
--- /dev/null
+++ b/ippisite/ippidb/templates/compound_card.html
@@ -0,0 +1,104 @@
+{% extends "base.html" %}
+
+
+{% block title %}compound detail{% endblock %}
+
+{% 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="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-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>
+ </div>
+ </div>
+ <div class="col-9">
+ <div class="tab-content" id="v-pills-tabContent">
+ <div class="tab-pane fade show active" id="v-pills-compound" role="tabpanel" aria-labelledby="v-pills-compound-tab">
+ <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>
+ <li class="list-group-item">IUPAC name: {{ compound.iupac_name }}</li>
+ <li class="list-group-item">Aromatic ratio: {{ compound.aromatic_ratio }}</li>
+ <li class="list-group-item">Balaban index: {{ compound.balaban_index }}</li>
+ <li class="list-group-item">Fsp3: {{ compound.fsp3 }}</li>
+ <li class="list-group-item">GC molar refractivity: {{ compound.gc_molar_refractivity }}</li>
+ <li class="list-group-item" title="Partition coefficient octanol-1/water, with pKa information">LogD: {{ compound.log_d }}</li>
+ <li class="list-group-item" title="Partition coefficient octanol-1/water">ALogP: {{ compound.a_log_p }}</li>
+ <li class="list-group-item" title="computed with VdW radii">Mean atom volume: {{ compound.mean_atom_vol_vdw }}</li>
+ <li class="list-group-item">Molecular weight: {{ compound.molecular_weight }}</li>
+ <li class="list-group-item">Number of hydrogen bond acceptors: {{ compound.nb_acceptor_h }}</li>
+ <li class="list-group-item">Number of aliphatics amines: {{ compound.nb_aliphatic_amines }}</li>
+ <li class="list-group-item">Number of aromatic bonds: {{ compound.nb_aromatic_bonds }}</li>
+ <li class="list-group-item">Number of aromatic ethers: {{ compound.nb_aromatic_ether }}</li>
+ <li class="list-group-item" title="Smallest Set of System Rings">Number of aromatic SSSRs: {{ compound.nb_aromatic_sssr }}</li>
+ <li class="list-group-item">Number of atoms: {{ compound.nb_atom }}</li>
+ <li class="list-group-item">Number of non hydrogen atoms: {{ compound.nb_atom_non_h }}</li>
+ <li class="list-group-item">Number of benzene-like rings: {{ compound.nb_benzene_like_rings }}</li>
+ <li class="list-group-item">Number of bonds: {{ compound.nb_bonds }}</li>
+ <li class="list-group-item">Number of bonds not involving a hydrogen: {{ compound.nb_bonds_non_h }}</li>
+ <li class="list-group-item">Number of Bromine atoms: {{ compound.nb_br }}</li>
+ <li class="list-group-item">Number of Carbon atoms: {{ compound.nb_c }}</li>
+ <li class="list-group-item">Number of chiral centers: {{ compound.nb_chiral_centers }}</li>
+ <li class="list-group-item">Number of circuits: {{ compound.nb_circuits }}</li>
+ <li class="list-group-item">Number of Chlorine atoms: {{ compound.nb_cl }}</li>
+ <li class="list-group-item">Number of sp2-hybridized carbon atoms: {{ compound.nb_csp2 }}</li>
+ <li class="list-group-item">Number of sp3-hybridized carbon atoms: {{ compound.nb_csp3 }}</li>
+ <li class="list-group-item">Number of hydrogen bond donors: {{ compound.nb_donor_h }}</li>
+ <li class="list-group-item">Number of double bonds: {{ compound.nb_double_bonds }}</li>
+ <li class="list-group-item">Number of Fluorine atoms: {{ compound.nb_f }}</li>
+ <li class="list-group-item">Number of Iodine atoms: {{ compound.nb_i }}</li>
+ <li class="list-group-item">Number of multiple bonds: {{ compound.nb_multiple_bonds }}</li>
+ <li class="list-group-item">Number of Nitrogen atoms: {{ compound.nb_n }}</li>
+ <li class="list-group-item">Number of Oxygen atoms: {{ compound.nb_o }}</li>
+ <li class="list-group-item">Number of rings: {{ compound.nb_rings }}</li>
+ <li class="list-group-item">Number of rotatable bonds: {{ compound.nb_rotatable_bonds }}</li>
+ <li class="list-group-item">Randic index: {{ compound.randic_index }}</li>
+ <li class="list-group-item" title="radial distribution function weighted by the atomic masses at 7Ã…">RDF070m: {{ compound.rdf070m }}</li>
+ <li class="list-group-item">Fraction of rotatable bonds: {{ compound.rotatable_bond_fraction }}</li>
+ <li class="list-group-item">Sum of atomic polarizabilities: {{ compound.sum_atom_polar }}</li>
+ <li class="list-group-item">Sum of atom volumes computed with VdW radii: {{ compound.sum_atom_vol_vdw }}</li>
+ <li class="list-group-item" title="Topological Polar Surface Area">TPSA: {{ compound.tpsa }}</li>
+ <li class="list-group-item">Unsaturation index: {{ compound.ui }}</li>
+ <li class="list-group-item">Wiener index: {{ compound.wiener_index }}</li>
+ </ul>
+ {% include "compound_db_links.html" %}
+ </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>
+ </div>
+ </div>
+ </div>
+ </main><!-- .site-main -->
+ </div>
+ </div><!-- div main -->
+ </div>
+</div>
+{% endblock %}
diff --git a/ippisite/ippidb/templates/compound_db_links.html b/ippisite/ippidb/templates/compound_db_links.html
new file mode 100644
index 0000000000000000000000000000000000000000..0a59ecb0487e718ee6dfa2f63d4ab5c5362eb2fe
--- /dev/null
+++ b/ippisite/ippidb/templates/compound_db_links.html
@@ -0,0 +1,14 @@
+ {%if compound.pubchem_id or compound.chembl_id or compound.chemspider_id %}
+ <p>in other databases</p>
+ <ul class="list-group">
+ {% if compound.pubchem_id %}
+ <li class="list-group-item">PubChem: <a href="https://pubchem.ncbi.nlm.nih.gov/compound/{{ compound.pubchem_id }}" target="_blank">{{ compound.pubchem_id }}</a></li>
+ {% endif %}
+ {% if compound.chembl_id %}
+ <li class="list-group-item">ChEMBL: <a href="https://www.ebi.ac.uk/chembldb/compound/inspect/{{ compound.chembl_id}}" target="_blank">{{ compound.chembl_id}}</a></li>
+ {% endif %}
+ {% if compound.chemspider_id %}
+ <li class="list-group-item">ChemSpider: <a href="http://www.chemspider.com/Chemical-Structure.{{ compound.chemspider_id}}.html" target="_blank">{{ compound.chemspider_id}}</a></li>
+ {% endif %}
+ </ul>
+ {% endif %}
diff --git a/ippisite/ippidb/templates/compound_list.html b/ippisite/ippidb/templates/compound_list.html
index 07d0e1f0bca3308248aac1b32b65982841e1f757..5139a4126f68d40f93096fdc9ece7add33ecaebf 100644
--- a/ippisite/ippidb/templates/compound_list.html
+++ b/ippisite/ippidb/templates/compound_list.html
@@ -73,6 +73,25 @@
</div>
{% endfor %}
</fieldset>
+ <fieldset class="form-group row border border-info m-2">
+ <div class="bg-info col-12"><legend>Organism</legend></div>
+ {% for taxonomy in selected_taxonomies %}
+ <div class="form-check col-12">
+ <label class="form-check-label">
+ <input class="form-check-input text-right" type="checkbox" checked value="{{ taxonomy.id }}" onchange="this.form.submit()" name="taxonomy" style="width: auto; margin-right: 1em;">
+ {{ taxonomy.name }}
+ </label>
+ </div>
+ {% endfor %}
+ {% for taxonomy in taxonomies|slice:":5" %}
+ <div class="form-check col-12">
+ <label class="form-check-label">
+ <input class="form-check-input text-right" type="checkbox" value="{{ taxonomy.id }}" onchange="this.form.submit()" name="taxonomy" style="width: auto; margin-right: 1em;">
+ {{ taxonomy.name }}
+ </label>
+ </div>
+ {% endfor %}
+ </fieldset>
</form>
</div>
<main class="col-12 col-md-9 col-xl-10 pl-md-5 bd-content" role="main">
diff --git a/ippisite/ippidb/templates/pubchem_img.html b/ippisite/ippidb/templates/pubchem_img.html
new file mode 100644
index 0000000000000000000000000000000000000000..ac4019068fde60ffde98f8ef48db9b9bcca64b7e
--- /dev/null
+++ b/ippisite/ippidb/templates/pubchem_img.html
@@ -0,0 +1 @@
+<img src="https://pubchem.ncbi.nlm.nih.gov/image/imagefly.cgi?cid={{ compound.pubchem_id }}&width=300&height=300" style="width:300px;height:300px;"/>
diff --git a/ippisite/ippidb/urls.py b/ippisite/ippidb/urls.py
index 5c1215153fb21041bf994d6e7f3ef5a38294ae18..e656cf7f5604fba3afa5439d5f39d66923e7662d 100644
--- a/ippisite/ippidb/urls.py
+++ b/ippisite/ippidb/urls.py
@@ -22,6 +22,7 @@ urlpatterns = [
url(r'^biblio/(?P<source>\w{2})(?P<id_source>\w+)$', views.biblio_card, name='biblio_card'),
url(r'^biblio/$', views.biblio_list, name='biblio_list'),
url(r'^compound/$', views.compound_list, name='compound_list'),
+ url(r'^compound/(?P<compound_id>\w+)$', views.compound_card, name='compound_card'),
url(r'^tutorials$', views.tutorials, name='tutorials'),
url(r'^admin-session$', views.adminSession, name='admin-session'),
url(r'^admin-session/add/(?P<step>.+)/$',
diff --git a/ippisite/ippidb/views.py b/ippisite/ippidb/views.py
index 987f3472ac40b8d13a8794e5d75a719c3a8530bc..e229aeabc55d93e5ce1726e8993a50ca547efcce 100644
--- a/ippisite/ippidb/views.py
+++ b/ippisite/ippidb/views.py
@@ -5,7 +5,7 @@ from django.http import HttpResponseRedirect, Http404
from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
from formtools.wizard.views import SessionWizardView, NamedUrlSessionWizardView
from .forms import IdForm, BibliographyForm, PDBForm, ProteinForm, ProteinDomainComplexTypeForm, ProteinDomainComplexForm, PpiForm, PpiComplexForm, ProteinFormSet,ActivityForm, CompoundForm, CompoundFormSet
-from .models import Protein, Bibliography, ProteinDomainComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi, Disease
+from .models import Protein, Bibliography, ProteinDomainComplex, RefCompoundBiblio, TestActivityDescription, Compound, Ppi, Disease, Taxonomy
from .ws import get_pdb_uniprot_mapping
@@ -199,6 +199,8 @@ def compound_list(request):
ppis = Ppi.objects.exclude(id__in=request.GET.getlist('ppi'))
selected_diseases = Disease.objects.filter(id__in=request.GET.getlist('disease'))
diseases = Disease.objects.exclude(id__in=request.GET.getlist('disease'))
+ selected_taxonomies = Taxonomy.objects.filter(id__in=request.GET.getlist('taxonomy'))
+ taxonomies = Taxonomy.objects.exclude(id__in=request.GET.getlist('taxonomy'))
# handle pagination in compounds list
paginator = Paginator(compounds, 5)
page = request.GET.get('page')
@@ -214,4 +216,13 @@ def compound_list(request):
'selected_ppis': selected_ppis,
'ppis': ppis,
'selected_diseases': selected_diseases,
- 'diseases': diseases})
+ 'diseases': diseases,
+ 'selected_taxonomies': selected_taxonomies,
+ 'taxonomies': taxonomies})
+
+def compound_card(request, compound_id):
+ try:
+ compound = Compound.objects.get(id=int(compound_id))
+ except Compound.DoesNotExist:
+ raise Http404("No compound data for %s:%s" % (compound_id))
+ return render(request, 'compound_card.html', {'compound': compound})