diff --git a/ippisite/ippidb/templates/about-general.html b/ippisite/ippidb/templates/about-general.html
new file mode 100644
index 0000000000000000000000000000000000000000..1877a5f811ffcc4abf15c69c51a268fa3cc41371
--- /dev/null
+++ b/ippisite/ippidb/templates/about-general.html
@@ -0,0 +1,18 @@
+{% extends "about.html" %}
+
+{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
+
+{% block pagetitle %}GENERAL INFORMATION{% endblock%}
+
+{% block view_content %}
+<ul>
+ <li>Number of compounds: {{ compounds_count }}</li>
+ <li>Total number of binding data: {{ car_count }}</li>
+ <li>Total number of biochemical binding data: {{ bioch_car_count }}</li>
+ <li>Total number of cellular binding data: {{ cell_car_count }}</li>
+ <li>Number of proteins: {{ proteins_count }}</li>
+ <li>Number of families: {{ families_count }}</li>
+ <li>Number of PPI targets: {{ ppis_count }}</li>
+ <li>Number of bibliographic sources: {{ biblio_count }}</li>
+</ul>
+{% endblock %}
diff --git a/ippisite/ippidb/templates/about-pharmacology.html b/ippisite/ippidb/templates/about-pharmacology.html
new file mode 100644
index 0000000000000000000000000000000000000000..a71166c69edd48411f02bdfeaed21bc8b531db6d
--- /dev/null
+++ b/ippisite/ippidb/templates/about-pharmacology.html
@@ -0,0 +1,130 @@
+{% extends "about.html" %}
+
+
+{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
+
+{% block pagetitle %}PHARMACOLOGY{% endblock%}
+
+{% block view_content %}
+<div class="row">
+ <div class="card col-sm-12 col-md-6">
+ <canvas id="pxc_by_test_type" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-6">
+ <canvas id="bioch_tests_histo" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-6">
+ <canvas id="data_per_ppi_family" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-6">
+ <canvas id="cell_tests_histo" style="width:300px; height:200px;"></canvas>
+ </div>
+</div>
+<div class="row">
+ <div class="card col-md-12">
+ <canvas id="le_lle_biplot" style="width:300px; height:200px;"></canvas>
+ </div>
+</div>
+
+<script>
+
+ var biochTestData = {
+ labels: {{ biochemical_tests_count_by_name.labels|safe }},
+ datasets: [{
+ label: 'Number of activity test results',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ biochemical_tests_count_by_name.values }}
+ }]
+ };
+
+ drawBarChart('bioch_tests_histo',
+ biochTestData,
+ 'Biochemical Tests',
+ 'biochtest');
+
+ var cellTestData = {
+ labels: {{ cellular_tests_count_by_name.labels|safe }},
+ datasets: [{
+ label: 'Number of activity test results',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ cellular_tests_count_by_name.values }}
+ }]
+ };
+
+ drawBarChart('cell_tests_histo',
+ cellTestData,
+ 'Cellular Tests',
+ 'celltest');
+
+ var bindingDataPerPPIFamily = {
+ labels: {{ compounds_per_ppi_family.labels|safe }},
+ datasets: [
+ {
+ label: 'Number of binding data',
+ backgroundColor: "rgba(46,87,139,0.6)",
+ borderColor: "rgba(46,87,139,1)",
+ borderWidth: 1,
+ data: {{ binding_data_per_ppi_family.values }}
+ },
+ {
+ label: 'Number of unique compounds',
+ backgroundColor: "rgba(185,45,92,1)",
+ borderColor: "rgba(185,45,92,0.6)",
+ borderWidth: 1,
+ data: {{ compounds_per_ppi_family.values }}
+ },
+ ]
+ };
+
+ drawBarChart('data_per_ppi_family',
+ bindingDataPerPPIFamily,
+ 'Compounds and binding data available in iPPI-DB per PPI target'
+ );
+
+
+ var bindingDataPerPXC50Bins = {
+ labels: ['Biochemical', 'Cellular'],
+ datasets: [
+ {
+ label: 'pXC50>=8',
+ backgroundColor: "rgba(46,87,139,1)",
+ borderColor: "rgba(46,87,139,1)",
+ borderWidth: 1,
+ data: [{{cell_tests_pxc50_gte8}},{{bioch_tests_pxc50_gte8}}],
+ },
+ {
+ label: '8>pXC50>=7',
+ backgroundColor: "rgba(185,45,92,1)",
+ borderColor: "rgba(185,45,92,1)",
+ borderWidth: 1,
+ data: [{{cell_tests_pxc50_gte7_lt8}},{{bioch_tests_pxc50_gte7_lt8}}],
+ },
+ {
+ label: '7>pXC50>=6',
+ backgroundColor: "rgba(209,224,253,1)",
+ borderColor: "rgba(209,224,253,1)",
+ borderWidth: 1,
+ data: [{{cell_tests_pxc50_gte6_lt7}},{{bioch_tests_pxc50_gte6_lt7}}],
+ },
+ {
+ label: '6>pXC50',
+ backgroundColor: "rgba(242,202,255,1)",
+ borderColor: "rgba(242,202,255,1)",
+ borderWidth: 1,
+ data: [{{cell_tests_pxc50_lt6}},{{bioch_tests_pxc50_lt6}}],
+ }
+ ]
+ };
+
+ drawHorizontalStackedBarChart('pxc_by_test_type',
+ bindingDataPerPXC50Bins,
+ 'Distribution of the binding data across bins of activity in pXC50 units');
+
+ drawCompoundsBiplotChart('le_lle_biplot', preparePerFamilyBiplotData({{ le_lle_biplot_data | safe }}), 'pharmacology');
+
+</script>
+{% endblock %}
diff --git a/ippisite/ippidb/templates/about-physicochemistry.html b/ippisite/ippidb/templates/about-physicochemistry.html
new file mode 100644
index 0000000000000000000000000000000000000000..fe928ae4c64ebf0a507d8c58f5dfec73448decb1
--- /dev/null
+++ b/ippisite/ippidb/templates/about-physicochemistry.html
@@ -0,0 +1,193 @@
+{% extends "about.html" %}
+
+{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
+
+{% block pagetitle %}PHYSICOCHEMISTRY{% endblock%}
+
+{% block view_content %}
+<div class="row">
+ <div class="card col-sm-12 col-md-4">
+ <canvas id="fsp3_dist" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-4">
+ <canvas id="mw_dist" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-4">
+ <canvas id="chiral_dist" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-4">
+ <canvas id="arom_dist" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-4">
+ <canvas id="rotbonds_dist" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-4">
+ <canvas id="haccept_dist" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-4">
+ <canvas id="hdon_dist" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-4">
+ <canvas id="tpsa_dist" style="width:300px; height:200px;"></canvas>
+ </div>
+ <div class="card col-sm-12 col-md-4">
+ <canvas id="alogp_dist" style="width:300px; height:200px;"></canvas>
+ </div>
+</div>
+<script>
+
+ var fsp3Data = {
+ labels: {{ fsp3_dist.labels|safe }},
+ datasets: [{
+ label: 'Compounds in FSP3 range',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ fsp3_dist.values }}
+ }]
+ };
+
+ drawBarChart('fsp3_dist',
+ fsp3Data,
+ 'Fsp3',
+ null,
+ 'bar');
+
+ var mwData = {
+ labels: {{ mw_dist.labels|safe }},
+ datasets: [{
+ label: 'Molecular Weight',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ mw_dist.values }}
+ }]
+ };
+
+ drawBarChart('mw_dist',
+ mwData,
+ 'Molecular Weight',
+ null,
+ 'bar');
+
+ var chiralData = {
+ labels: {{ chiral_dist.labels|safe }},
+ datasets: [{
+ label: 'Number of chiral centers',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ chiral_dist.values }}
+ }]
+ };
+
+ drawBarChart('chiral_dist',
+ chiralData,
+ 'Number of chiral centers',
+ null,
+ 'bar');
+
+ var aromData = {
+ labels: {{ arom_dist.labels|safe }},
+ datasets: [{
+ label: 'Number of aromatic rings',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ arom_dist.values }}
+ }]
+ };
+
+ drawBarChart('arom_dist',
+ aromData,
+ 'Number of aromatic rings',
+ null,
+ 'bar');
+
+ var rotbondsData = {
+ labels: {{ rotbonds_dist.labels|safe }},
+ datasets: [{
+ label: 'Number of rotatable bonds',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ rotbonds_dist.values }}
+ }]
+ };
+
+ drawBarChart('rotbonds_dist',
+ rotbondsData,
+ 'Number of rotatable bonds',
+ null,
+ 'bar');
+
+ var hacceptData = {
+ labels: {{ haccept_dist.labels|safe }},
+ datasets: [{
+ label: 'Number of H acceptors',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ haccept_dist.values }}
+ }]
+ };
+
+ drawBarChart('haccept_dist',
+ hacceptData,
+ 'Number of H acceptors',
+ null,
+ 'bar');
+
+ var hdonData = {
+ labels: {{ hdon_dist.labels|safe }},
+ datasets: [{
+ label: 'Number of H donors',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ hdon_dist.values }}
+ }]
+ };
+
+ drawBarChart('hdon_dist',
+ hdonData,
+ 'Number of H donors',
+ null,
+ 'bar');
+
+ var tpsaData = {
+ labels: {{ tpsa_dist.labels|safe }},
+ datasets: [{
+ label: 'TPSA',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ tpsa_dist.values }}
+ }]
+ };
+
+ drawBarChart('tpsa_dist',
+ tpsaData,
+ 'TPSA',
+ null,
+ 'bar');
+
+ var alogpData = {
+ labels: {{ alogp_dist.labels|safe }},
+ datasets: [{
+ label: 'ALogP',
+ backgroundColor: "rgba(70,130,180,0.6)",
+ borderColor: "rgba(70,130,180,1)",
+ borderWidth: 1,
+ data: {{ alogp_dist.values }}
+ }]
+ };
+
+ drawBarChart('alogp_dist',
+ alogpData,
+ 'ALogP',
+ null,
+ 'bar');
+
+</script>
+{% endblock %}
diff --git a/ippisite/ippidb/templates/about.html b/ippisite/ippidb/templates/about.html
index 799b064161e5aeb9ef8c3255b303d98701dbc2d3..367f3e3a3915965b3d6d5ca4b0bec2c538040192 100644
--- a/ippisite/ippidb/templates/about.html
+++ b/ippisite/ippidb/templates/about.html
@@ -4,42 +4,31 @@
{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
{% block content %}
-{% block secondarynav %}
<div id="mainnav">
<nav class="secondary-nav">
<div class="inner-wrap">
<ul>
<li>
- <a href="/about/general">General informations</a>
+ <a href="/about-general">General information</a>
</li>
<li>
- <a href="/about/pharmacology">Pharmacology</a>
+ <a href="/about-pharmacology">Pharmacology</a>
</li>
<li>
- <a href="/about/physicochemistry">Physicochemistry</a>
- </li>
- <li>
- <a href="/about/drug-candidate">Drug candidate</a>
+ <a href="/about-physicochemistry">Physicochemistry</a>
</li>
</ul>
</div>
</nav>
</div>
-{% endblock %}
<div class="inner-wrap">
- <nav class="breadcrumb breadNav" role="navigation">
- <div class="breadNav-label">You are here</div>
- <div aria-labelledby="breadcrumb-label">
- {% block breadcrumb %} {{block.super}}About{% endblock %}
- </div>
- </nav>
<div id="main-wrapper" class="page">
<div id="main">
<div id="content" class="main-content">
<div class="section">
<main role="main">
- <h1 class="page-title"> ABOUT </h1>
+ <h1 class="page-title"> {% block pagetitle %}ABOUT{% endblock%} </h1>
<div class="tabs"></div>
<div class="main__inner">
<div class="region region-content">
@@ -50,7 +39,8 @@
<div class="block block-system block-system-main">
<div class="content">
<div class="view-content">
-
+{% block view_content %}
+{% endblock %}
</div>
</div>
</div>
diff --git a/ippisite/ippidb/templates/base.html b/ippisite/ippidb/templates/base.html
index 18a1e3d53942fb9d312c48def1d1134858746134..13b7b497202ba061d73e2a5685f79073a12630a5 100644
--- a/ippisite/ippidb/templates/base.html
+++ b/ippisite/ippidb/templates/base.html
@@ -51,16 +51,19 @@
window.location = modifiedUrl;
$('#loadingModal').modal();
};
+
var changeSelection = function(paramName){
var selectedFields = $('input[name='+ paramName +']:checked').map(function(_, el) { return $(el).val(); }).get();
modifyUrl(paramName, selectedFields);
}
+
var removeFromSelection = function(paramName, value){
var url = new URL(location.href);
var selectedValues = url.searchParams.getAll(paramName);
selectedValues.splice(selectedValues.indexOf(value), 1);
modifyUrl(paramName, selectedValues);
}
+
var multiselectTypeAhead = function(idSearch, selection, onSelect){
var bh = new Bloodhound({
datumTokenizer: Bloodhound.tokenizers.obj.whitespace('name'),
@@ -130,7 +133,7 @@
maintainAspectRatio: false
}});
};
- var drawCompoundsBiplotChart = function(canvasId, compoundId, compoundFamily, plotData, tabHash){
+ var prepareCompoundFamilyBiplotData = function(compoundId, compoundFamily, plotData){
var currentCompoundData = [];
var currentFamilyData = [];
var otherFamiliesData = [];
@@ -162,6 +165,55 @@
data: currentCompoundData
}
]};
+ return scatterData;
+ }
+
+ var getPpiFamilyColor = function(ppiName){
+ return {
+ 'BCL2-Like / BAX': '#0E5C97',
+ 'Beta-catenin / TCF-4': '#FAB362',
+ 'Bromodomain / Histone': '#C9862D',
+ 'CD4 / gp120': '#FE8E85',
+ 'CD80 / CD28': '#DB0016',
+ 'E2 / E1': '#C4ADD1',
+ 'FAK / VEGFR3': '#6700FF',
+ 'IL2 / IL2R': '#FE6C00',
+ 'LEDGF / IN': '#971D19',
+ 'LFA / ICAM': '#9DD87E',
+ 'MDM2-Like / P53': '#96C5DC',
+ 'MENIN / MLL': '#EDBBFF',
+ 'Myc / Max': '#C04DC4',
+ 'NRP / VEGF': '#A8184B',
+ 'UPAR / UPA': '#CBDCFF',
+ 'VEGF / VEGFR': '#FED215',
+ 'WDR5/MLL': '#F5F6F7',
+ 'XIAP / Smac': '#128C6D',
+ 'ZipA / ftsZ': '#FEFE01',
+ }[ppiName];
+ }
+
+ var preparePerFamilyBiplotData = function(plotData){
+ var property = 'family_name';
+ var datasets = plotData.reduce(function (acc, obj) {
+ var family = obj[property];
+ if(!acc[family]){
+ acc[family] = {
+ label: family,
+ borderColor: getPpiFamilyColor(family),
+ backgroundColor: getPpiFamilyColor(family),
+ data: []
+ };
+ }
+ acc[family].data.push(obj);
+ return acc;
+ }, {});
+ var scatterData = {
+ 'datasets': Object.values(datasets)
+ };
+ return scatterData;
+ }
+
+ var drawCompoundsBiplotChart = function(canvasId, scatterData, tabHash){
var ctx = document.getElementById(canvasId).getContext('2d');
var scatterChart = new Chart(ctx, {
type: 'scatter',
@@ -231,6 +283,7 @@
window.location = '/compounds/' + id + '#' + tabHash;
};
};
+
var setUpSliderForModal = function(paramName){
$('#'+paramName).slider();
$('#'+paramName).on('slide', function(slideEvt) {
@@ -238,6 +291,7 @@
$('#'+paramName+'_textvalue_max').text(slideEvt.value[1]);
});
}
+
var toggleCheckBox = function(id){
var cb = $('#'+id);
if(cb.prop('checked')==true){
@@ -246,6 +300,82 @@
modifyUrl(id,null);
}
}
+
+ var drawBarChart = function(elementId, data, caption, queryFilter, orientation){
+ var ctx = document.getElementById(elementId).getContext('2d');
+ if(orientation==null){
+ orientation = 'horizontalBar'
+ }
+ var myHorizontalBar = new Chart(ctx, {
+ type: orientation,
+ data: data,
+ options: {
+ elements: {
+ rectangle: {
+ borderWidth: 20,
+ }
+ },
+ responsive: true,
+ legend: {
+ position: 'bottom',
+ },
+ title: {
+ display: true,
+ text: caption
+ }
+ }
+ });
+ if(queryFilter!=null){
+ document.getElementById(elementId).onclick = function(evt){
+ var activePoints = myHorizontalBar.getElementAtEvent(evt);
+ var datasetIndex = activePoints[0]._datasetIndex;
+ var selectedIndex = activePoints[0]._index;
+ var id = myHorizontalBar.data.labels[datasetIndex];
+ window.location = '/compounds/?'+ queryFilter + '=' + id;
+ };
+ }
+ }
+
+ var drawHorizontalStackedBarChart = function(elementId, data, caption, queryFilter){
+ var ctx = document.getElementById(elementId).getContext('2d');
+ var myHorizontalBar = new Chart(ctx, {
+ type: 'horizontalBar',
+ data: data,
+ options: {
+ elements: {
+ rectangle: {
+ borderWidth: 20,
+ }
+ },
+ responsive: true,
+ legend: {
+ position: 'bottom',
+ },
+ title: {
+ display: true,
+ text: caption
+ },
+ scales: {
+ xAxes: [{
+ stacked: true
+ }],
+ yAxes: [{
+ stacked: true
+ }]
+ }
+ }
+ });
+ if(queryFilter!=null){
+ document.getElementById(elementId).onclick = function(evt){
+ var activePoints = myHorizontalBar.getElementAtEvent(evt);
+ var datasetIndex = activePoints[0]._datasetIndex;
+ var selectedIndex = activePoints[0]._index;
+ var id = myHorizontalBar.data.labels[datasetIndex];
+ window.location = '/compounds/?'+ queryFilter + '=' + id;
+ };
+ }
+ }
+
</script>
</head>
@@ -277,7 +407,7 @@
<a href="/">Home</a>
</li>
<li>
- <a href="/about">About</a>
+ <a href="/about-general">About</a>
</li>
<li>
<a href="/compounds">Query compounds</a>
@@ -323,7 +453,7 @@
<nav>
<ul>
<li>
- <a href="/about">About Us</a>
+ <a href="/about-general">About Us</a>
</li>
<li>
<a href="/query">Query</a>
diff --git a/ippisite/ippidb/templates/compound_card.html b/ippisite/ippidb/templates/compound_card.html
index ba50ab9442120e6841f61efebb475ec905c5076b..8bf98f4eff53cf2d8b98c7c21fed138d47ce94d5 100644
--- a/ippisite/ippidb/templates/compound_card.html
+++ b/ippisite/ippidb/templates/compound_card.html
@@ -125,7 +125,7 @@
<canvas id="pca_biplot" style="width:600px; height:600px;"></canvas>
<script>
- drawCompoundsBiplotChart('pca_biplot', {{ compound.id }}, '{{ compound.best_activity_ppi_family_name|default_if_none:"No target family identified" }}', {{ pca_biplot_data | safe }}, 'physicochemistry');
+ drawCompoundsBiplotChart('pca_biplot', prepareCompoundFamilyBiplotData({{ compound.id }}, '{{ compound.best_activity_ppi_family_name|default_if_none:"No target family identified" }}', {{ pca_biplot_data | safe }}), 'physicochemistry');
</script>
</div>
</div>
@@ -143,7 +143,7 @@
<div class="card-body">
<canvas id="le_lle_biplot"></canvas>
<script>
- drawCompoundsBiplotChart('le_lle_biplot', {{ compound.id }}, '{{ compound.best_activity_ppi_family_name|default_if_none:"No target family identified" }}', {{ le_lle_biplot_data | safe }}, 'pharmacology');
+ drawCompoundsBiplotChart('le_lle_biplot', prepareCompoundFamilyBiplotData({{ compound.id }}, '{{ compound.best_activity_ppi_family_name|default_if_none:"No target family identified" }}', {{ le_lle_biplot_data | safe }}), 'pharmacology');
</script>
</div>
</div>
diff --git a/ippisite/ippidb/templates/general.html b/ippisite/ippidb/templates/general.html
deleted file mode 100644
index 7c1f459a6b09ff44203867969380ca345b199074..0000000000000000000000000000000000000000
--- a/ippisite/ippidb/templates/general.html
+++ /dev/null
@@ -1,64 +0,0 @@
-{% extends "about.html" %}
-
-
-{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
-
-{% block content %}
-<div id="mainnav">
- <nav class="secondary-nav">
- <div class="inner-wrap">
- <ul>
- <li>
- <a href="/about/general">General informations</a>
- </li>
- <li>
- <a href="/about/pharmacology">Pharmacology</a>
- </li>
- <li>
- <a href="/about/physicochemistry">Physicochemistry</a>
- </li>
- <li>
- <a href="/about/drug-candidate">Drug Candidate</a>
- </li>
- </ul>
- </div>
- </nav>
-</div>
-<div class="inner-wrap">
- <nav class="breadcrumb breadNav" role="navigation">
- <div class="breadNav-label">You are here</div>
- <div aria-labelledby="breadcrumb-label">
- {% block breadcrumb %} <a href="/about" class="breadNav-link">{{block.super}}</a> > General informations {% endblock %}
- </div>
- </nav>
- <div id="main-wrapper" class="page">
- <div id="main">
- <div id="content" class="main-content">
- <div class="section">
- <main role="main">
- <h1 class="page-title"> GENERAL INFORMATIONS </h1>
- <div class="tabs"></div>
- <div class="main__inner">
- <div class="region region-content">
- <div class="page-intro">
- </div>
- <div class="color-wrap">
- <div class="region region-content">
- <div class="block block-system block-system-main">
- <div class="content">
- <div class="view-content">
-
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </main><!-- .site-main -->
- </div>
- </div>
- </div><!-- div main -->
- </div>
-</div>
-{% endblock %}
diff --git a/ippisite/ippidb/templates/physicochemistry.html b/ippisite/ippidb/templates/physicochemistry.html
deleted file mode 100644
index 0f6a83098645b491b1626b003d81d88e0ea7c9ea..0000000000000000000000000000000000000000
--- a/ippisite/ippidb/templates/physicochemistry.html
+++ /dev/null
@@ -1,64 +0,0 @@
-{% extends "about.html" %}
-
-
-{% block title %}inhibitors of Protein-Protein Interaction Database{% endblock %}
-
-{% block content %}
-<div id="mainnav">
- <nav class="secondary-nav">
- <div class="inner-wrap">
- <ul>
- <li>
- <a href="/about/general">General informations</a>
- </li>
- <li>
- <a href="/about/pharmacology">Pharmacology</a>
- </li>
- <li>
- <a href="/about/physicochemistry">Physicochemistry</a>
- </li>
- <li>
- <a href="/about/drug-candidate">Drug candidate</a>
- </li>
- </ul>
- </div>
- </nav>
-</div>
-<div class="inner-wrap">
- <nav class="breadcrumb breadNav" role="navigation">
- <div class="breadNav-label">You are here</div>
- <div aria-labelledby="breadcrumb-label">
- {% block breadcrumb %} <a href="/about/" class="breadNav-link">{{block.super}}</a> > Physicochemistry {% endblock %}
- </div>
- </nav>
- <div id="main-wrapper" class="page">
- <div id="main">
- <div id="content" class="main-content">
- <div class="section">
- <main role="main">
- <h1 class="page-title"> PHYSICOCHEMISTRY </h1>
- <div class="tabs"></div>
- <div class="main__inner">
- <div class="region region-content">
- <div class="page-intro">
- </div>
- <div class="color-wrap">
- <div class="region region-content">
- <div class="block block-system block-system-main">
- <div class="content">
- <div class="view-content">
-
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </div>
- </main><!-- .site-main -->
- </div>
- </div>
- </div><!-- div main -->
- </div>
-</div>
-{% endblock %}
diff --git a/ippisite/ippidb/urls.py b/ippisite/ippidb/urls.py
index d112f740a8c1a73da522779d333c666380eaa6d4..bb3f766bb593b5c7dff6b47bc75648c132f06417 100644
--- a/ippisite/ippidb/urls.py
+++ b/ippisite/ippidb/urls.py
@@ -13,8 +13,9 @@ ippidb_wizard = IppiWizard.as_view(FORMS,
urlpatterns = [
url(r'^$', views.index, name='index'),
- url(r'^about$', views.about, name='about'),
- url(r'^about/general/$', views.general, name='general'),
+ url(r'^about-general/$', views.about_general, name='general'),
+ url(r'^about-pharmacology/$', views.about_pharmacology, name='pharmacology'),
+ url(r'^about-physicochemistry/$', views.about_physicochemistry, name='physicochemistry'),
url(r'^compounds/$', views.CompoundListView.as_view(), name='compound_list'),
url(r'^compounds/IPPIDB-(?P<compound_id>\w+)$', views.CompoundCardBDCHEMRedirectView.as_view(), name='redirect_compound_card'),
url(r'^compounds/(?P<pk>\w+)$', views.CompoundDetailView.as_view(), name='compound_card'),
diff --git a/ippisite/ippidb/views/__init__.py b/ippisite/ippidb/views/__init__.py
index 377175cfd797a046f62fd0c6061dde5632c5b004..1eb3e43b4bd8c8c13ab43c0d52c48b1820f5a74a 100644
--- a/ippisite/ippidb/views/__init__.py
+++ b/ippisite/ippidb/views/__init__.py
@@ -18,11 +18,6 @@ from django.conf import settings
def index(request):
return render(request, 'index.html')
-
-def about(request):
- return render(request, 'about.html')
-
-
def general(request):
return render(request, 'general.html')
diff --git a/ippisite/ippidb/views/compound_query.py b/ippisite/ippidb/views/compound_query.py
index 532f9f5a4d630b52f2f94c918a7a4abe82116005..f35de390859c77b7e0a596b26aed3612cee79e01 100644
--- a/ippisite/ippidb/views/compound_query.py
+++ b/ippisite/ippidb/views/compound_query.py
@@ -5,7 +5,8 @@ iPPI-DB compound query view and related classes
import json
from collections import OrderedDict
-from django.db.models import Max, Min, F, Q
+from django.db.models import Max, Min, F, Q, Count, FloatField
+from django.db.models.functions import Cast, Floor
from django.shortcuts import render
from django.urls import reverse
from django.http import Http404, JsonResponse
@@ -14,7 +15,7 @@ from django.views.generic.detail import DetailView
from django.views.generic.base import RedirectView
from ippidb.utils import mol2smi, smi2mol
-from ippidb.models import Compound, Ppi, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Disease, Domain, Taxonomy, LeLleBiplotData, PcaBiplotData, PpiFamily, MolecularFunction, TestActivityDescription, create_tanimoto
+from ippidb.models import Compound, Ppi, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Disease, Domain, Taxonomy, LeLleBiplotData, PcaBiplotData, PpiFamily, MolecularFunction, TestActivityDescription, create_tanimoto, CompoundActivityResult, Bibliography, Protein
DEACTIVATION_MAPPING = {
'lipinsky': set(['molecular_weight', 'nb_acceptor_h', 'nb_donor_h', 'a_log_p']),
@@ -551,3 +552,79 @@ def convert_smi2mol(request):
mol_string = smi2mol(smi_string)
resp = {'mol': mol_string}
return JsonResponse(resp)
+
+def about_general(request):
+ compounds_count = Compound.objects.count()
+ car_count = CompoundActivityResult.objects.count()
+ bioch_car_count = CompoundActivityResult.objects.filter(test_activity_description__test_type='BIOCH').count()
+ cell_car_count = CompoundActivityResult.objects.filter(test_activity_description__test_type='CELL').count()
+ proteins_count = Protein.objects.count()
+ families_count = PpiFamily.objects.count()
+ ppis_count = Ppi.objects.count()
+ biblio_count = Bibliography.objects.count()
+ context = {
+ 'compounds_count': compounds_count,
+ 'car_count': car_count,
+ 'bioch_car_count': bioch_car_count,
+ 'cell_car_count': cell_car_count,
+ 'proteins_count': proteins_count,
+ 'families_count': families_count,
+ 'ppis_count': ppis_count,
+ 'biblio_count': biblio_count,
+ }
+ return render(request, 'about-general.html', context=context)
+
+def convert_to_bar_chart_data(data):
+ return {
+ 'labels': [item['label'] for item in data],
+ 'values': [item['value'] for item in data]
+ }
+
+def about_pharmacology(request):
+ biochemical_tests_count_by_name_qs = CompoundActivityResult.objects.filter(test_activity_description__test_type='BIOCH').values(label=F('test_activity_description__test_name')).order_by('label').annotate(value=Count('label')).order_by('-value')
+ biochemical_tests_count_by_name = convert_to_bar_chart_data(biochemical_tests_count_by_name_qs)
+ cellular_tests_count_by_name_qs = CompoundActivityResult.objects.filter(test_activity_description__test_type='CELL').values(label=F('test_activity_description__test_name')).order_by('label').annotate(value=Count('label')).order_by('-value')
+ cellular_tests_count_by_name = convert_to_bar_chart_data(cellular_tests_count_by_name_qs)
+ compounds_per_ppi_family_raw = PpiFamily.objects.annotate(value=Count('ppi__compoundaction__compound', distinct=True)).values(value=F('value'),label=F('name')).order_by('-value').all()
+ compounds_per_ppi_family = convert_to_bar_chart_data(compounds_per_ppi_family_raw)
+ binding_data_per_ppi_family_raw = PpiFamily.objects.annotate(value=Count('ppi__compoundaction')).values(value=F('value'),label=F('name')).order_by('-value')
+ binding_data_per_ppi_family = convert_to_bar_chart_data(binding_data_per_ppi_family_raw)
+ context = {
+ 'biochemical_tests_count_by_name': biochemical_tests_count_by_name,
+ 'cellular_tests_count_by_name': cellular_tests_count_by_name,
+ 'bioch_tests_pxc50_gte8': CompoundActivityResult.objects.filter(test_activity_description__test_type='BIOCH').filter(activity__gte=8).count(),
+ 'bioch_tests_pxc50_gte7_lt8': CompoundActivityResult.objects.filter(test_activity_description__test_type='BIOCH').filter(activity__gte=7).filter(activity__lt=8).count(),
+ 'bioch_tests_pxc50_gte6_lt7': CompoundActivityResult.objects.filter(test_activity_description__test_type='BIOCH').filter(activity__gte=6).filter(activity__lt=7).count(),
+ 'bioch_tests_pxc50_lt6': CompoundActivityResult.objects.filter(test_activity_description__test_type='BIOCH').filter(activity__lt=6).count(),
+ 'cell_tests_pxc50_gte8': CompoundActivityResult.objects.filter(test_activity_description__test_type='CELL').filter(activity__gte=8).count(),
+ 'cell_tests_pxc50_gte7_lt8': CompoundActivityResult.objects.filter(test_activity_description__test_type='CELL').filter(activity__gte=7).filter(activity__lt=8).count(),
+ 'cell_tests_pxc50_gte6_lt7': CompoundActivityResult.objects.filter(test_activity_description__test_type='CELL').filter(activity__gte=6).filter(activity__lt=7).count(),
+ 'cell_tests_pxc50_lt6': CompoundActivityResult.objects.filter(test_activity_description__test_type='CELL').filter(activity__lt=6).count(),
+ 'compounds_per_ppi_family': compounds_per_ppi_family,
+ 'binding_data_per_ppi_family': binding_data_per_ppi_family,
+ 'le_lle_biplot_data': LeLleBiplotData.objects.get().le_lle_biplot_data,
+ }
+ return render(request, 'about-pharmacology.html', context=context)
+
+def about_physicochemistry(request):
+ fsp3_counts = Compound.objects.annotate(label=Cast(Floor(F('fsp3')*10),FloatField())/10).values('label').order_by('label').annotate(value=Count('label')).values('value','label').exclude(value=0)
+ mw_counts = Compound.objects.annotate(label=Cast(Floor(F('molecular_weight')/100),FloatField())*100).values('label').order_by('label').annotate(value=Count('label')).values('value','label').exclude(value=0)
+ chiral_counts = Compound.objects.annotate(label=F('nb_chiral_centers')).values('label').order_by('label').annotate(value=Count('label')).values('value','label').exclude(value=0)
+ arom_counts = Compound.objects.annotate(label=F('nb_aromatic_sssr')).values('label').order_by('label').annotate(value=Count('label')).values('value','label').exclude(value=0)
+ rotbonds_counts = Compound.objects.annotate(label=F('nb_rotatable_bonds')).values('label').order_by('label').annotate(value=Count('label')).values('value','label').exclude(value=0)
+ haccept_counts = Compound.objects.annotate(label=F('nb_acceptor_h')).values('label').order_by('label').annotate(value=Count('label')).values('value','label').exclude(value=0)
+ hdon_counts = Compound.objects.annotate(label=F('nb_donor_h')).values('label').order_by('label').annotate(value=Count('label')).values('value','label').exclude(value=0)
+ tpsa_counts = Compound.objects.annotate(label=Cast(Floor(F('tpsa')/10),FloatField())*10).values('label').order_by('label').annotate(value=Count('label')).values('value','label').exclude(value=0)
+ alogp_counts = Compound.objects.annotate(label=Cast(Floor(F('a_log_p')),FloatField())).values('label').order_by('label').annotate(value=Count('label')).values('value','label').exclude(value=0)
+ context = {
+ 'fsp3_dist': convert_to_bar_chart_data(fsp3_counts),
+ 'mw_dist': convert_to_bar_chart_data(mw_counts),
+ 'chiral_dist': convert_to_bar_chart_data(chiral_counts),
+ 'arom_dist': convert_to_bar_chart_data(arom_counts),
+ 'rotbonds_dist': convert_to_bar_chart_data(rotbonds_counts),
+ 'haccept_dist': convert_to_bar_chart_data(haccept_counts),
+ 'hdon_dist': convert_to_bar_chart_data(hdon_counts),
+ 'tpsa_dist': convert_to_bar_chart_data(tpsa_counts),
+ 'alogp_dist': convert_to_bar_chart_data(alogp_counts),
+ }
+ return render(request, 'about-physicochemistry.html', context=context)