From 426d6e460b36690e8fbbc0d09ad34e7bacade61a Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Sat, 17 Oct 2020 18:22:35 +0530
Subject: [PATCH] added Molecule Properties and Alerts

---
 app/misc.ini                           | 13 +++-
 app/templates/base.html                |  9 +++
 app/templates/home.html                | 10 ++-
 app/templates/mol-characteristics.html | 66 +++++++++++++++++++
 app/views.py                           | 90 +++++++++++++++++++++++++-
 5 files changed, 184 insertions(+), 4 deletions(-)
 create mode 100644 app/templates/mol-characteristics.html

diff --git a/app/misc.ini b/app/misc.ini
index c474556..9587e56 100644
--- a/app/misc.ini
+++ b/app/misc.ini
@@ -13,4 +13,15 @@ DB02 = Unknown Hostname, failed to connect to the database.
 
 CW01 = Looks like an invalid PDB ID
 
-PC00 = Could not find any compound on PubChem matching the query.
\ No newline at end of file
+PC00 = Could not find any compound on PubChem matching the query.
+
+RD00 = Failed to import RDKit.
+RD01 = Could not convert SMILES to molecule, please check the SMILES 
+
+[ALERT_SMARTS]
+ESTER = [#6][CX3](=O)[OX2H0][#6]
+ANILINE = [NX3][$(C=C),$(cc)]
+
+[ALERT_DESCRIPTION]
+ESTER = The given compound contains Ester. For more details read the paper.
+ANILINE = None
\ No newline at end of file
diff --git a/app/templates/base.html b/app/templates/base.html
index e4ae447..0936f80 100644
--- a/app/templates/base.html
+++ b/app/templates/base.html
@@ -29,6 +29,15 @@
           <li class="{{ 'nav-item active' if active_page == 'about' else 'nav-item' }}">
             <a class="nav-link" href="{{ url_for('about') }}">About</a>
           </li>
+          <li class="{{ 'nav-item dropdown active' if active_page == 'analyse' else 'nav-item dropdown' }}">
+            <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
+              Analyse
+            </a>
+            <div class="dropdown-menu" aria-labelledby="navbarDropdown">
+              <a class="dropdown-item" href="{{ url_for('propalert') }}">Property and Alerts</a>
+              <a class="dropdown-item" href="#">Druggability</a>
+            </div>
+          </li>
           <li class="{{ 'nav-item dropdown active' if active_page == 'dock' else 'nav-item dropdown' }}">
             <a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
               Dock and Report
diff --git a/app/templates/home.html b/app/templates/home.html
index 7e0e352..d67cac7 100644
--- a/app/templates/home.html
+++ b/app/templates/home.html
@@ -5,7 +5,7 @@
     <h2>Curie Web Demo</h2>
     <p>Curie-Web is a part of The Curie Project which aims to make the process of Computer-Aided Drug Design as fast as possible.</p>
     <p>The following are the currently active modules</p>
-    <h3>Docking</h3>
+    <h3>Dock and Generate Reports</h3>
     <ul>
         <li><a href="{{ url_for('dock_manual') }}">Dock and Report (Manual)</a> - You can enter your AutoDock Vina configuration, upload the PDBQT files and it will perform the molecular docking and generate a PDF with proper visualisations and protein-interaction profillings (Using PLIP) </li>
         <li><a href="{{ url_for('dock_automatic') }}">Dock and Report (Automatic)</a> - You just enter in the PDB Code, target compound's SMILES structure and name, it will automatically find a binding location and then perform docking and report generation</li>
@@ -16,13 +16,19 @@
         <li><a href="{{ url_for('generate') }}">Generate</a> - You can use this to generate completely new compounds</li>
     </ul>
 
-    <h3>Researching</h3>
+    <h3>Research</h3>
     <ul>
         <li><a href="{{ url_for('pubmed') }}">PubMed Search</a> - Handy PubMed search with direct download links</li>
         <li><a href="{{url_for('pubchem')}}">PubChem Search</a> - Get Compound SMILES</li>
         <li>Qrious App - You can enter a question for a set of papers (e.g. ChemRxiv preprints) and it uses AI to answer it for each individual paper based on their abstract</li>
     </ul>
 
+    <h3>Analyse</h3>
+    <ul>
+        <li><a href="{{ url_for('propalert') }}">Chemical Properties and Alerts</a> - Find Chemical properties and check structure for alerts.</li>
+        <li><a href="#">Druggability</a> - Classify druggability of a compound using a ML Model.</li>
+    </ul>
+
     <h3>Misc.</h3>
     <ul>
         <li>API - <a href="/docs">Swagger UI</a> or <a href="/redoc">ReDoc</a> - API access for the server</li>
diff --git a/app/templates/mol-characteristics.html b/app/templates/mol-characteristics.html
new file mode 100644
index 0000000..c7fc945
--- /dev/null
+++ b/app/templates/mol-characteristics.html
@@ -0,0 +1,66 @@
+{% extends 'base.html' %}
+{% set active_page = "analyse" %}
+{% block main %}
+    <h1>Chemical Properties and Alerts</h1>
+    <form action="{{ url_for('propalert') }}" method="post" enctype="multipart/form-data">
+        {% include 'flash_messages.html' %}
+        {{ form.csrf_token }}
+        <div class="form-row">
+                {{ form.query.label }}
+                {{ form.query(class="form-control")}}
+        </div>
+        <!--<div class="form-row">
+            {\{ form.modelSelection.label }}
+            {\{ form.modelSelection(class="form-control")}}
+        </div>-->
+        <br>
+        <div class="form-row">
+            <button type="submit" class="btn btn-primary">Search</button>
+        </div>
+    </form>
+
+    {% if complete %}
+      <br>
+        <h3>Properties</h3>
+
+        <table class="table table-dark">
+          <thead>
+            <tr>
+              <th scope="col">Property</th>
+              <th scope="col">Value</th>
+            </tr>
+          </thead>
+        {% for x in prop %}
+          <tbody>
+            <tr>
+              <th scope="row">{{x}}</th>
+              <td>{{prop[x]}}</td>
+            </tr>
+          </tbody>
+        {% endfor %}
+      </table>
+
+      {% if perfect %}
+        <h3>No alerts for the given compound.</h3>
+      {% endif %}
+
+        <div class="card-deck row-cols-2">
+        {% for x in range(result|length) %}
+
+        <div class="card" style="width: 18rem;">
+          <div class="card-img-top">
+            {{result[x]["SVG"] | safe }}
+          </div>
+          <div class="card-body">
+            <h5 class="card-title">{{result[x]["Name"]}}</h5>
+            <p class="card-text">{{result[x]["Description"]}}</p>
+            <a href="#" class="btn btn-primary">Read Paper</a>
+          </div>
+        </div>
+        {% endfor %}
+        </div>
+    {% endif %}
+
+    
+
+{% endblock %}
\ No newline at end of file
diff --git a/app/views.py b/app/views.py
index 47a37ac..bf2d401 100644
--- a/app/views.py
+++ b/app/views.py
@@ -17,6 +17,8 @@ import subprocess
 import mysql.connector as con
 from mysql.connector.errors import InterfaceError,DatabaseError
 
+
+
 import requests
 
 import logging
@@ -31,6 +33,8 @@ import configparser
 misc = configparser.ConfigParser()
 misc.read('app/misc.ini')
 errors = misc['ERRORS']
+AlertSMARTS = misc['ALERT_SMARTS']
+AlertDescription = misc['ALERT_DESCRIPTION']
 
 base = os.getcwd()
 
@@ -121,6 +125,47 @@ def pubchem():
         return render_template('search-pubchem.html',result=search,form=form)
     return render_template('search-pubchem.html',form=form)
 
+@app.route('/Properties',methods=['GET','POST'])
+def propalert():
+    form = PyMedSearch()
+
+    if request.method == 'POST' and form.validate_on_submit():
+        q = form.query.data
+        result = []
+        perfect = False
+        complete = False
+
+        try:
+            from rdkit import Chem
+        except ImportError:
+            return render_template('error.html',code="RD00",description=errors["RD00"])
+
+        if Chem.MolFromSmiles(q.strip()) is None:
+            print("invalid smiles")
+            return render_template('error.html',code="RD01",description=errors["RD01"])
+
+        for alert in AlertSMARTS:
+            print("Checking",alert,AlertSMARTS[alert])
+            records = {}
+            records['Name'] = alert
+            try:
+                records['SVG'] = get_svg(q,AlertSMARTS[alert])
+            except:
+                continue
+            records['Description'] = AlertDescription[alert]
+            result.append(records)
+
+        prop = get_prop(q)
+        print(prop)
+
+        complete = True
+
+        if len(result) == 0:
+            perfect = True
+
+        return render_template('mol-characteristics.html',complete=complete,result=result,form=form,perfect=perfect,prop=prop)
+    return render_template('mol-characteristics.html',form=form)
+
 @app.route('/Status',methods=['GET','POST'])
 def status():
     taskStatusForm = statusForm()
@@ -426,4 +471,47 @@ def page_not_found(error):
 
 
 if __name__ == '__main__':
-    app.run(debug=True, host="0.0.0.0", port="8080")
\ No newline at end of file
+    app.run(debug=True, host="0.0.0.0", port="8080")
+
+def get_svg(base,pattern):
+    try:
+        from rdkit.Chem.Draw import rdMolDraw2D
+        from rdkit import Chem
+    except:
+        return None # Need to add logic
+
+    mol = Chem.MolFromSmiles(base)
+    patt = Chem.MolFromSmarts(pattern)
+    hit_ats = list(mol.GetSubstructMatch(patt))
+    hit_bonds = []
+    for bond in patt.GetBonds():
+        aid1 = hit_ats[bond.GetBeginAtomIdx()]
+        aid2 = hit_ats[bond.GetEndAtomIdx()]
+        hit_bonds.append(mol.GetBondBetweenAtoms(aid1,aid2).GetIdx())
+    d = rdMolDraw2D.MolDraw2DSVG(500, 500)
+    rdMolDraw2D.PrepareAndDrawMolecule(d, mol, highlightAtoms=hit_ats, highlightBonds=hit_bonds)
+    return d.GetDrawingText().replace("width='500' height='500'","").replace("width='500px' height='500px'","")
+
+def get_prop(base):
+    try:
+        from rdkit import Chem
+        from rdkit.Chem import Crippen
+        from rdkit.Chem import Descriptors
+        from rdkit.Chem import rdMolDescriptors
+        from rdkit.Chem import Lipinski
+    except:
+        return None # Need to add logic
+    result = {}
+
+    mol = Chem.MolFromSmiles(base)
+    result["cLogP"] = Crippen.MolLogP(mol)
+    result["Molecular Weight"] = Descriptors.MolWt(mol)
+    result["TPSA"] = rdMolDescriptors.CalcTPSA(mol)
+    result["Hydrogen Bond Acceptors"] = Lipinski.NumHAcceptors(mol)
+    result["Hydrogen Bond Donors"] = Lipinski.NumHDonors(mol)
+    result["Rotable Bonds"] = Lipinski.NumRotatableBonds(mol)
+    result["Fraction SP3"]  = Lipinski.FractionCSP3(mol)
+
+
+    return result
+