added pubchem search

app/forms.py

@@ -52,4 +52,4 @@ class generatePDBQTS(FlaskForm):
     name = StringField('Compound Name (Optional)')
 
 class PyMedSearch(FlaskForm):
-    query = StringField('Search Query for PubMed',default="Covid-19",validators=[DataRequired()])
+    query = StringField('Search Query for PubMed',default="Query",validators=[DataRequired()])

app/misc.ini

@@ -9,4 +9,6 @@ PL01 = Failed to fetch the PDB, please check the PDB Code
 
 DB01 = This Job ID does not exist 😠. If you think this is an error, please contact us.
 
-CW01 = Looks like an invalid PDB ID
+CW01 = Looks like an invalid PDB ID
+
+PC00 = Could not find any compound on PubChem matching the query.

app/templates/error.html

@@ -3,7 +3,7 @@
 
 {% block main %}
     <h2>Oh Snap! An error occured</h2>
-    <p>Error Code: {{code}}</p>
+    <div class="alert alert-warning" role="alert">Error Code: {{code}}</div>
     <p>Error Description: {{description}}</p>
     <!--<section>
         <style>

app/templates/home.html

@@ -18,6 +18,7 @@
     <h3>Researching</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>
 

app/templates/search-pubchem.html

@@ -0,0 +1,48 @@
+{% extends 'base.html' %}
+
+{% block main %}
+    <h1>SMILES Search</h1>
+    <p>Get Compound SMILES through PubChem.</p>
+    <form action="{{ url_for('pubchem') }}" 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 result %}
+        <h3>Search Results</h3>
+        {% for x in range(result|length) %}
+        <!--<i>{\{result}}</i>-->
+        <!--<p>{{result[x]}}</p>-->
+        <div class="card mb-3">
+            <div class="row no-gutters">
+                <div class="col-md-4 text-white bg-dark">
+                    <div class="card-body">
+                    <img src="https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{{result[x]['CID']}}/PNG" class="card-img">
+                </div>
+            </div>
+              <div class="col-md-8">
+                <div class="card-body">
+                  <h5 class="card-title"><b>CID:</b> <a href="https://pubchem.ncbi.nlm.nih.gov/compound/{{result[x]['CID']}}">{{result[x]["CID"]}}</a></h5>
+                  <p class="card-text"><b>Canonical SMILES: </b>{{result[x]["CanonicalSMILES"]}}</p>
+                  <p class="card-text"><b>Isomeric SMILES: </b>{{result[x]["IsomericSMILES"]}}</p>
+                  <p class="card-text"><b>2D Fingerprint </b>{{result[x]["Fingerprint2D"]}}</p>
+                </div>
+              </div>
+            </div>
+          </div>
+        {% endfor %}
+    {% endif %}
+
+{% endblock %}

app/views.py

@@ -14,6 +14,8 @@ from datetime import datetime,date
 import json
 import subprocess
 
+import requests
+
 import logging
 import logzero
 from logzero import logger
@@ -100,6 +102,20 @@ def pubmed():
     flash_errors(form)
     return render_template('search.html',form=form)
 
+@app.route('/Compound-Search',methods=['GET','POST'])
+def pubchem():
+    form = PyMedSearch()
+    
+    if request.method == 'POST' and form.validate_on_submit():
+        q = form.query.data
+        response = requests.get('https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/%s/property/Fingerprint2D,CanonicalSMILES,IsomericSMILES/JSON' % q.strip())
+        if response.status_code == 404:
+            return render_template('error.html',code="PC00",description=errors["PC00"])
+        search = response.json()["PropertyTable"]["Properties"]
+        print(search)
+        return render_template('search-pubchem.html',result=search,form=form)
+    return render_template('search-pubchem.html',form=form)
+
 @app.route('/Status',methods=['GET','POST'])
 def status():
     taskStatusForm = statusForm()