added pubchem search
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@ -52,4 +52,4 @@ class generatePDBQTS(FlaskForm):
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name = StringField('Compound Name (Optional)')
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name = StringField('Compound Name (Optional)')
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class PyMedSearch(FlaskForm):
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class PyMedSearch(FlaskForm):
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query = StringField('Search Query for PubMed',default="Covid-19",validators=[DataRequired()])
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query = StringField('Search Query for PubMed',default="Query",validators=[DataRequired()])
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@ -10,3 +10,5 @@ PL01 = Failed to fetch the PDB, please check the PDB Code
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DB01 = This Job ID does not exist 😠. If you think this is an error, please contact us.
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DB01 = This Job ID does not exist 😠. If you think this is an error, please contact us.
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CW01 = Looks like an invalid PDB ID
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CW01 = Looks like an invalid PDB ID
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PC00 = Could not find any compound on PubChem matching the query.
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@ -3,7 +3,7 @@
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{% block main %}
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{% block main %}
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<h2>Oh Snap! An error occured</h2>
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<h2>Oh Snap! An error occured</h2>
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<p>Error Code: {{code}}</p>
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<div class="alert alert-warning" role="alert">Error Code: {{code}}</div>
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<p>Error Description: {{description}}</p>
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<p>Error Description: {{description}}</p>
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<!--<section>
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<!--<section>
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<style>
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<style>
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@ -18,6 +18,7 @@
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<h3>Researching</h3>
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<h3>Researching</h3>
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<ul>
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<ul>
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<li><a href="{{ url_for('pubmed') }}">PubMed Search</a> - Handy PubMed search with direct download links</li>
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<li><a href="{{ url_for('pubmed') }}">PubMed Search</a> - Handy PubMed search with direct download links</li>
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<li><a href="{{url_for('pubchem')}}">PubChem Search</a> - Get Compound SMILES</li>
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<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>
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<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>
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</ul>
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</ul>
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@ -0,0 +1,48 @@
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{% extends 'base.html' %}
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{% block main %}
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<h1>SMILES Search</h1>
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<p>Get Compound SMILES through PubChem.</p>
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<form action="{{ url_for('pubchem') }}" method="post" enctype="multipart/form-data">
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{% include 'flash_messages.html' %}
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{{ form.csrf_token }}
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<div class="form-row">
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{{ form.query.label }}
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{{ form.query(class="form-control")}}
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</div>
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<!--<div class="form-row">
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{\{ form.modelSelection.label }}
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{\{ form.modelSelection(class="form-control")}}
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</div>-->
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<br>
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<div class="form-row">
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<button type="submit" class="btn btn-primary">Search</button>
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</div>
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</form>
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{% if result %}
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<h3>Search Results</h3>
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{% for x in range(result|length) %}
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<!--<i>{\{result}}</i>-->
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<!--<p>{{result[x]}}</p>-->
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<div class="card mb-3">
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<div class="row no-gutters">
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<div class="col-md-4 text-white bg-dark">
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<div class="card-body">
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<img src="https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{{result[x]['CID']}}/PNG" class="card-img">
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</div>
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</div>
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<div class="col-md-8">
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<div class="card-body">
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<h5 class="card-title"><b>CID:</b> <a href="https://pubchem.ncbi.nlm.nih.gov/compound/{{result[x]['CID']}}">{{result[x]["CID"]}}</a></h5>
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<p class="card-text"><b>Canonical SMILES: </b>{{result[x]["CanonicalSMILES"]}}</p>
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<p class="card-text"><b>Isomeric SMILES: </b>{{result[x]["IsomericSMILES"]}}</p>
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<p class="card-text"><b>2D Fingerprint </b>{{result[x]["Fingerprint2D"]}}</p>
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</div>
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</div>
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</div>
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</div>
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{% endfor %}
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{% endif %}
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{% endblock %}
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16
app/views.py
16
app/views.py
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@ -14,6 +14,8 @@ from datetime import datetime,date
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import json
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import json
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import subprocess
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import subprocess
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import requests
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import logging
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import logging
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import logzero
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import logzero
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from logzero import logger
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from logzero import logger
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@ -100,6 +102,20 @@ def pubmed():
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flash_errors(form)
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flash_errors(form)
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return render_template('search.html',form=form)
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return render_template('search.html',form=form)
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@app.route('/Compound-Search',methods=['GET','POST'])
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def pubchem():
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form = PyMedSearch()
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if request.method == 'POST' and form.validate_on_submit():
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q = form.query.data
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response = requests.get('https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/%s/property/Fingerprint2D,CanonicalSMILES,IsomericSMILES/JSON' % q.strip())
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if response.status_code == 404:
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return render_template('error.html',code="PC00",description=errors["PC00"])
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search = response.json()["PropertyTable"]["Properties"]
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print(search)
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return render_template('search-pubchem.html',result=search,form=form)
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return render_template('search-pubchem.html',form=form)
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@app.route('/Status',methods=['GET','POST'])
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@app.route('/Status',methods=['GET','POST'])
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def status():
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def status():
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taskStatusForm = statusForm()
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taskStatusForm = statusForm()
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