diff options
| -rw-r--r-- | app/forms.py | 2 | ||||
| -rw-r--r-- | app/misc.ini | 4 | ||||
| -rw-r--r-- | app/templates/error.html | 2 | ||||
| -rw-r--r-- | app/templates/home.html | 1 | ||||
| -rw-r--r-- | app/templates/search-pubchem.html | 48 | ||||
| -rw-r--r-- | app/views.py | 16 |
6 files changed, 70 insertions, 3 deletions
diff --git a/app/forms.py b/app/forms.py index eaaf547..fb2ecf0 100644 --- a/app/forms.py +++ b/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()])
\ No newline at end of file + query = StringField('Search Query for PubMed',default="Query",validators=[DataRequired()])
\ No newline at end of file diff --git a/app/misc.ini b/app/misc.ini index 875fa7d..cdf439c 100644 --- a/app/misc.ini +++ b/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
\ No newline at end of file +CW01 = Looks like an invalid PDB ID + +PC00 = Could not find any compound on PubChem matching the query.
\ No newline at end of file diff --git a/app/templates/error.html b/app/templates/error.html index b605430..54656ba 100644 --- a/app/templates/error.html +++ b/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> diff --git a/app/templates/home.html b/app/templates/home.html index 10724d7..8386dac 100644 --- a/app/templates/home.html +++ b/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> diff --git a/app/templates/search-pubchem.html b/app/templates/search-pubchem.html new file mode 100644 index 0000000..9b8e7cb --- /dev/null +++ b/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 %}
\ No newline at end of file diff --git a/app/views.py b/app/views.py index dfd33e2..142229b 100644 --- a/app/views.py +++ b/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() |