I posted topics about rdkitjs before.
The library can render molecule as SVG format. It was very useful for me.
But, sometime I write webapp using python. So I want to draw molecule from python.
There are a lots of web framework in python and my favorite is “Flask”. 😉
So, I tested render molecule as SVG from python using Flask.
At first, I coded app.py that is base app.
Sample code is following.
This web app will render molecule if user access the url ‘localhost:5000/’.
from __future__ import print_function
from flask import Flask
from flask import render_template
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from HTMLParser import HTMLParser
def smitosvg( smi, molSize=( 400,200 ) ):
mol = Chem.MolFromSmiles( smi )
print(smi)
mc = Chem.Mol( mol.ToBinary() )
if not mc.GetNumConformers():
rdDepictor.Compute2DCoords( mc )
drawer = rdMolDraw2D.MolDraw2DSVG( molSize[0], molSize[1] )
opts = drawer.drawOptions()
drawer.DrawMolecule( mc )
drawer.FinishDrawing()
svg = drawer.GetDrawingText()
svg = svg.replace('svg:','')
return svg
app = Flask(__name__)
@app.route( '/top/<smi>' )
def top( smi ):
return render_template( '/top.html', svg = smitosvg( smi ), smi =smi )
if __name__ == '__main__':
app.run( debug=True )
And I wrote top.html in templates folder.
It’s manner of Flask.
<!DOCTYPE=HTML>
<html>
<head>
<title>render smi</title>
</head
>
<body>
<h1>Render Smiles</h1>
{{ svg|safe }} </br>
This is your query    {{ smi }}
</body>
</html>
The argument of “|safe” is important to escape html tag.
OK! Just do it!
Run the app and access sample url.
$ python app.py
Then access “http://127.0.0.1:5000/top/Fc1cc(c(F)cc1F)C%5BC@@H%5D(N)CC(=O)N3Cc2nnc(n2CC3)C(F)(F)F”
I got following image.
Work fine.
It’s very simple stuff. I’ll make more advanced app ASAP. 😉
