CODEWITHSUNDEEP
pythonchemistryrdkit
hehe
hehe

Reputation: 775

Create a scaled molecule rdkit

I am using RDKit in python to draw a molecule, and I want to get a high-definition image

This is my current code

mol = Chem.MolFromSmiles("CCO")
mol = Chem.AddHs(mol)
img = Draw.MolToImage(mol)

I want it to be ~ 2000x1000 pixels

I tried: img = Draw.MolToImage(mol, size = (2000,1000)) but although the canvas increases in size, the line width and font size remains constant.

Scaling with img.resize() is not ok because I want to get a non-pixelated output.

The closes to an answer is this. However when I try creating its parent class I get an error:

>> a = Draw.rdMolDraw2D.MolDraw2D()
RuntimeError: This class cannot be instantiated from Python

tldr; I am trying to find out a way to scale the image while it is rendering.

I am also ok using an alternative to RDKit, all I need is a way to display chemical structures from SMILES in a high-def (2000x1000) image.

Side question: Is there a way to show carbon atoms too? Can't find any docs for both these questions.

Upvotes: 0

Views: 61

Answers (2)

pippo1980
pippo1980

Reputation: 3061

This code works, see RDKit SetScale method for drawing:

import rdkit
print('\n-------------------------------')
print('\n rdkit Version : ', rdkit.__version__)
print('\n-------------------------------')

from rdkit import Chem

from rdkit.Chem import Draw

from rdkit.Geometry.rdGeometry import Point2D

from PIL import Image
from io import BytesIO


mol = Chem.MolFromSmiles("CCO")
mol = Chem.AddHs(mol)

# drawer = Draw.MolDraw2DSVG(200, 400, 200, 200)

drawer = Draw.MolDraw2DCairo(200, 400, 200, 200)

minv = Point2D(1000, 1000)

maxv = Point2D(-1000, -1000)

drawer.SetScale(10, 10, minv, maxv)

drawer.DrawMolecule(mol)

drawer.SetOffset(0, 200)

drawer.DrawMolecule(mol)

drawer.FinishDrawing()

print('drawer.GetDrawingText() : ', drawer.GetDrawingText() , type(drawer.GetDrawingText()))

bio = BytesIO(drawer.GetDrawingText())

img = Image.open(bio)

img.save('test.png')

img.show()

Output:

enter image description here

But I still don't understand how SetScale works, especially the minv and maxv paramters in:

drawer.SetScale(50, 50, minv, maxv)

Upvotes: 0

hehe
hehe

Reputation: 775

I ended up first rendering as a svg and then scaling + converting to a png, here is the implementation:

from rdkit import Chem
from rdkit.Chem import Draw
import cairosvg  #You can use some toher library to convert svg to png

mol = Chem.MolFromSmiles("CCO")
mol = Chem.AddHs(mol)

drawer = Draw.MolDraw2DSVG(300, 150) #You can adjust this, however to keep it looking good, both width,height should be between 150-400 inclusive.
drawer.DrawMolecule(mol)
drawer.FinishDrawing()

svg_data = drawer.GetDrawingText()
cairosvg.svg2png(bytestring=svg_data.encode('utf-8'), write_to="molecule.png", scale=10) #Adjust scale for higher-def image

Upvotes: 0

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