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.
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