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I am using jupyter lab to draw chemical structures. But the output image resolution is too low. How can I improve it?

from rdkit import Chem
from rdkit.Chem import Draw
smiles = 'C1=CC(=C(C=C1C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)O)O)O'
m = Chem.MolFromSmiles(smiles)
Draw.MolToImage(m)

Thanks a lot

Wang
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2 Answers2

4

For those looking for a solution with higher resolution molecule output AND export. The cairosvg library (also command-line program) has export options for file types including .svg, .pdf, .png, .eps (https://cairosvg.org/).

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdMolDraw2D
import cairosvg
import io


def molecule_to_pdf(mol, file_name, width=300, height=300):
    """Save substance structure as PDF"""

    # Define full path name
    full_path = f"./figs/2Dstruct/{file_name}.pdf"

    # Render high resolution molecule
    drawer = rdMolDraw2D.MolDraw2DSVG(width, height)
    drawer.DrawMolecule(mol)
    drawer.FinishDrawing()

    # Export to pdf
    cairosvg.svg2pdf(bytestring=drawer.GetDrawingText().encode(), write_to=full_path)

# Example
m = Chem.MolFromSmiles('Cn1cnc2n(C)c(=O)n(C)c(=O)c12')
molecule_to_pdf(m, "myfav")
BLT
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  • This works great! Writing the svg directly is also an option (https://github.com/rdkit/rdkit-tutorials/blob/master/notebooks/006_save_rdkit_mol_as_image.ipynb), but pdf is better supported. Quick question, do you know how to remove the white background? I cannot make much of this: https://github.com/rdkit/rdkit/issues/616 – Adriaan Jul 27 '23 at 13:04
3

I have found a solution, more information can be found here

from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from IPython.display import SVG

smiles = 'C1=CC(=C(C=C1C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)O)O)O' 
m = Chem.MolFromSmiles(smiles)

def moltosvg(mol, molSize = (300,300), kekulize = True):
    mc = Chem.Mol(mol.ToBinary())
    if kekulize:
        try:
            Chem.Kekulize(mc)
        except:
            mc = Chem.Mol(mol.ToBinary())
    if not mc.GetNumConformers():
        rdDepictor.Compute2DCoords(mc)
    drawer = rdMolDraw2D.MolDraw2DSVG(molSize[0],molSize[1])
    drawer.DrawMolecule(mc)
    drawer.FinishDrawing()
    svg = drawer.GetDrawingText()
    return svg.replace('svg:','')

SVG(moltosvg(m))
Wang
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    Yes, the RDKit has SVG rendering code which is higher quality. Also the CoordGen library can be activated in RDKit: this supports more sensible poses for drawings of molecules. And also there are some newer drawing functions in the most recent release: http://rdkit.blogspot.com/2020/04/new-drawing-options-in-202003-release.html – JoshuaBox May 12 '20 at 17:00