[Python] How to change highlight color using MolsToGridImage in RDKit using python?

The cheminformatics RDKit tool features the RDKit Cookbook with example code for a range of applications. One of them is to Highlight the Differences between 2 Molecules, here by using fMCS to map similarities, then marking those residues which are not shared. This example works well, the code is here

I need the change the highlight color, but cannot get it to work. Based on the code link above, I've tried so far:

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import rdFMCS
from rdkit.Chem.Draw import rdDepictor
rdDepictor.SetPreferCoordGen(True)
IPythonConsole.drawOptions.minFontSize=20
IPythonConsole.drawOptions.setHighlightColour=(0,1,0)
from collections import defaultdict


This had no effect at all, pic was drawn with default highlight.

d2g = Draw.MolsToGridImage([mol1, mol2])
opts = d2g.drawOptions()
opts.setHighlightColour = (0,1,0)
d2g([mol1, mol2],highlightAtomLists=[target_atm1, target_atm2])


This throws the error

AttributeError: 'Image' object has no attribute 'drawOptions'
​

Then I got it to work with this one:

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw import rdMolDraw2D
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import rdFMCS
from rdkit.Chem.Draw import rdDepictor
rdDepictor.SetPreferCoordGen(True)
IPythonConsole.drawOptions.minFontSize=20
from collections import defaultdict

mol1 = Chem.MolFromSmiles('FC1=CC=C2C(=C1)C=NN2')
mol2 = Chem.MolFromSmiles('CCC1=C2NN=CC2=CC(Cl)=C1')

from PIL import Image
from io import BytesIO
def show_mol(d2d,mol,legend='',highlightAtoms=[]):
d2d.DrawMolecule(mol,legend=legend, highlightAtoms=highlightAtoms)
d2d.FinishDrawing()
bio = BytesIO(d2d.GetDrawingText())
return Image.open(bio)
def show_images(imgs,buffer=5):
height = 0
width = 0
for img in imgs:
height = max(height,img.height)
width += img.width
width += buffer*(len(imgs)-1)
res = Image.new("RGBA",(width,height))
x = 0
for img in imgs:
res.paste(img,(x,0))
x += img.width + buffer
return res

mcs = rdFMCS.FindMCS([mol1,mol2])
mcs_mol = Chem.MolFromSmarts(mcs.smartsString)
match1 = mol1.GetSubstructMatch(mcs_mol)
target_atm1 = []
for atom in mol1.GetAtoms():
if atom.GetIdx() not in match1:
target_atm1.append(atom.GetIdx())
match2 = mol2.GetSubstructMatch(mcs_mol)
target_atm2 = []
for atom in mol2.GetAtoms():
if atom.GetIdx() not in match2:
target_atm2.append(atom.GetIdx())

img1 = []
d2dx = Draw.MolDraw2DCairo(350,300)
doptsx = d2dx.drawOptions()
doptsx.setHighlightColour((1,0.84,0,.5))
img1.append(show_mol(d2dx,mol1,highlightAtoms=target_atm1))
d2dx = Draw.MolDraw2DCairo(350,300)
doptsx = d2dx.drawOptions()
doptsx.setHighlightColour((1,0.84,0,.5))
img1.append(show_mol(d2dx,mol2, highlightAtoms=target_atm2))
pic = show_images(img1)
pic.save('hallo.png')
pic


Problems are, 1) I need an svg output and, 2) if the molecules have different size or alternate SMILE config is used, only MolsToGrid places them properly adjacent within same subpanel boundaries. So I need to use MolsToGrid for scientific publication-quality images.

I am a complete python n00b using jupyter lab on a windows 11 PC.

Python 3.8.18 (default, Sep 11 2023, 13:39:12) [MSC v.1916 64 bit (AMD64)] :: Anaconda, Inc. on win32
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