Github4043.ipynb

Github4043.ipynb

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      "source": "from rdkit import Chem\nfrom rdkit.Chem import Draw\nfrom rdkit.Chem import rdDepictor\nimport rdkit\nprint(rdkit.__version__)",
      "execution_count": 1,
      "outputs": [
        {
          "output_type": "stream",
          "text": "2021.03.1\n",
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      "source": "m = Chem.MolFromSmiles('C(C(N)=O)c(c)c',sanitize=False)\nChem.SanitizeMol(m,sanitizeOps=(Chem.SanitizeFlags.SANITIZE_ALL^Chem.SanitizeFlags.SANITIZE_KEKULIZE^Chem.SanitizeFlags.SANITIZE_SETAROMATICITY))\nrdDepictor.Compute2DCoords(m)",
      "execution_count": 2,
      "outputs": [
        {
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          "execution_count": 2,
          "data": {
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      ]
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      "cell_type": "code",
      "source": "from IPython.display import SVG\nd2d = Draw.MolDraw2DSVG(250,200)\nd2d.drawOptions().prepareMolsBeforeDrawing=False\nd2d.DrawMolecule(m)\nd2d.FinishDrawing()\nSVG(d2d.GetDrawingText())",
      "execution_count": 3,
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        {
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Thank you very much for your time and effort to prepare this notebook.
I tried to do the same with "Draw.MolsToGridImage" (since I have several smiles and I would like to use smiles as legend to the image).

I tried the following code:

from rdkit import Chem
from rdkit.Chem import Draw
from rdkit.Chem.Draw.MolDrawing import DrawingOptions

smile_1 = 'C(C(N)=O)c(c)c'
smile_2 = 'o(cn)c(c)c'

m1 = Chem.MolFromSmiles(smile_1,sanitize=False)
Chem.SanitizeMol(m1, sanitizeOps=(Chem.SanitizeFlags.SANITIZE_ALL^Chem.SanitizeFlags.SANITIZE_KEKULIZE^Chem.SanitizeFlags.SANITIZE_SETAROMATICITY))
m2 = Chem.MolFromSmiles(smile_2,sanitize=False)
Chem.SanitizeMol(m2, sanitizeOps=(Chem.SanitizeFlags.SANITIZE_ALL^Chem.SanitizeFlags.SANITIZE_KEKULIZE^Chem.SanitizeFlags.SANITIZE_SETAROMATICITY))

UpdatedDrawingOptions = DrawingOptions()
UpdatedDrawingOptions.prepareMolsBeforeDrawing=False

Draw.MolsToGridImage([m1, m2], legends = [smile_1, smile_2], drawOptions=UpdatedDrawingOptions)

But, an error came up:

TypeError: MolsToGridImage() got multiple values for keyword argument 'drawOptions'

I looked at the source code of "Draw.MolsToGridImage". There is an if-condition as below:

if drawOptions is not None:
    d2d.SetDrawOptions(drawOptions)

However, I couldn't understand how to pass Draw Options to "Draw.MolsToGridImage".

Also, if I remove UpdatedDrawingOptions.prepareMolsBeforeDrawing=False and use "Draw.MolsToGridImage" without "drawOptions", I get another error:

AtomKekulizeException: non-ring atom 4 marked aromatic

Sorry for the trouble but any help is really appreciated. Thank you.

please ask rdkit-related questions on the discussions tab in the rdkit github repo