Introduction

In RDKit, I would like to define a reaction pattern in SMARTS and generate a product from the reactant based on that pattern.

environment

Windows 10
RDkit 2019.03.3.0

Method

Please refer to the references.

Reaction I tried this time

This time I would like to try the hydroxylation reaction of carbon atoms. The SMARTS pattern is as follows.

[C:1]>>[C:1][OH]

For the reaction product, the following compounds were tried.

Source

The source is as follows. I tried to output all the products produced by the reaction to an image.

from rdkit.Chem import AllChem
from rdkit.Chem.Draw import rdMolDraw2D
from io import BytesIO
from cairosvg import svg2png
from IPython.display import SVG
from rdkit import Chem

#Image output
def generate_image(mol, size, path, name):

    image_data = BytesIO()
    view = rdMolDraw2D.MolDraw2DSVG(size[0], size[1])
    tm = rdMolDraw2D.PrepareMolForDrawing(mol)

    view.DrawMolecule(tm)
    view.FinishDrawing()
    svg = view.GetDrawingText()
    SVG(svg.replace('svg:', ''))
    print(path + "/" + name)
    try:
        svg2png(bytestring=svg, write_to=path + "/" + name + ".png ")
    except:
        pass


def main():
    reactant_1 = Chem.MolFromSmiles('COc2ccc1cccc(CCNC(C)=O)c1c2')
    reaction_pattern = '[C:1]>>[C:1][OH]'
    rxn = AllChem.ReactionFromSmarts(reaction_pattern)
    x = rxn.RunReactants([reactant_1])
    for i, mol in enumerate(x):
        print(mol[0])
        try:
            Chem.SanitizeMol(mol[0])
            generate_image(mol[0], (300, 300), "tmp", "metablite_{0}".format(i))
        except:
            print("Error")
            print(Chem.MolToMolBlock(mol[0]))


if __name__ == "__main__":
    main()

Verification

Four products were obtained. One was an error due to the charge when sanitizing. Let's check the result with an image.

Product 1

Product 2

Product 3

Product 4

Product 5 (charge error due to sanitizing process)

Consideration

--The result is as expected. --There was no reaction of the aromatic ring to the C atom, but the reason is not clear. It is necessary to confirm the specifications (future issues) —— In any case, it will be necessary to determine whether the produced reactant is a valid compound.

References

-Chemical reaction with RDKit: How to handle reaction formulas in chemoinformatics -Story of playing with SMARTS notation and RDKit chemical reaction

Define the reaction pattern with SMARTS with RDKit and generate a reactant