RDKit | 基于RDKit的指定原子或键高亮

基于RDKit的指定原子或键高亮

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指定原子或键高亮

HilightChemAtom.py 

from rdkit import Chem
from rdkit.Chem.Draw import rdMolDraw2D
from IPython.display import SVG
from io import BytesIO
from PIL import Image
from cairosvg import svg2png
import argparse


def generate_image(mol, highlight_atoms, highlight_bonds, atomColors, bondColors, radii, size, output, isNumber=False):

    print(highlight_atoms)
    print(highlight_bonds)
    print(atomColors)
    print(bondColors)

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

    option = view.drawOptions()
    if isNumber:
        for atom in mol.GetAtoms():
            option.atomLabels[atom.GetIdx()] = atom.GetSymbol() + str(atom.GetIdx() + 1)

    view.DrawMolecule(tm, highlightAtoms=highlight_atoms, highlight