RDKit | 可视化分子来自于xyz文件

                                              通过xyz文件可视化小分子

导入库

from __future__ import print_function
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from IPython.display import SVG

from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D

定义mol转svg函数

def moltosvg(mol,molSize=(450,150),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

def render_svg(svg):
    return SVG(svg.replace(