rdkit：如何绘制高分辨率化学结构

Question

我正在使用 jupyter 实验室绘制化学结构。但输出图像分辨率太低。我该如何改进它？from rdkit import Chemfrom rdkit.Chem import Drawsmiles = 'C1=CC(=C(C=C1C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)O)O)O'm = Chem.MolFromSmiles(smiles)Draw.MolToImage(m)

Answer 1

对于那些寻找具有更高分辨率分子输出和输出的解决方案的人。该cairosvg库（也是命令行程序）具有文件类型的导出选项，包括 .svg、.pdf、.png、.eps ( https://cairosvg.org/ )。

from rdkit import Chem

from rdkit.Chem import Draw

from rdkit.Chem.Draw import rdMolDraw2D

import cairosvg

import io

def molecule_to_pdf(mol, file_name, width=300, height=300):

    """Save substance structure as PDF"""

    # Define full path name

    full_path = f"./figs/2Dstruct/{file_name}.pdf"

    # Render high resolution molecule

    drawer = rdMolDraw2D.MolDraw2DSVG(width, height)

    drawer.DrawMolecule(mol)

    drawer.FinishDrawing()

    # Export to pdf

    cairosvg.svg2pdf(bytestring=drawer.GetDrawingText().encode(), write_to=full_path)

# Example

m = Chem.MolFromSmiles('Cn1cnc2n(C)c(=O)n(C)c(=O)c12')

molecule_to_pdf(m, "myfav")

Answer 2

我找到了解决方案，更多信息可以在这里找到

from rdkit import Chem

from rdkit.Chem.Draw import IPythonConsole

from rdkit.Chem import rdDepictor

from rdkit.Chem.Draw import rdMolDraw2D

from IPython.display import SVG

smiles = 'C1=CC(=C(C=C1C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)O)O)O' 

m = Chem.MolFromSmiles(smiles)

def moltosvg(mol, molSize = (300,300), 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.replace('svg:','')

SVG(moltosvg(m))