如何将“IPython.core.display.SVG”保存为 PNG 文件？

Question

我正在尝试在 Jupyter Notebook 环境中将数据类型为“IPython.core.display.SVG”的变量保存为 PNG 文件。

首先我尝试过：

with open('./file.png','wb+') as outfile:
    outfile.write(my_svg.data)

我得到了错误：

TypeError: a bytes-like object is required, not 'str'

接下来，我尝试了：

with open('./file.png','wb+') as outfile:
    outfile.write(my_svg.data.encode('utf-8'))

但是，我无法打开“file.png”。操作系统报错：

The file “file.png” could not be opened. It may be damaged or use a file format that Preview doesn’t recognize.

我可以使用“svg”扩展名保存“my_svg”，如下所示：

with open('./file.svg','wb+') as outfile:
    outfile.write(my_svg.data.encode('utf-8'))

但是，当我想通过以下方式将“file.svg”转换为“file.png”时：

import cairosvg
cairosvg.svg2png(url="./file.svg", write_to="./file.png")

我得到错误：

ValueError: unknown locale: UTF-8

这就是我在 Jupyter Notebook 中获得“IPython.core.display.SVG”数据类型的方式：

from rdkit import Chem
from rdkit.Chem.Draw import rdMolDraw2D
from IPython.display import SVG


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))

mols = [m1, m2]
legends = ["smile_1", "smile_2"]

molsPerRow=2
subImgSize=(200, 200)
nRows = len(mols) // molsPerRow
if len(mols) % molsPerRow:
  nRows += 1
  
fullSize = (molsPerRow * subImgSize[0], nRows * subImgSize[1])
d2d = rdMolDraw2D.MolDraw2DSVG(fullSize[0], fullSize[1], subImgSize[0], subImgSize[1])
d2d.drawOptions().prepareMolsBeforeDrawing=False
d2d.DrawMolecules(list(mols), legends=legends)
d2d.FinishDrawing()
SVG(d2d.GetDrawingText())

环境：

• macOS 11.2.3
• python 3.6
• RDKit 版本 2020.09.1

非常感谢任何帮助。

Answer 1

与其使用 rdkit 创建 SVG 并尝试将其转换为 PNG，不如直接创建一个 PNG？

from rdkit.Chem import Draw
from rdkit import Chem

# create rdkit mol
smile = 'CCCC'
mol = Chem.MolFromSmiles(smile)

# create png
d2d = Draw.MolDraw2DCairo(200, 200)
d2d.DrawMolecule(mol)
d2d.FinishDrawing()
png_data = d2d.GetDrawingText()

# save png to file
with open('mol_image.png', 'wb') as png_file:
    png_file.write(png_data)

我不确定为什么 MolDraw2DCairo 不适合你，但使用你提到的包 (cairosvg) 你可以很容易地扩展你的代码示例：

# extra imports
import cairosvg
import tempfile

# replace molecule drawing part
d2d = rdMolDraw2D.MolDraw2DSVG(fullSize[0], fullSize[1], subImgSize[0], subImgSize[1])
d2d.drawOptions().prepareMolsBeforeDrawing=False
d2d.DrawMolecules(list(mols), legends=legends)
d2d.FinishDrawing()
svg_text = d2d.GetDrawingText()

# save to png file
with tempfile.NamedTemporaryFile(delete=True) as tmp:
    tmp.write(svg_text.encode())
    tmp.flush()
    cairosvg.svg2png(url=tmp.name, write_to="./mol_img.png")