TA貢獻(xiàn)1744條經(jīng)驗 獲得超4個贊
對于那些尋找具有更高分辨率分子輸出和輸出的解決方案的人。該cairosvg庫（也是命令行程序）具有文件類型的導(dǎo)出選項，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")
TA貢獻(xiàn)1827條經(jīng)驗 獲得超8個贊
我找到了解決方案，更多信息可以在這里找到
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))
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