如何在 RDKit 中用粗红线将分子的子结构突出显示为 SVG（高分辨率）

Question

我有以下代码：

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


m = Chem.MolFromSmiles('c1cc(C(=O)O)c(OC(=O)C)cc1')
substructure = Chem.MolFromSmarts('C(=O)O')
print(m.GetSubstructMatches(substructure))
m

产生以下情节。

但是上面的代码不会生成高分辨率图像。我想要 SVG。我试过这个：

drawer = rdMolDraw2D.MolDraw2DSVG(400,200)
drawer.DrawMolecule(m,highlightAtoms=m.GetSubstructMatch(Chem.MolFromSmarts('C(=O)O')))
drawer.FinishDrawing()
svg = drawer.GetDrawingText().replace('svg:','')
SVG(svg)

但我得到：

正确的做法是什么？

代码可以在我的Google Colab.

中测试

Answer 1

GetSubstructMatch returns 只有第一场比赛。使用 GetSubstructMatches。根据您安装的 rdkit 版本，这里有多种情况。在最新的rdkit版本（2021.09.2）中，下面的代码应该可以工作。

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
from copy import deepcopy


def increase_resolution(mol, substructure, size=(400, 200)):
    mol = deepcopy(mol)
    substructure = deepcopy(substructure)
    drawer = rdMolDraw2D.MolDraw2DSVG(size[0], size[1])
    
    # highlightAtoms expects only one tuple, not tuple of tuples. So it needs to be merged into a single tuple
    matches = sum(mol.GetSubstructMatches(substructure), ())
    drawer.DrawMolecule(mol, highlightAtoms=matches)
    
    drawer.FinishDrawing()
    svg = drawer.GetDrawingText()
    
    return svg.replace('svg:','')


mol = Chem.MolFromSmiles('c1cc(C(=O)O)c(OC(=O)C)cc1')
substructure = Chem.MolFromSmarts('C(=O)O')
SVG(increase_resolution(mol, substructure))

如果您收到 Value Error: Bad Conformer id 错误，请将 rdkit 包更新到最新版本或尝试以下操作：

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
from copy import deepcopy


def increase_resolution(mol, substructure, size=(400, 200), kekulize=True):
    mol = deepcopy(mol)
    substructure = deepcopy(substructure)
    rdDepictor.Compute2DCoords(mol)
    if kekulize:
        Chem.Kekulize(mol) # Localize the benzene ring bonds
        
    drawer = rdMolDraw2D.MolDraw2DSVG(size[0], size[1])
    
    # highlightAtoms expects only one tuple, not tuple of tuples. So it needs to be merged into a single tuple
    matches = sum(mol.GetSubstructMatches(substructure), ())
    drawer.DrawMolecule(mol, highlightAtoms=matches)
    
    drawer.FinishDrawing()
    svg = drawer.GetDrawingText()
    return svg.replace('svg:','')


mol = Chem.MolFromSmiles('c1cc(C(=O)O)c(OC(=O)C)cc1')
substructure = Chem.MolFromSmarts('C(=O)O')
SVG(increase_resolution(mol, substructure, kekulize=True))

如果对于某些情况，例如作为 SMILES 字符串的一部分在其中引入手性的结构，它可能无法工作。对于这种情况，设置 kekulize=False.

如何在 RDKit 中用粗红线将分子的子结构突出显示为 SVG（高分辨率）

How to highlight the substructure of a molecule with thick red lines in RDKit as SVG (high res)

python

rdkit