RDKit | 基于RDKit获取分子3D距离矩阵

获取分子的3D距离矩阵时，使用Get3DDistanceMatrix方法。
 

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 导入库

from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdDistGeom as molDG

mol = Chem.MolFromSmiles('CCC')
bm = molDG.GetMoleculeBoundsMatrix(mol)
bm

array([[0.        , 1.524     , 2.51279063],
       [1.504     , 0.        , 1.524     ],
       [2.43279063, 1.504     , 0.        ]])

AllChem.EmbedMolecule(mol)

0

dm=AllChem.Get3DDistanceMatrix(mol)
dm

array([[0.        , 1.50401361, 2.47848679],
       [1.50401361, 0.        , 1.50913087],
       [2.47848679, 1.50913087, 0.        ]])

mol1 = Chem.MolFromSmil