RDKit|RDKitに基づいて分子3 D距離行列を取得
分子の3 D距離行列を取得する場合,Get 3 DDistanceMatrix法を用いた.
入庫
0
入庫
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.MolFromSmiles('c1ccncc1')
bm1 = molDG.Get