RDKit | 基于RDKit从分子中提取3D药效团特征

从分子中提取3D药效团特征

导入库

import os
from rdkit import Geometry
from rdkit import RDConfig
from rdkit.Chem import AllChem
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem.Pharm3D import Pharmacophore

载入数据，计算3D药效团特征 

FEAT = os.path.join(RDConfig.RDDataDir, "BaseFeatures.fdef")
featfact = ChemicalFeatures.BuildFeatureFactory(FEAT)
mol = Chem.MolFromSmiles('c1cccnc1')
AllChem.EmbedMolecule(mol)
feats = featfact.GetFeaturesForMol(mol)
for feat in feats:
    print(feat.GetFamily())
    pos = feat.GetPos()
    print(pos.x, pos.y, pos.z)

Acceptor
-0.7520182725486869 1.1296446496915278 0.019479874267963344
Aromatic
-6.938893903907228e-16 -4.85722573273506e-16 -5.206338832275392e-16