RDKit | 基于RDKit计算3D药效团指纹

3D Pharmacophore指纹

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导入库

from rdkit import Chem, DataStructs, RDConfig
from rdkit.Chem import AllChem
from rdkit.Chem.Pharm2D import Gobbi_Pharm2D, Generate

载入数据，产生3D结构

mol = Chem.MolFromSmiles( 'O=C2C(Cc1ccc(cc1)C(C(=O)O)C)CCC2' )
AllChem.EmbedMolecule(mol) #gen 3d

计算3D Pharmacophore指纹

factory = Gobbi_Pharm2D.factory
#calc 3d p4 fp
fp = Generate.Gen2DFingerprint(mol, factory, dMat = Chem.Get3DDistanceMatrix(mol))
fp

len(fp)

39972

fp.GetNum