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

文章来源: drugai.blog.csdn.net，作者：DrugAI，版权归原作者所有，如需转载，请联系作者。

原文链接：drugai.blog.csdn.net/article/details/105030253