RDKit：化合物骨架分析（基于Python3）

基于RDKit的骨架分析

代码实例：

  

   

    

     

    
    

     

      # In[1]:
     
    
   

    

     

    
    

     

      #!/usr/bin/env python3
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

      from rdkit import Chem
     
    
   

    

     

    
    

     

      from rdkit.Chem import Draw
     
    
   

    

     

    
    

     

      from rdkit.Chem.Scaffolds import MurckoScaffold
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

      # In[2]:
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

      drugbank_input = Chem.SDMolSupplier('drugbank.sdf')
     
    
   

    

     

    
    

     

      drugbank = [m for m in drugbank_input if m]
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

      # In[3]:
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

      basic_structure = drugbank[222]
     
    
   

    

     

    
    

     

      atomic_scaffold = MurckoScaffold.GetScaffoldForMol(basic_structure)
     
    
   

    

     

    
    

     

      atomic_scaffold.Compute2DCoords()
     
    
   

    

     

    
    

     

      graph_scaffold = MurckoScaffold.MakeScaffoldGeneric(atomic_scaffold)
     
    
   

    

     

    
    

     

      Draw.MolsToGridImage([basic_structure, atomic_scaffold, graph_scaffold])
     
    
  
 

  

   

    

     

    
    

     

      # In[4]:
     
    
   

    

     

    
    

     
 
     
    
   

    

     

    
    

     

      drugbank_atomic_scaffolds = [MurckoScaffold.GetScaffoldForMol(mol) for mol in drugbank]
     
    
   

    

     

    
    

     

      for i in
     
    
  
 

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/82082317