Source code for Scaffolds

# -*- coding: utf-8 -*-
#  Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
#  All rights reserved.
#  This file is part of the PyBioMed.
#  The contents are covered by the terms of the BSD license
#  which is included in the file license.txt, found at the root
#  of the PyBioMed source tree.
"""
##############################################################################
This module provides standard Murcko-type decomposition of molecules into scaffolds. 

If you have any question please contact me via email.

Bemis, G. W.; Murcko, M. A. “The Properties of Known Drugs. 1. Molecular Frameworks.” 
J. Med. Chem. 39:2887-93 (1996).

2016.11.15

@author: Zhijiang Yao and Dongsheng Cao

Email: gadsby@163.com and oriental-cds@163.com

##############################################################################
"""

from rdkit import Chem
from rdkit.Chem.Scaffolds import MurckoScaffold

def GetScaffold(mol, generic_framework = False):
    """
    #################################################################
    Calculate Scaffold
    
    Usage:
        
        result = GetScaffold(mol)
        
        Input: mol is a molecule object.
        
        generic_framework is boolean value. If the generic_framework is True, the
        
        result returns a generic framework.
        
        Output: result is a string form of the molecule's scaffold.
    #################################################################
    """
    core = MurckoScaffold.GetScaffoldForMol(mol)
    if generic_framework == True:
        fw = MurckoScaffold.MakeScaffoldGeneric(core)
        mol_generic_framework = Chem.MolToSmiles(fw)    
        return mol_generic_framework
    else:
        mol_scafflod = Chem.MolToSmiles(core)
        return mol_scafflod
  

def GetUniqueScaffold(mols, generic_framework = False):
    """
    #################################################################
    Calculate molecules' unique scaffolds
    
    Usage:
        
        result = GetUniqueScaffold(mols)
        
        Input: mols is molecules object.
        
        generic_framework is boolean value. If the generic_framework is True, the
        
        result returns a generic framework dictionary.
        
        Output: result is a tuple form. The first is the list of 
        
        unique scaffolds. The second is a dict form whose keys are the 
        
        scaffolds and the values are the scaffolds' count. 
    #################################################################
    """
    scaffolds_dict = {}
    if generic_framework == True:
        for mol in mols:
            scaffold = GetScaffold(mol,generic_framework = True)
            if scaffold not in scaffolds_dict:
                scaffolds_dict[scaffold] = 1
            else:
                scaffolds_dict[scaffold] += 1
    else:    
        for mol in mols:
            scaffold = GetScaffold(mol)
            if scaffold not in scaffolds_dict:
                scaffolds_dict[scaffold] = 1
            else:
                scaffolds_dict[scaffold] += 1
    return scaffolds_dict.keys(),scaffolds_dict
    
  



if __name__ == '__main__':    
    m1 = Chem.MolFromSmiles('O=C1N=C(Nc2ncc(nc12)CNc1ccc(cc1)C(=O)N[C@@H](CCC(O)=O)C(O)=O)N')
    print GetScaffold(m1)
    print GetScaffold(m1,generic_framework = True)
    mols = [m1]*3
    print GetUniqueScaffold(mols)