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  • 分子指纹相似度的可视化

    rdkit有一个很炫酷的功能,那就是能可视化显示两个分子的相似性。

    以下面两个分子为例:

    D-Aspartate and L-Sep Molecules

    计算相似度

    from rdkit import Chem
    from rdkit.Chem import AllChem, DataStructs
    from rdkit.Chem.Fraggle import FraggleSim
    
    # define TanimotoSim calculator for convinience.
    def calctc(mol1,mol2):
        fp1=AllChem.GetMorganFingerprintAsBitVect(mol1,2)
        fp2=AllChem.GetMorganFingerprintAsBitVect(mol2,2)
        return DataStructs.TanimotoSimilarity(fp1,fp2)
    
    # make molecule from smiles.
    mol=Chem.MolFromSmiles("N[C@H](CC(=O)O)C(=O)O")
    mol2=Chem.MolFromSmiles("N[C@@H](CO)C(=O)O")
    
    # calc. molecular similarity like ECFP4.
    In [26]: calctc(mol,mol2)
    Out[26]: 0.3333333333333333
    #only N,C difference but low similarity !
     
    # calc Fraggle sim.
    In [27]:FraggleSim.GetFraggleSimilarity(mol,mol2)
    Out[27]: (1.0, '[*]c1ccccc1.[*]c1ccccc1')
    # near my feeling.
    

    将相似度映射到分子图像

    %matplotlib inline
    %pylab inline
    from IPython.display import Image
     
    from rdkit.Chem import AllChem as Chem
    from rdkit.Chem.Draw import IPythonConsole
    from rdkit.Chem.Draw import SimilarityMaps
     
    smiles1 = 'N[C@H](CC(=O)O)C(=O)O' #ZINC000000895218 (D-Aspartate)
    smiles2 = 'N[C@@H](CO)C(=O)O' #ZINC000000895034 (L-Ser)
     
    mol1 = Chem.MolFromSmiles(smiles1)
    mol2 = Chem.MolFromSmiles(smiles2)
     
    SimilarityMaps.GetSimilarityMapForFingerprint(mol2, mol1, SimilarityMaps.GetMorganFingerprint)
    

    结果如下:

    Similarity

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  • 原文地址:https://www.cnblogs.com/liulunyang/p/14302723.html
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