python聚类_Python脚本：聚类小分子数据集

聚类分子（Clustering molecules）

聚类是一种有价值的化学信息学技术，用于将大型化合物数据集合细分为单个小组相似化合物。其中一个优点是处理非常大的小分子数据集时特别有用。通常用于分析高通量筛选结果、虚拟筛选或对接研究的分析。

基于RDKit的Python脚本用于聚类分子

#!/usr/bin/python3
# coding: utf-8
#http://www.rdkit.org/docs/Cookbook.html  - - -Clustering molecules
#AspirinCode.20180725
 
def ClusterFps(fps,cutoff=0.2):
    from rdkit import DataStructs
    from rdkit.ML.Cluster import Butina
 
    # first generate the distance matrix:
    dists = []
    nfps = len(fps)
    for i in range(1,nfps):
        sims = DataStructs.BulkTanimotoSimilarity(fps[i],fps[:i])
        dists.extend([1-x for x in sims])
 
    # now cluster the data:
    cs = Butina.ClusterData(dists,nfps,cutoff,isDistData=True)
    return cs
 
from rdkit import Chem
from rdkit.Chem import AllChem
 
#generate fingerprints
ms = [x for x in Chem.ForwardSDMolSupplier('ApprovedDrugs.sdf') if x is not None]
fps = [AllChem.GetMorganFingerprintAsBitVect(x,2,1024) for x in ms]
 
#cluster
clusters=ClusterFps(fps,cutoff=0.4)
 
# show one of the clusters
print(clusters[20])
 
#now display structures from one of the clusters
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
 
#look at a specific cluster
m1 = ms[1630]
m2 = ms[1010]
m3 = ms[1022]
m4 = ms[1023]
m5 = ms[1034]
m6 = ms[1043]
mols=(m1,m2,m3,m4,m5,m6)
Draw.MolsToGridImage(mols)

Jupyter Notebook运行效果

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