使用pubchempy批量获取sdf格式2d分子结构（jupyter notebook实现）

CID为txt格式的pubchem中CID列

PATH为sdf格式的2d分子结构保存路径 

结果

import pubchempy as pcp

import urllib
import pubchempy as pcp
import pandas as pd
import numpy as np

with open(r'C:UserslenovoDesktopCID.txt','r',encoding='utf-8-sig') as file1:
    file_lines = file1.readlines()
    name_list=[]
#readlines读取的每行是字符串格式，采用以下代码将其转换成列表格式
    for i in file_lines:
        j=i.strip() #去掉每行头尾空白
        name_list.append(str(j))

PATH = 'D:Download'

import os
import pubchempy as pcp
for cid in name_list:
    sdfpath = os.path.join(PATH, "{}.sdf".format(cid))
    pcp.download('SDF',sdfpath, overwrite=True, identifier=cid)