网络药理学：SwissADME和PubChem和TCMSP互通（TCMSP爬虫批量得到化合物名称或Mol ID、批量转换为SDF文件/SMILES序列号/CID）

TCMSP爬虫批量得到化合物名称或Mol ID

见我的另一篇博客：http://t.csdnimg.cn/lTg6k

通过化合物名称批量获得SMILES序列号/CID序列号

import pubchempy
import pandas as pd
import itertools
import time

def read_file(file_name) -> list:
    """
    读取化合物名称
    :param file_name: 含有化合物名称的txt或csv格式文件（含路径）
    :return: list
    """
    try:
        df = pd.read_csv(file_name, sep=',', encoding='utf-8-sig')
        if 'Molecule Name' in df.columns.values:
            return df['Molecule Name'].tolist()
    except pd.errors.ParserError:  # 如果文件不是CSV格式，说明是txt格式，继续尝试
        pass

    with open(file_name, 'r', encoding='utf-8-sig') as file:
        return [line.strip() for line in file.readlines()]


def get_compound_info(name: list):
    """
    获取化合物信息
    :param name: 化合物名称列表
    """
    try:
        compounds = pubchempy.get_compounds(name, 'name')
        for compound in compounds:
            result = {
                'name': name,
                'molecular_formula': compound.molecular_formula,
                'molecular_weight': compound.molecular_weight,
                'smiles': compound.isomeric_smiles,
                'synonyms': compound.synonyms,
                'cid': compound.cid
            }
            print(
                f"CID: {compound.cid}\tMass: {compound.exact_mass}\tName: {compound.iupac_name}\tMolfor: {compound.molecular_formula}\tSmi: {compound.isomeric_smiles}\tSyn: {compound.synonyms}")
            yield result
    except Exception as e:
        print("occurred error when processing compound", name)
        print(str(e))
        return


def chemName_to_Smiles_or_CID(input_file_name, output_file_name):
    """
    通过化合物名称批量获得SMILES序列号/CID序列号
    :param input_file_name:含有化合物名称的txt格式文件（含路径），一行一个化合物名称，换行符分隔
    :param output_file_name: 输出文件（含路径）
    """

    start_time = time.time()

    # 输入
    name_list = read_file(input_file_name)
    # 生成器优化循环遍历
    results = itertools.chain.from_iterable(get_compound_info(name) for name in name_list)
    # 输出
    dataframe = pd.DataFrame(results)
    dataframe.to_csv(output_file_name, index=False, sep=',')
    
    # 结束计时
    end_time = time.time()
    print(f"Total queries: {len(dataframe)}")
    print(f"Elapsed time: {end_time - start_time:.2f} seconds")


if __name__ == '__main__':
    print("start convert")

    input_file_name = "1-TCMSP.csv"
    output_file_name = "smiles_and_cid.csv"

    chemName_to_Smiles_or_CID(input_file_name, output_file_name)