Request SDF files in batch

This code download SDF files of molecules in batch when provided SMILES files. The code background is: Frontend colleagues need molecular files with geometry information stored in their database. They used JavaScript library 3Dmol.js to visualize 3D molecular structrues on web application when provided sdf or pdf format files. Example SMILES txt file can be checked here. All codes mentioned in Scripts section are placed in this folder.

import requests,os
import numpy as np
from pathlib import Path
import zipfile

def download_sdf_files(smiles,path):
    # request data from pubchem
    # url_2d = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/{smiles}/SDF"
    url_3d = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/{smiles}/SDF?record_type=3d"
    response = requests.get(url_3d)
    
    # If the requests succeed, obtain the content
    if response.status_code == 200:
        sdf_content = response.content
        
        # save 3D SDF files
        with open(path/f'3d_{smiles}.sdf', 'wb') as f:
            f.write(sdf_content)
        
        print("SDF files downloaded successfully.")
    else:
        print(f"Failed to download SDF files. Status code: {response.status_code}")


if __name__=="__main__":

    dirpath = r'C:\Users\YOUR\DESTINATION\DIRECTORY\FOLDER'
    if os.getcwd() != dirpath:
        os.chdir(dirpath)
    output_head = Path.cwd()/'files'
    if not os.path.exists(output_head):
        os.mkdir(output_head)
    
    
    # ex1：given single smiles, download the 3D SDF file
    smiles = "C1=CC=C(C=C1)C=O"
    download_sdf_files(smiles,output_head)
    
    # ex2：download 3D SDF file in SMILES txt file
    mols = np.loadtxt(Path.cwd()/'SMILES.txt',dtype=str)
    for mol in mols:
        download_sdf_files(mol,output_head)

    # compress files into one file:files.zip
    with zipfile.ZipFile(Path.cwd()/'files.zip', 'w', zipfile.ZIP_DEFLATED) as myzip:
        print(os.listdir(output_head))
        for file in os.listdir(output_head):
            myzip.write(Path('./files')/file) # Relative path