科研小白0126 发表于 2025-8-20 15:59
您好方便问一下您这是chemdraw哪个版本吗，我的ChemDraw 22.0.0 64未找到该工具

其实不需要使用工具来写键接位点，直接使用文本编辑，在键接位点处用文本写入*即可（注意对其位点）

王纪峰 发表于 2025-8-20 20:12
后台发现您这边输入的单体SMILES过于复杂，在转化为SMILES转化为3D结构的过程出现了问题，导致失败，目前 ...

好的谢谢您

科研小白0126 发表于 2025-8-19 21:50
大佬我这是smile格式不对吗，纯小白
Failed to run notebook: 2_Polymer_chg_and_Polymer_creation_ Linea ...

后台发现您这边输入的单体SMILES过于复杂，在转化为SMILES转化为3D结构的过程出现了问题，导致失败，目前正在想方法解决。

科研小白0126 发表于 2025-8-20 18:12
打扰您了，我这个两个任务正在进行是只有完全结束才会显示在下面的任务历史的吗

这两个任务是我的吗老师，我看下面历史记录和我提交的时间不一样

打扰您了，我这个两个任务正在进行是只有完全结束才会显示在下面的任务历史的吗

科研小白0126 发表于 2025-8-20 15:59
您好方便问一下您这是chemdraw哪个版本吗，我的ChemDraw 22.0.0 64未找到该工具

你能给某个原子标正负电荷，就能标上那个*

我用的很旧了，还是2012版的

牧生 发表于 2025-8-20 12:22
一般情况下，很多人用chemdraw画结构式，没有很注意那个连接位点，包括我自己也从来就没注意过那个*号表示 ...

您好方便问一下您这是chemdraw哪个版本吗，我的ChemDraw 22.0.0 64未找到该工具

王纪峰 发表于 2025-8-20 10:29
认真看帖子，写的SMILES明显不对，键接位点呢

万分感谢您的回复

牧生 发表于 2025-8-20 12:22
一般情况下，很多人用chemdraw画结构式，没有很注意那个连接位点，包括我自己也从来就没注意过那个*号表示 ...

感谢大神终于知道怎么在smiles里找连接位点了

It sounds good. I'll try it.

一般情况下，很多人用chemdraw画结构式，没有很注意那个连接位点，包括我自己也从来就没注意过那个*号表示连接点。。

我在这里帖一下方法。。

用丙烯酸为例：

因为组合成聚合物链，是一个重复过程，所以，必须画重复的单元，*号视为那个连接的点，需要在两端分别点上一个*号，且电荷必须正确。



得到的结果就是这样的结构式


然后复制为SMILES



得到

SMILES的问题在上面已经回答的非常详细了，请仔细核对SMILES是否正确，类似问题不再回答

科研小白0126 发表于 2025-8-19 21:50
大佬我这是smile格式不对吗，纯小白
Failed to run notebook: 2_Polymer_chg_and_Polymer_creation_ Linea ...

认真看帖子，写的SMILES明显不对，键接位点呢

大佬我这是smile格式不对吗，纯小白
Failed to run notebook: 2_Polymer_chg_and_Polymer_creation_ Linear_polymer.ipynb
Return Code: 1
Standard Output:

Standard Error:
[NbConvertApp] Converting notebook /data/jupyternotebook_public/Project15_AI_ML_BMS_JZZ/cemp/media/Polymer/GeneratePolymer/20250819_212106_f3b689/2_Polymer_chg_and_Polymer_creation_ Linear_polymer.ipynb to notebook
Traceback (most recent call last):
  File "/data/jiazheju/anaconda3/envs/cemp_env/bin/jupyter-nbconvert", line 10, in
    sys.exit(main())
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/jupyter_core/application.py", line 283, in launch_instance
    super().launch_instance(argv=argv, **kwargs)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/traitlets/config/application.py", line 1075, in launch_instance
    app.start()
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/nbconvertapp.py", line 420, in start
    self.convert_notebooks()
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/nbconvertapp.py", line 597, in convert_notebooks
    self.convert_single_notebook(notebook_filename)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/nbconvertapp.py", line 563, in convert_single_notebook
    output, resources = self.export_single_notebook(
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/nbconvertapp.py", line 487, in export_single_notebook
    output, resources = self.exporter.from_filename(
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/exporters/exporter.py", line 201, in from_filename
    return self.from_file(f, resources=resources, **kw)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/exporters/exporter.py", line 220, in from_file
    return self.from_notebook_node(
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/exporters/notebook.py", line 36, in from_notebook_node
    nb_copy, resources = super().from_notebook_node(nb, resources, **kw)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/exporters/exporter.py", line 154, in from_notebook_node
    nb_copy, resources = self._preprocess(nb_copy, resources)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/exporters/exporter.py", line 353, in _preprocess
    nbc, resc = preprocessor(nbc, resc)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/preprocessors/base.py", line 48, in __call__
    return self.preprocess(nb, resources)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 103, in preprocess
    self.preprocess_cell(cell, resources, index)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbconvert/preprocessors/execute.py", line 124, in preprocess_cell
    cell = self.execute_cell(cell, index, store_history=True)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/jupyter_core/utils/__init__.py", line 165, in wrapped
    return loop.run_until_complete(inner)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/asyncio/base_events.py", line 647, in run_until_complete
    return future.result()
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbclient/client.py", line 1062, in async_execute_cell
    await self._check_raise_for_error(cell, cell_index, exec_reply)
  File "/data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/nbclient/client.py", line 918, in _check_raise_for_error
    raise CellExecutionError.from_cell_and_msg(cell, exec_reply_content)
nbclient.exceptions.CellExecutionError: An error occurred while executing the following cell:
------------------
if __name__ == '__main__':
    main()
------------------

----- stdout -----
--------PQx-IT-------PQx-IT----------PQx-IT--------PQx-IT---------PQx-IT-------PQx-IT----------PQx-IT--------PQx-IT--------
------------------

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[26], line 2
      1 if __name__ == '__main__':
----> 2     main()

Cell In[25], line 16, in main()
     14 smiles = df.loc[df['Name'] == name, 'SMILES'].values[0]
     15 n = int(df.loc[df['Name'] == name, 'repeating unit'].values[0])
---> 16 processing(name, smiles, n)
     17 print(f"--------{name}-------{name}----------{name}--------{name}---------{name}-------{name}----------{name}--------{name}--------")

Cell In[24], line 16, in processing(polymer_name, smiles, n, nproc, mem)
     13 mol = Chem.MolFromSmiles(smiles)
     15 # 获取聚合物链重复单元的原子电荷
---> 16 repeat_unit_charges = repeat_unit_charge_list(chg_filename)
     18 # 获取聚合物链端基聚合位点的原子电荷信息
     19 end_group_atom_charges_dict = create_end_group_atom_charges_dict(repeat_unit_charges, mol, n)

Cell In[5], line 7, in repeat_unit_charge_list(chg_filename)
      3 '''
      4 chg_filename：聚合物单个重复单元的电荷信息文件
      5 '''
      6 repeat_unit_charges = []
----> 7 with open(chg_filename, 'r') as file:
      8     for line in file:
      9         # 假设电荷信息在每行的最后一列
     10         repeat_unit_charges.append(float(line.split()[-1]))

File /data/jiazheju/anaconda3/envs/cemp_env/lib/python3.9/site-packages/IPython/core/interactiveshell.py:284, in _modified_open(file, *args, **kwargs)
    277 if file in {0, 1, 2}:
    278     raise ValueError(
    279         f"IPython won't let you open fd={file} by default "
    280         "as it is likely to crash IPython. If you know what you are doing, "
    281         "you can use builtins' open."
    282     )
--> 284 return io_open(file, *args, **kwargs)

FileNotFoundError: [Errno 2] No such file or directory: 'PQx-IT.chg'