Bugfix/update chemtorch tutorial

[tonyzamyatin]

Updated ChemTorch CLI commands in the "Deep Learning of Reaction Barrier Heights with ChemTorch" due to latest changes in the ChemTorch API.

[tonyzamyatin]

This PR can be squashed into one commit with the commit message of the last commit

[timmyte]

Dear @tonyzamyatin

Thank for updating the notebook. Looks good to me.

Please include and update (if necessary) the disclaimer from the previous version and then we are good to merge:

# Deep Learning of Reaction Barrier Heights with ChemTorch

----

**Disclaimer**  
This community notebook was kindly supplied by [Anton Zamyatin](https://github.com/tonyzamyatin) and [Esther Heid](https://github.com/hesther) for OPI version 1.0.0.

----

[tonyzamyatin]

done, I believe we can merge now

[timmyte]

@tonyzamyatin

Thanks for the last fix! Please make sure your PR is update with the target branch, as it still has conflicts.

[timmyte]

@tonyzamyatin
Sorry for our late response to your PR.

I currently fail to execute the notebook, there we postpone the merge.
@haneug Please take a look.

The error:

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[16], line 2
      1 # > Load predictions from the CSF file
----> 2 df = pd.read_csv("predictions.csv")
      3 delta_E_act_kcal_predicted = df["prediction"].values[0]

File /opi_pr_154.3bQ/opi/.venv/lib/python3.13/site-packages/pandas/io/parsers/readers.py:873, in read_csv(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, skip_blank_lines, parse_dates, date_format, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, encoding_errors, dialect, on_bad_lines, low_memory, memory_map, float_precision, storage_options, dtype_backend)
    861 kwds_defaults = _refine_defaults_read(
    862     dialect,
    863     delimiter,
   (...)    869     dtype_backend=dtype_backend,
    870 )
    871 kwds.update(kwds_defaults)
--> 873 return _read(filepath_or_buffer, kwds)

File /opi_pr_154.3bQ/opi/.venv/lib/python3.13/site-packages/pandas/io/parsers/readers.py:300, in _read(filepath_or_buffer, kwds)
    297 _validate_names(kwds.get("names", None))
    299 # Create the parser.
--> 300 parser = TextFileReader(filepath_or_buffer, **kwds)
    302 if chunksize or iterator:
    303     return parser

File /opi_pr_154.3bQ/opi/.venv/lib/python3.13/site-packages/pandas/io/parsers/readers.py:1645, in TextFileReader.__init__(self, f, engine, **kwds)
   1642     self.options["has_index_names"] = kwds["has_index_names"]
   1644 self.handles: IOHandles | None = None
-> 1645 self._engine = self._make_engine(f, self.engine)

File /opi_pr_154.3bQ/opi/.venv/lib/python3.13/site-packages/pandas/io/parsers/readers.py:1904, in TextFileReader._make_engine(self, f, engine)
   1902     if "b" not in mode:
   1903         mode += "b"
-> 1904 self.handles = get_handle(
   1905     f,
   1906     mode,
   1907     encoding=self.options.get("encoding", None),
   1908     compression=self.options.get("compression", None),
   1909     memory_map=self.options.get("memory_map", False),
   1910     is_text=is_text,
   1911     errors=self.options.get("encoding_errors", "strict"),
   1912     storage_options=self.options.get("storage_options", None),
   1913 )
   1914 assert self.handles is not None
   1915 f = self.handles.handle

File /opi_pr_154.3bQ/opi/.venv/lib/python3.13/site-packages/pandas/io/common.py:926, in get_handle(path_or_buf, mode, encoding, compression, memory_map, is_text, errors, storage_options)
    921 elif isinstance(handle, str):
    922     # Check whether the filename is to be opened in binary mode.
    923     # Binary mode does not support 'encoding' and 'newline'.
    924     if ioargs.encoding and "b" not in ioargs.mode:
    925         # Encoding
--> 926         handle = open(
    927             handle,
    928             ioargs.mode,
    929             encoding=ioargs.encoding,
    930             errors=errors,
    931             newline="",
    932         )
    933     else:
    934         # Binary mode
    935         handle = open(handle, ioargs.mode)

FileNotFoundError: [Errno 2] No such file or directory: 'predictions.csv'

[timmyte]

Waiting for @haneug to review before merge.

[tonyzamyatin]

Hi @timmyte, did you successfully run the ChemTorch command specified in the notebook? It is not a cell but has to be manually exectued from the terminal (in the chemtorch directory) by the user. If there was an error or unexpected behavior please let me know!

[haneug]

Hi @tonyzamyatin I tried to install ChemTorch as described in the notebook but in the opi_tutorial branch there is no environment.yml file available to set up the conda env.
EDIT: The OPI part looks really nice!