Generalize `download_opls_xml` Function

[shehan807]

Summary

Include a summary of major changes in bullet points:

• Feature 1: src/atomate2/openmm contains utils.py, for which the LigParGen server is accessed; currently, the download_opla_xml function allows only SMILES string inputs. This feature generalizes this by modifying the input dictionary (dict[str, str]) to a dictionary of dictionaries (dict[str, dict[str, str]]), where the new input handles the molecule's charge and number of optimization iterations. A working dictionary, then, follows:

mols = {
        'benzene':{
            'smiles':'c1ccccc1'
            },
        'TMA':{
            'smiles':'C[N+](C)(C)C',
            'checkopt':3,
            'charge':"+1"
            }
        }

• Fix 1: The LigParGen server output creates an .XML file that results in an error while copying it to the new file, so shutil.copy(file, final_file) resolves this issue.

Additional dependencies introduced (if any)

• shutil: code like Path(file).rename(final_file) can fail for environments where the .XML file from LigParGen is created in a /tmp folder. shutil allows a standard copy; it is possible that, in a high-throughput test case, this results in performance loss.
• selenium.webdriver.support.ui.WebDriverWait and selenium.webdriver.support.expected_conditions: both are from selenium and safeguard from LigParGen server crashes

TODO (if any)

If this is a work-in-progress, write something about what else needs to be done.

• Feature 1 supports utils.py, but has not been updated in tests/openmm_md/test_utils.py.

Checklist

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[utf]

Thanks @shehan807. This looks good to me. Can you install and run the linter on your changes to ensure they match the style guidelines: https://materialsproject.github.io/atomate2/dev/dev_install.html#installing-pre-commit

pip install pre-commit
pre-commit run --all

[shehan807]

Hi @utf, I just wanted to follow up on this. It seems like the only issue is regarding the changes I've made using the time.sleep function--all I've done is added a dependence to the number of optimization iterations selected in LigParGen since this may increase the time it takes to output .xml/.pdb files.

On a slightly separate note, I wanted to raise the issue regarding version control of LigParGen. Based on my issue on the LigParGen repository (https://github.com/Isra3l/ligpargen/issues/31#issue-2639431963), I learned that the server has only kept up with BOSS v4.9 (the program managed by the Jorgenson group that operates under the hood for LigParGen). Perhaps @orionarcher could comment here, since in the case of high throughput OPLS-AA simulations, I wonder if extending the current download_opls_xml function to interface with the BOSS source code is a feasible option. The BOSS v5.1 source code is available online (https://zarbi.chem.yale.edu/software.html), but I am unsure how licensing works with incorporating it into atomate2. I'm happy to contribute to whatever extent this may be useful!

[orionarcher]

One comment but LGTM, thanks @shehan807.

It should be fine to build an integration that works if BOSS is available as an executable. Atomate2 has integrations with other closed-source codes like VASP.

[shehan807]

The changes in this PR are now merged with #1111