Add timeout decorator to RMSD calculations to prevent occasional process deadlocks

[amorehead]

• Adds a timeout decorator to the _rmsd function to prevent occasional process deadlocks.
• The timeout is set to 30 seconds by default.

[maabuu]

Thank you for the suggestion. Three things would have to be addressed before we include a timeout in the RMSD module.

1. All the tests must pass, including the "validation" check which checks that the pre-commit hooks ran.
2. The signal module in the standard Python library should be used instead of introducing a third party dependency.
3. It might change the results of the paper. I should add a test for this.

[maabuu]

Out of personal interest, could you share which molecules cause these deadlocks? In my experience, highly symmetric molecules like Phytic acid cause (very) long run times because of the large number of possible bijections to calculate RMSDs for.

[github-actions[bot]]

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