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Minimization convergence tests (#20)
* be more explicit with source of molecular topology * minimization test * adding drugbank * Add ContinuousProgressReporter class for reporting simulation progress * Skip molecules containing phosphores during minimum test detection * Fix exception handling in run_detect_minimum_test function * Refactor stability protocol and molecule generation functions * Add simulation parameters classes and initialize_ml_system function * Fix code formatting and update file paths --------- Co-authored-by: wiederm <[email protected]>
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