Fix various bugs and improve code readability #103
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…e unnecessary variable
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This pull request includes several commits that fix various bugs and improve the readability of the code. The changes include removing lines with errors, correcting typos, and removing unnecessary variables and functions. Additionally, the code has been optimized in several areas, such as the loadStructure() function, setChains function, and setup function. The import handling for Openmm has also been improved. Furthermore, the code now includes functions to create simulation contexts, initialize reporters, and run simulations. The code has also been updated to include version checking and a new software format for saving structures. Overall, these changes enhance the functionality and maintainability of the codebase.