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Breaking Change: Renamed functions System::group_by_resid and System::group_by_resname to System::atoms_split_by_resid and System::atoms_split_by_resname, respectively.
Breaking Change: Revised the return type of System::group_create from Result<(), Box<dyn Error>> to Result<(), GroupError>. This change simplifies pattern matching when handling the result of the function. Additionally, the error type SelectError, previously returned by the function, is now encapsulated within the new error variant GroupError::InvalidQuery.
Updated selection macros according to Gromacs definitions, and introduced new macros for identifying DNA (@dna) and RNA (@rna).
Introduced new functions: System::group_split_by_resid for splitting groups of atoms by their residue ID and System::group_split_by_resname for splitting by residue name.
Added functions System::group_remove for removing groups and System::group_rename for renaming them.
Introduced System::group_create_from_geometry which allows to construct groups of atoms that are inside some geometric shape in the current simulation frame.
Restructured codebase:
Split the system.rs file into multiple smaller files.
Grouped files related to IO operations into a dedicated directory.
Organized files containing System-related methods into a separate directory.
Placed files defining fundamental data structures into their own directory.