…on sphere functions

…refmoleclist_xyz and handle_error functions

…on and properties

…sistency

…d_adjacency and split_species functions

…onnected_groups function in Metal class

…rix in Specie class

…_reference_molecules function Cell class

- Removed the cell2mol_mode function from final_c2m_module.py, simplifying the interface for running cell2mol.
- Consolidated the unit cell reconstruction logic into a new function, reconstruct_unitcell, in cell_reconstruction.py.
- Updated unitcell.py to directly call reconstruct_unitcell, enhancing clarity and reducing complexity.

…plex molecules

WIP

feat: add ProtonationGroupResult to type registry

…ctions

…plitting to detect extra or missing bonds

…nd enhance valence problem handling

…support and improve logging details

…order

…n compare_species function

feat(connectivity): update return type of build_adjacency function to allow None

feat(element_utils): update POST_TRANSITION_METALS set and update function signatures for type hints

…gic, increase atol to 5e-1

…fety for charge state functions

…ng of protonation states

…bonds

…s and numpy arrays

…atoms and metals

…and coordinates

…ecify protonation type

…nd unitcell attributes

… and connected atoms

…and metals

…t attribute and computed properties

…and attributes

…d attributes

…tes and methods

… As, Sb

Co-authored-by: Copilot <copilot@github.com>

…metaclass

… SMILES processing