Feat/pydantic#6
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…on sphere functions
…refmoleclist_xyz and handle_error functions
…on and properties
…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
…ation in generate_charge_state
…plitting to detect extra or missing bonds
…nd enhance valence problem handling
…support and improve logging details
…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
…s and numpy arrays
…ecify protonation type
…nd unitcell attributes
… and connected atoms
…t attribute and computed properties
Co-authored-by: Copilot <copilot@github.com>
… SMILES processing
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