…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

- Introduced a new script `rf.py` for training a Random Forest classifier.
- Added hapticity in features
- Included cross-validation for model evaluation with metrics such as accuracy and F1 score.
- Saved the trained model and its metadata, including feature importance.

- enumerate  protonation states
- resolve charge states for species
- balance and validate total molecular or unit cell charge
- process SMILES and generate bond order information

- Updated logging messages in Group and Ligand classes to provide clearer context.
- Removed debug parameters from methods where they were unnecessary.
- Changed import paths for charge-related functions to reflect new module structure.
- Simplified charge assignment logic in Molecule class and removed redundant debug prints.
- Enhanced error assessment in Molecule class to categorize error cases.
- Cleaned up commented-out debug logs for better readability.
- Adjusted default values for cov_factor and metal_factor in Specie class to use config constants.

…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

… resonance structure evaluation

…rove resonance structure handling

…c groups "C"

…efault values

…in macrocycle identification

…or porphyrins and fullerene handling

…erenes, noble gases, teflate, and Sb-halides

These species were previously skipped or forced through the general
AC2mol bond-order search, which either can't scale to them (60+ atom
fullerene cages) or produces chemically implausible charge-separated
resonance structures. Each now gets a direct, connectivity-based
charge assignment instead:

- Fullerene cages: closed-shell Kekule structure via a perfect matching
  on the 3-regular cage graph (Petersen's theorem), replacing the old
  "skip entirely" behavior.
- Noble gas solvate/lattice atoms: always neutral.
- Teflate (-OTeF5): fixed hexacoordinate Te(VI) pattern with charge on
  the terminal O.
- Sb-halide-only species: per-center formal charge for mononuclear
  cases, and charge distributed round-robin across terminal halogens
  for polynuclear/bridged clusters.

Also:
- Route As/Sb/Bi/Se/Te always through the AC2BO search regardless of
  whether their degree matches a "normal" valence.
- Detect non-coordinated carboxylate/sulfonate moieties to size ligand
  max-charge ranges, replacing the plain terminal-oxygen count.
- Add dedicated porphyrin charge handling and disable charged
  fragments when a porphyrin's candidate charge is 0.