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…ssignment and connectivity modules, updating 'protonation' to 'Protonation', 'charge_state' to 'ChargeState', and 'molecule' to 'Molecule'. This improves code readability and maintains uniformity in naming conventions.
…module accessibility and code organization.
- Add type annotations and Pydantic BaseModel inheritance to all classes - Implement computed fields for dynamic properties like atnum, block, formula - Add serialization support for circular references - Include version, type, and subtype fields for consistency - Update my_types.py with proper type definitions
adding initial CITATION document
This commit enhances the handling of circular references in Pydantic models by introducing a registry system for object resolution during deserialization. UUID strings are now used as placeholders and resolved to actual objects post-deserialization. It also updates type annotations to support both object references and UUID strings, adds deserialization logic for RDKit Mol objects, and fixes serialization issues in the Protonation class.
Implement support for saving and loading `Cells` objects in both JSON and pickle formats, with a preference for JSON as the default format. Deprecate pickle usage with appropriate warnings.
refactor: update logging filename from cell2mol.out to cell2mol.log fix: change empty coordinates check from size to length in normalize_structure
feat(cell): rename error map key for clarity and remove commented code feat(write_results): enhance Metal info output with group details
… analysis for merged groups
…pes for Ligand and Molecule
…rges in ChargeState
…tion state enumeration. - introduce new haptic types - use missing hydrogen detection for non-local protonation sites
… improved error handling
… make ring_atoms as list type
…haptic_group for improved logging
…for merged groups feat(coordination): replace print statements with logger warnings for better error tracking
… handle non-carbon atoms in _handle_haptic_group
…ed_groups function
…l_coordination function - get_denticity function should be changed later
…nnected metals for oxygen ligands
…ed_atoms - Primary: hydrogens, Secondary: Furthest distance first
… enhance hydrogen addition logic
…g and update attributes
… attributes and improve charge correction logic
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