Summary:

Executes a major refactoring of the core data models within scream-core, replacing the previous Vec-based storage and usize indexing with slotmap. This provides stable, generational IDs (AtomId, ResidueId, ChainId), which guarantees that references remain valid even after additions or deletions of other entities. This change fundamentally enables safe mutability, introducing methods to add and remove entities directly from the MolecularSystem. Consequently, the separate MolecularSystemBuilder has been removed, and its functionality is now integrated into MolecularSystem itself, leading to a more robust, performant, and ergonomic API.

Changes:

• Stable ID Generation with slotmap:

  • Introduced the slotmap crate to manage Atom, Residue, and Chain collections, replacing the fragile Vec/usize index system.
  • Created stable, typed IDs: AtomId, ResidueId, and ChainId in a new ids.rs module.

• Data Structure and API Refactoring:

  • Restructured MolecularSystem to use SlotMap for primary data storage, flattening the hierarchy for direct access to all entities.
  • Implemented methods for safe, direct mutation of the molecular system: add_atom_to_residue, add_bond, remove_atom, and remove_residue.
  • Removed the MolecularSystemBuilder and integrated its construction logic directly into MolecularSystem's public methods (add_chain, add_residue, etc.).
  • Updated Atom, Residue, Chain, and Bond models to use the new stable IDs, simplifying their structure.

• Performance Enhancements:

  • Added a bond_adjacency SecondaryMap to MolecularSystem for efficient, cached lookups of an atom's bonded neighbors.
  • Changed file I/O operations to use BufWriter, improving write performance.

• BGF Parser/Writer Update:

  • Completely refactored the BgfFile parser and writer (core::io::bgf) to work with the new slotmap-based data models and mutable API.
  • The parser now handles entity creation and bond connections more robustly, with improved error handling for missing atoms in CONECT records.