Description:

This task executes a major architectural refactor to distinguish between the chemical connectivity provided by the user and the physical force field topology required for simulation. Currently, "Aromatic" is treated as a bond type that persists through the pipeline, and resonance detection relies on a broad, third-party algorithm that often over-assigns conjugation. This update separates InputBondOrder from TopologyBondOrder, ensuring that "Resonant" bonds are treated strictly as a derived property. Furthermore, the resonance perception logic will be rewritten to remove external dependencies and rely on a strict "allowlist" of motifs (Aromatic systems, Carboxylates, Nitro groups, Guanidinium, and Amides). This ensures that only chemically significant delocalization results in a partial bond order in the final topology.

Tasks:

• Phase 1: Refactor Core Data Structures

  • In src/core/properties.rs, replace the single BondOrder enum with two distinct types:
    • InputBondOrder: Variants Single, Double, Triple, Aromatic. Used by MolecularGraph.
    • TopologyBondOrder: Variants Single, Double, Triple, Resonant. Used by MolecularTopology.
  • Update src/core/graph.rs to use InputBondOrder in MolecularGraph and BondEdge.
  • Update src/core/graph.rs to use TopologyBondOrder in the final Bond struct within MolecularTopology.
  • Update src/perception/model.rs so AnnotatedMolecule uses InputBondOrder (or a Kekulized equivalent) for internal adjacency, while preparing to store resonance metadata separately.

• Phase 2: Reimplement Resonance Perception

  • Remove the pauling crate dependency from Cargo.toml.
  • In src/perception/model.rs, add a resonance_systems: Vec<ResonanceSystem> field to AnnotatedMolecule. A ResonanceSystem should track both atom IDs and bond IDs involved.
  • Rewrite src/perception/resonance.rs to implement Strict Resonance Detection:
    • Aromatic Import: Automatically treat all atoms and internal bonds of detected aromatic rings as a resonance system. (Note: Inter-ring bonds like in biphenyl must remain single).
    • Carboxylate Detector: Identify C(=O)O- motifs.
    • Nitro Detector: Identify N(=O)O- motifs.
    • Guanidinium Detector: Identify C(N)3+ motifs.
    • Amide Detector: Identify O=C-N motifs.
  • Ensure that is_in_conjugated_system and is_resonant atom flags are updated based solely on membership in these strict systems.

• Phase 3: Upgrade Topology Builder

  • In src/builder/mod.rs, update the build_bonds function.
  • Logic Change: Instead of copying bond orders directly:
    • Check if a bond ID belongs to any ResonanceSystem identified in Phase 2.
    • If yes, assign TopologyBondOrder::Resonant.
    • If no, map the Kekulized InputBondOrder (Single/Double/Triple) to the corresponding TopologyBondOrder.

• Phase 4: Verification and Cleanup

  • Update all integration tests in tests/cases/ to use the new InputBondOrder enum variants in their blueprints.
  • Verify that biphenyl-like structures correctly produce Resonant bonds within rings but a Single bond between rings.
  • Verify that Amides and Carboxylates correctly generate Resonant bond orders in the final topology.