Summary:

Refactors the core bond representation to explicitly distinguish between input bond orders (GraphBondOrder) and final topology bond orders (TopologyBondOrder). This decoupling allows for precise control over how aromatic and resonant systems are perceived and represented in the output. Additionally, the integration test suite has been significantly enhanced to strictly verify these final bond orders, ensuring that resonance systems (like carboxylates, amides, and aromatic rings) are correctly identified and assigned the Resonant bond order.

Changes:

• Decoupled Bond Order Types:

  • Introduced GraphBondOrder (Single, Double, Triple, Aromatic) for input MolecularGraph construction.
  • Introduced TopologyBondOrder (Single, Double, Triple, Resonant) for output MolecularTopology.
  • Updated all core data structures and public APIs (add_bond, Bond) to use these specific types, preventing ambiguity.

• Implemented Strict Resonance Perception:

  • Updated the perception pipeline to correctly promote bonds within detected resonance systems (aromatic rings, carboxylates, nitro groups, etc.) to TopologyBondOrder::Resonant.
  • Non-resonant bonds retain their localized Kekulé orders (Single/Double).

• Enhanced Test Suite:

  • Updated the MoleculeTestCase harness to include expected_bonds, allowing rigorous verification of final bond orders.
  • Refactored all existing integration tests (amino acids, nucleic acids, DREIDING paper examples) to specify both input GraphBondOrder and expected output TopologyBondOrder.
  • Added a new test case for Diglycine to verify peptide bond resonance handling.

• Documentation and Examples:

  • Updated README.md and crate-level documentation to reflect the new GraphBondOrder API and provide correct usage examples.
  • Refined architectural documentation (01_pipeline.md) to clarify the distinction between graph and topology representations.