Summary:

Refactors the core energy model to calculate absolute total system energy, moving away from a relative optimization score. This is achieved by introducing a new fixed_energy task that computes a constant energy offset from all non-optimizable parts of the system (e.g., static backbone, environment, fixed sidechains). The final energy of any solution is now the sum of this fixed offset, the pre-computed EL energy, and the pairwise interaction energy. This change provides more physically meaningful energy values.

This refactoring also significantly streamlines the parameterization and data loading pipeline. Topology information is now managed by a dedicated TopologyRegistry, loaded from a single file, which decouples rotamer placement logic from the rotamer library itself. Consequently, the forcefield and rotamer libraries are now simpler and more focused.

Changes:

• Implemented Absolute Energy Model:

  • fixed_energy.rs: A new task that calculates the interaction energy of all static parts of the system (backbone, fixed sidechains, water, ligands) to establish a constant energy offset.
  • total_energy.rs: Removed this task and integrated its logic into the main workflow, which now combines the fixed energy offset, EL energy, and interaction energy to report an absolute total energy for each solution.
  • Solution: The Solution struct in the engine::state module was updated to store both total_energy and optimization_score.

• Introduced Topology Registry:

  • topology/registry.rs: Created a TopologyRegistry to load and manage residue topology definitions (anchor and sidechain atoms) from a single TOML file (registry.toml).
  • The RotamerLibrary no longer loads placement info; instead, it and the placement functions consume the TopologyRegistry.
  • The CLI and configuration system were updated to accept a --topology-registry path.

• Streamlined forcefield and rotamer Modules:

  • forcefield/parameterization.rs: The Parameterizer is now responsible for assigning atom roles (Backbone, Sidechain, etc.) based on the TopologyRegistry. It was simplified by removing the logic for building bonds and assigning charges, which are now defined in the rotamer library.
  • rotamer/library.rs: The rotamer library loader now also loads intra-rotamer bond information from the TOML file, making rotamers self-contained topological units.
  • Atom struct now includes an AtomRole enum to clearly define its function.

• Enhanced I/O and CLI:

  • io/sorting.rs: Introduced a canonical atom sorter for generating deterministic and clean BGF output. The old utils::identifiers module was removed in favor of this more comprehensive system.
  • io/bgf.rs: The BGF writer was completely refactored to use the new canonical sorter, renumbering all atoms sequentially and producing clean, standard-compliant files.
  • cli.rs: The CLI help text for output files was improved to detail the available placeholders ({energy}, {score}, etc.).

• Performance and Reliability Improvements:

  • The Scorer now correctly excludes 1-2 and 1-3 bonded interactions from non-bonded calculations.
  • VDW parameters are now cached directly on the Atom struct as CachedVdwParam, improving performance by avoiding repeated string-based lookups.