Implement Analysis Workflow

[TKanX]

Description:

This task focuses on creating a dedicated analysis workflow. Instead of optimizing a structure, this workflow uses the SCREAM++ force field and scoring engine to perform specific calculations on a given molecular system and report the results. This provides a powerful utility for users to probe molecular interactions and properties.

Tasks:

• run Function Signature: Define the main function in workflows/analyze.rs that accepts an initial_system, an AnalyzeConfig, and a ProgressReporter, returning a Result<AnalysisReport, EngineError>.
• Phase 0: Setup: Load the Forcefield and fully parameterize a copy of the input system.
• Phase 1: Dispatch & Execute:
  • Implement a match statement on the analysis_type field from the AnalyzeConfig to dispatch to the correct analysis logic.
  • For Interaction Analysis:
    • Resolve the two AtomSelection groups (e.g., Residue A, Chain B) into concrete Vec<AtomId>.
    • Create a Scorer instance.
    • Call score_interaction on the two resolved atom groups.
    • Populate and return an AnalysisReport with the resulting EnergyTerm breakdown (VDW, Coulomb, HBond).
  • For ClashDetection Analysis:
    • Resolve the selection of atoms to check for clashes (e.g., all atoms).
    • Iterate through all relevant non-bonded atom pairs in the selection.
    • Calculate the interaction energy for each pair using the Scorer.
    • If the energy exceeds the configured threshold_kcal_mol, add the pair's details (atom identifiers, distance, energy) to a list within the AnalysisReport.
    • Return the final AnalysisReport.