Summary:

Introduces a complete forcefield module designed for molecular energy calculation and system parameterization. It includes a robust system for loading forcefield parameters from data files, a Parameterizer to apply these settings to a MolecularSystem, and a Scorer to calculate non-bonded interaction energies. This module establishes the core functionality for evaluating molecular interactions, enabling scoring, minimization, and future simulation tasks. It also includes the necessary parameter data files for a baseline forcefield implementation.

Changes:

• Created a Comprehensive Parameter System (params.rs):

  • Defined structs (VdwParam, HBondParam, ChargeParam, DeltaParam) to represent forcefield parameters, using serde for deserialization.
  • Implemented Forcefield::load to parse parameters from TOML (for non-bonded) and CSV (for charges, deltas, etc.) files.
  • Provided robust error handling (ParamLoadError) for file I/O and parsing issues.
  • Added a data/ directory containing CSV files for charges, deltas, and other parameters.

• Implemented Core Energy Potentials (potentials.rs):

  • Provided implementations for standard potential energy functions:
    • Lennard-Jones (12-6) and Buckingham (exp-6) for van der Waals interactions.
    • Coulomb's law for electrostatic interactions.
    • Dreiding-style (12-10) for hydrogen bond interactions.
  • Implemented logic for "flat-bottom" potentials (apply_flat_bottom_vdw, apply_flat_bottom_hbond) to handle the delta parameter.

• Developed an Energy Calculation Engine (energy.rs):

  • Created a stateless EnergyCalculator to compute specific interaction energies (VDW, Coulomb, H-bond).
  • The calculator correctly handles the mixing of different VDW parameter types (e.g., Lennard-Jones with Buckingham) between two atoms.

• Introduced a Parameterizer for System Setup (parameterization.rs):

  • Developed a Parameterizer to apply a loaded Forcefield to a MolecularSystem.
  • It assigns forcefield types, partial charges, delta values, and cached VDW parameters to each atom.
  • It automatically builds both intra-residue bonds based on topology definitions and inter-residue peptide bonds.

• Provided a High-Level Scorer API (scoring.rs):

  • Implemented a Scorer to calculate the total interaction energy (VDW, Coulomb, H-bond) between two distinct groups of atoms (e.g., a query and its environment).
  • The Scorer correctly handles exclusion rules, such as ignoring intra-residue interactions.
  • It intelligently identifies and scores hydrogen bonds by looking for donor-hydrogen-acceptor triplets.

• Enhanced Core Models and Utilities:

  • Removed the AtomFlags bitflags from the Atom model, simplifying its structure.
  • Added get_bonded_neighbors to MolecularSystem for efficient topology lookups.
  • Added a bond_angle utility function to the geometry module.