Summary:

Introduces a comprehensive rotamers module designed to load, manage, and apply pre-calculated sidechain conformations. The core component is a RotamerLibrary that reads rotamer definitions and placement instructions from TOML files. A key aspect of this implementation is that each rotamer is fully parameterized on-the-fly using the existing forcefield module during the loading process. This ensures that rotamers are not just coordinate sets but are immediately ready for accurate energy scoring and conformational sampling within the system.

Changes:

• Implemented Rotamer Library (rotamers::library):

  • Created a RotamerLibrary to serve as the central repository for all loaded rotamer conformations.
  • Implemented RotamerLibrary::load to parse rotamer data from a TOML file, mapping conformations to their respective ResidueType.
  • Provided a robust LibraryLoadError enum for handling I/O, parsing, and logical errors during the loading process.

• Integrated On-the-Fly Parameterization:

  • Added a new public method parameterize_atom to the Parameterizer. This function applies forcefield settings (topology, VDW, delta, etc.) to a single Atom.
  • The RotamerLibrary uses this new method during loading to ensure every atom in every rotamer is fully parameterized and ready for use in energy calculations.

• Developed a Placement Information System (rotamers::placement):

  • Implemented PlacementInfo and PlacementRegistry to define how a rotamer should be aligned and placed onto a protein backbone.
  • This system specifies anchor atoms for alignment, sidechain atoms for replacement, and connection points, loaded from a dedicated TOML registry file.

• Defined Core Rotamer Data Structures (rotamers::rotamer):

  • Created RotamerData and RotamerAtomData as serde-compatible structs for deserializing rotamer definitions from files.
  • Defined the in-memory Rotamer struct, which holds a collection of fully parameterized Atom objects.

• Established New Module Structure:

  • Created a new top-level rotamers module in scream-core.
  • Organized the functionality into logical submodules: library, placement, and rotamer.