Summary:

Implemented a modular I/O framework within scream-core to handle the reading and writing of molecular file formats, with BGF (.bgf) being the first supported format. This work introduces a generic MolecularFile trait for future expansion. A significant refactoring of the core data models was performed, including a redesigned Atom struct that uses bitflags for state and a more organized MolecularSystemBuilder. Error handling has also been improved by introducing custom error types with thiserror.

Changes:

• Implemented Modular I/O Framework:

  • Created a new core::io module to house file format handlers.
  • Introduced a generic MolecularFile trait with methods for reading from and writing to readers/writers and file paths, ensuring a consistent API for all supported formats.

• Added BGF File Support:

  • Implemented BgfFile as the first concrete implementation of the MolecularFile trait.
  • Reading: Parses ATOM, HETATM, and CONECT records from a BGF file, correctly identifying chain types (Protein, Water, Ligand) and building a MolecularSystem via the builder.
  • Writing: Capable of writing a MolecularSystem back into a valid BGF file format, including atom records and connectivity information.
  • Added a comprehensive test suite for BGF reading and writing logic.

• Core Data Model Refactoring:

  • Redesigned Atom Struct:
    • The Element enum has been removed.
    • The Atom struct now contains more descriptive topological fields (res_name, res_id, chain_id) and SCREAM-specific parameters (flags, delta, vdw_radius, etc.).
  • Introduced AtomFlags:
    • Added an AtomFlags struct using the bitflags crate to efficiently manage boolean atom properties like IS_FIXED_ROLE and IS_VISIBLE_INTERACTION.
  • Enhanced MolecularSystemBuilder:
    • Moved the builder to its own module (core::models::builder) for better code organization.
    • Updated the builder to construct the new, more detailed Atom and MolecularSystem structures.

• Dependency and Error Handling Improvements:

  • Added bitflags and thiserror as new dependencies to scream-core.
  • Implemented a custom BgfError enum using thiserror for clearer and more ergonomic error handling during file parsing.
  • Updated other error types (e.g., ParseChainTypeError) to use thiserror.