Description:

This task represents the evolution of dreid-forge from a core library into a versatile command-line utility for DREIDING force field parameterization. The objective is to build a user-friendly CLI that exposes the parameterization engine through two primary workflows: bio for biomolecular structures (PDB/mmCIF) and chem for small molecules (MOL2/SDF).

The implementation will introduce a new binary target at src/bin/dreidforge.rs, organized into a modular architecture under src/bin/cli/. The CLI will utilize clap for robust argument parsing, anyhow for top-level error handling, and indicatif for progress feedback during parameterization. The I/O layer must abstract away file vs. stdin/stdout differences, enabling seamless integration with existing computational chemistry workflows.

Tasks:

• Phase 1: Project Scaffolding

  • Add CLI dependencies to Cargo.toml: clap, anyhow, indicatif, is-terminal.
  • Define the binary target: [[bin]] name = "dreidforge" path = "src/bin/dreidforge.rs".
  • Create the module structure: src/bin/cli/mod.rs.
  • Implement the root Cli struct with global arguments:
    • -i, --input: Input path (defaults to stdin if missing).
    • -o, --output: Output path(s) (defaults to stdout if missing).
    • --out-format: Force output format.
    • -q, --quiet: Suppress progress output.

• Phase 2: I/O Abstraction Layer

  • Implement format inference from file extensions.
  • Handle file opening vs. stdin/stdout for streams.
  • Support multiple output targets with paired formats.
  • Implement LAMMPS dual-file output (.data + .in.settings).

• Phase 3: Subcommand Implementation

  • Bio (cli/bio.rs):
    • Structure preparation: --no-water, --no-ions, --no-hetero, --keep, --remove.
    • Protonation: --no-protonate, --ph, --his (hid/hie/random/network).
    • Solvation: --solvate, --solv-margin, --cation, --anion.
    • Topology building with --hetero-template and --ss-cutoff.
  • Chem (cli/chem.rs):
    • Direct parameterization of small molecules.
    • Support MOL2 and SDF input formats.
  • Shared Forge Options:
    • Charge method: --charge (none/qeq) with QEq solver options.
    • Potential types: --bond, --angle, --vdw.
    • Custom parameters: --params, --rules.

• Phase 4: User Interface Polish

  • Implement ASCII art banner for branding.
  • Add braille spinner progress indicators.
  • Render result tables (parameters, atom types, chain breakdown).
  • Display timing information and success footer.

• Phase 5: Testing and Documentation

  • Verify stdin/stdout piping works correctly.
  • Verify round-trip format conversion.
  • Ensure non-zero exit codes and readable error messages.
  • Update README with CLI usage examples.