feat(io): Support Context-Aware Histidine Salt Bridge Protonation

[TKanX]

Summary:

Updated dreid-forge to leverage the salt bridge detection capabilities introduced in bio-forge v0.4.0. This enhancement allows for context-aware histidine protonation, where histidine residues near carboxylate anions (ASP⁻, GLU⁻, C-terminal COO⁻) are automatically assigned the doubly-protonated HIP form to model stabilizing salt bridge interactions. This behavior is enabled by default but can be disabled via configuration.

Changes:

• Updated Dependency:

  • Upgraded bio-forge to version 0.4.0.

• Enhanced Protonation Configuration:

  • Added his_salt_bridge field to ProtonationConfig in src/io/mod.rs (defaults to true).
  • Updated to_bf_hydro_config in src/io/util.rs to pass this setting to the bio-forge engine.

• Updated CLI:

  • Added --no-his-salt-bridge flag to dforge bio to optionally disable this feature.
  • Updated CLI configuration builder in src/bin/dforge/config/bio.rs.
  • Refined progress reporting in src/bin/dforge/commands/bio.rs to indicate salt bridge detection status.

• Documentation:

  • Updated MANUAL.md with the new CLI flag documentation.
  • Updated ARCHITECTURE.md to reflect the new capability in the protonation stage description.
  • Added RustDoc comments explaining the salt bridge logic in ProtonationConfig.

[Copilot]

Pull request overview

This PR updates dreid-forge’s biomolecular protonation pipeline to use bio-forge v0.4.0’s salt-bridge-aware histidine handling, allowing automatic HIS→HIP assignment near carboxylate anions (enabled by default, configurable/disableable via CLI).

Changes:

• Bump bio-forge dependency to 0.4.0 and plumb new salt-bridge toggle into the hydro/protonation config conversion.
• Add his_salt_bridge to ProtonationConfig (default true) and expose --no-his-salt-bridge CLI flag.
• Update CLI progress text and documentation to reflect the new capability.

Reviewed changes

Copilot reviewed 5 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
Cargo.toml	Upgrades bio-forge dependency to 0.4.0.
src/io/mod.rs	Adds his_salt_bridge to ProtonationConfig with docs + default behavior.
src/io/util.rs	Passes the new toggle into bf::ops::HydroConfig and extends tests.
src/bin/dforge/cli.rs	Adds --no-his-salt-bridge CLI flag.
src/bin/dforge/config/bio.rs	Maps CLI option into ProtonationConfig.his_salt_bridge.
src/bin/dforge/commands/bio.rs	Updates progress substep text to reflect salt-bridge behavior.
MANUAL.md	Documents the new CLI flag.
ARCHITECTURE.md	Updates dependency/version references and protonation-stage description.

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