feat(cli): Implement DREID-Forge Command-Line Interface#10
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…flect CLI implementation
…file format detection
…utputTarget enums
…tom type information
…mmand line progress display
…n, Solvation, and Topology options
…, and lammps submodules
…nd parameterization
…s including Acetaminophen, Aspirin, and others
…for structure images
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Pull request overview
This PR introduces a comprehensive CLI tool (dforge) for the DREID-Forge molecular parameterization library, exposing the complete pipeline from structure preparation to force field generation. The implementation follows good practices with modular architecture, proper error handling, and rich user experience features. Key changes also include critical bug fixes in the core library for deterministic atom ordering and robust parsing.
Key Changes:
- Implemented full-featured CLI with
bioandchemsubcommands for different molecular workflows - Replaced
BTreeMapwithIndexMapin topology conversion for deterministic ordering - Fixed edge cases in SDF parsing and BGF writing for Unicode safety
- Added interactive progress reporting and detailed error diagnostics
Reviewed changes
Copilot reviewed 27 out of 68 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
src/io/util.rs |
Switched to IndexMap for deterministic atom ordering in bio topology conversion |
src/io/sdf/reader.rs |
Fixed potential panics with .get() for safe string slicing |
src/io/mod.rs |
Split LAMMPS format into separate Data and Settings variants |
src/io/bgf/writer.rs |
Fixed truncation to handle Unicode properly with char boundaries |
src/forge/config.rs |
Updated documentation comment for clarity |
src/bin/dforge/main.rs |
CLI entry point with context detection and error handling |
src/bin/dforge/cli.rs |
Comprehensive argument parsing with clap |
src/bin/dforge/commands/ |
Command handlers for bio and chem workflows |
src/bin/dforge/config/ |
Configuration builders mapping CLI args to library types |
src/bin/dforge/io/ |
I/O abstraction layer with format inference |
src/bin/dforge/display/ |
Progress reporting, error display, and summary tables |
src/bin/dforge/util/ |
Text wrapping and truncation utilities |
examples/drugs/ |
Example drug molecules with documentation |
examples/large/ |
Large biomolecule examples |
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Summary:
Introduced
dforge, a feature-rich command-line interface (CLI) for the DREID-Forge library. This tool exposes the complete parameterization pipeline—from structure preparation to force field generation—through two intuitive subcommands:dforge biofor biological macromolecules anddforge chemfor small molecule chemistry. It includes robust I/O handling, interactive progress reporting, and extensive configuration options for fine-tuning the DREIDING force field application.Changes:
Implemented CLI Architecture:
src/bin/dforgestructure with modular command handlers (commands/bio.rs,commands/chem.rs).clapfor argument parsing with subcommands, aliases (b/c), and grouped help messages.Developed
dforge bioCommand:bio-forgepreparation pipeline: cleaning (water/ions/hetero removal), protonation (pH, His tautomers), and solvation (box size, ion concentration).Developed
dforge chemCommand:Enhanced User Experience:
indicatiffor rich, interactive progress spinners and step completion reporting.Configuration & Flexibility:
CleanConfig,ProtonationConfig,ForgeConfig,LammpsConfig) to CLI flags.Documentation:
MANUAL.mdas a definitive user guide for the CLI.examples/directory.README.mdwith CLI installation and usage instructions.Performance & Refactoring:
BTreeMapwithIndexMapinto_bio_topologyto ensure deterministic atom ordering, critical for reproducible simulations.SDFparsing andBGFwriting.