v2.0.0-alpha.1

gdock has evolved 🦀

v2.0.0-alpha.1 is a full re-write of gdock into Rust

The previous versions relied completely on dcomplex as its scoring function, which now unfortunately is no longer distributed. Thus it was no longer functional. After looking for a while for some alternatives I decided that it was time to evolve gdock into a software that is completely self-contained and able to do its own scoring evaluations.

Key Highlights

• Blazing Fast: Generate an acceptable model in 0.04s (on 16 cores)—a dramatic improvement from the previous ~1 hour.
• Self-Contained Scoring: No longer relies on external scoring functions. I've fully incorporated the OPLS-AA forcefield and implemented functions for VdW, Desolvation, and Electrostatics energy calculations.
• Information-Driven Docking: Continues the philosophy heavily inspired by HADDOCK, now with a powerful, modern engine.

Major Changes

• Full Rust Rewrite: The entire codebase has been migrated from Python to Rust for performance and reliability.
• Eliminated Dependency: The legacy dependency on dcomplex has been removed, resolving a critical failure point and making gdock functional again.
• Native Scoring Engine: All scoring calculations are now performed internally using our custom-built OPLS-AA implementation (see toppar.rs).

Alpha Release Notice

⚠️ v2.0.0-alpha.1 is not yet ready for production. The code requires further review and the algorithm needs a comprehensive benchmark. However, it provides a stable and incredibly fast foundation for future development.

Remember that everything eventually becomes a crab 🦀