v2.0.0-rc.2

rc2!

More code cleaning and documentation minor changes + paper to be soon submitted to JOSS

v2.0.0-rc.1

rc1 !

The first release candidate has been completed, polishing some rough edged and making minor tweaks to the code.

v2.0.0-beta.2

Beta 2!

In this version the pipeline to create/run a docking benchmark was established, clustering was implemented and the weights were tweaked to avoid clashing models.

v2.0.0-beta.1

Beta started!

In this beta-1 what was added was a systematic way to identify the best weights to be used in the scoring function (calibration).

v2.0.0-alpha.3

This adds support to scoring ensembles and formats the scoring output to a more parser friendly output.

This is the last release in the alpha cycle! In beta cycle the focus will be fine tuning the scoring and code review. 🦀

v2.0.0-alpha.2

• Added tests (#47)
• Introduced debug mode with optimizations for development and troubleshooting
• Updated scoring interface for better usability and consistency (#46)
• Added detailed metrics printing during scoring
• Added BSD Zero Clause License file for clear licensing terms
• QoL: Better documentation and usage examples
• QoL: Cleaner codebase organization
• QoL: More informative output during execution

Alpha Release Notice

⚠️ v2.0.0-alpha.2 continues as a pre-production release. While there are now tests and code is stable, the algorithm still requires comprehensive benchmarking before production use.

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 🦀

v1.1.0

Changes:

• Many, many code optimizations
• Better documentation
• Adding restraint satisfaction as fitness
• Introduction of the scoring module
• Notable success rate performance increase in comparison to previous version
• Replacing dockq with profit (mostly for performance reasons) for benchmarking

v1.0.0

First release of gdock.