perf: Speed up of 7 times of DOCK3.8.5#4

Open

phonglam3103 wants to merge 11 commits intodocking-org:mainfrom

phonglam3103:main

Commits on Mar 20, 2026

feat: Python scripts to convert db2 format to db2binary format. Requires zstandard for more efficient zipping.
phonglam3103
committed
perf: Matching optimization by bucket-based degeneracy and canonical ordering of the ligand matching spheres
phonglam3103
committed
fix: Small fix related to mismatch between the types of variables and signal sending
phonglam3103
committed
perf: Scoring optimization, done by lazy-evaluation; SIMD optimization and atom bump early exit
phonglam3103
committed
perf: Binary DB2 support, helping to accelerate the parsing process, avoid type conversion
phonglam3103
committed
feat: A bunch of code lines for measuring the performance of each process (DB2 parsing, matching, and scoring)
phonglam3103
committed
Change the folder name
phonglam3103
committed
refactor: Remove standalone DB2 to binary converter, enhance recursive version, and add script documentation.
phonglam3103
committed
fix: Fix a bug that apolar desolvation was not calculated correctly
phonglam3103
committed

Commits on Mar 21, 2026