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

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phonglam3103 wants to merge 11 commits into

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Commits on Mar 20, 2026

feat: Python scripts to convert db2 format to db2binary format. Requires zstandard for more efficient zipping.
phonglam3103
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9ae399b
perf: Matching optimization by bucket-based degeneracy and canonical ordering of the ligand matching spheres
phonglam3103
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27da92c
fix: Small fix related to mismatch between the types of variables and signal sending
phonglam3103
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ba48111
perf: Scoring optimization, done by lazy-evaluation; SIMD optimization and atom bump early exit
phonglam3103
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d80cb8a
perf: Binary DB2 support, helping to accelerate the parsing process, avoid type conversion
phonglam3103
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1ed6811
feat: A bunch of code lines for measuring the performance of each process (DB2 parsing, matching, and scoring)
phonglam3103
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f6ab149
Change the folder name
phonglam3103
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14f78b5
refactor: Remove standalone DB2 to binary converter, enhance recursive version, and add script documentation.
phonglam3103
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9bd8b71
fix: Fix a bug that apolar desolvation was not calculated correctly
phonglam3103
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e82a6bd

Commits on Mar 21, 2026

Change portland compilers to the updated nvfortrans
phonglam3103
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59bdee9
Precompiled dock64 for convenient testing
phonglam3103
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8446bfc