perf: Speed up of 7 times of DOCK3.8.5

[phonglam3103]

Hi @jir322 ,

Sorry for taking so long to contribute the changes, but here we are ;). This PR includes several changes to all the phases:

1. DB2 parsing

• Support for binary format parsing
• Included a conversion script from standard DB2 to binary format
• Enable via use_binary_db2: yes in the INDOCK configuration

2. Matching optimization

• Implemented bucket-based degeneracy checks
• Added canonical ordering for ligand sphere matching

3. Scoring optimization

• Introduced lazy evaluation
• Applied SIMD optimizations
• Added early exit on atom bump detection

4. FYI, I changed the portland compilers to nvfortran as that is what we have from our side.
   DOCK optimization.pdf

I’ve also attached a PDF with additional details for reference. You might also find the precompiled version of dock64 (named dock64_optimized) in the main directory, which you can test directly without recompiling it.

Happy to hear any feedback—feel free to take a look through the code!
Phong.