[Yarv-devel] Speedup

[Daniel Amelang]

I've attached a zip file with the program (just the beginning of it; 
I've just started, really). It's called riposuc and it does structural 
comparision of proteins. If you want input data files for the program, I 
can send those too.

There are three files:

bsearch.rb for performing a binary search on sorted arrays

riposuc.rb is the module that does most of the work. Actually, most of 
the work is just in the score_against method of the RIPOSUC::Protein class.

score.rb is the 'driver' that is invoked from the command line

It's about 200 lines total, so it should be easy to get an idea of what 
it's doing.

About your question, I do quite a bit of float comparisons, Math.sqrt 
and **2. I know I can do x*x instead of x**2, but I haven't really 
reached that level of optimization yet. The code is already pretty messy 
already with ugly speed optimizations.

Dan

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