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tanlongzhi / dip-c

Tools to analyze Dip-C (or other 3C/Hi-C) data
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In the old pipeline, Is it possible to generate models at a higher resolution? #36

Closed tarak77 closed 4 years ago

tarak77 commented 5 years ago

Hey @tanlongzhi , Will it be possible to pass in particle size list with resolutions higher than 20kb? what would cause it to fail? Thanks!

tanlongzhi commented 5 years ago

Hey @tarak77, yes it should work but will be much slower. Keep in mind that the time complexity to keep track of particles is O(N) and even worse for exclusion volumes (collision detection).

tarak77 commented 4 years ago

Now that I am thinking, do you have any idea for an efficient method for collision detection?

tanlongzhi commented 4 years ago

Hi @tarak77, yes, @lh3 has already developed an efficient method using AVL tree. This has been implemented as the 3D modeling functionality of hickit. More specifically, the relevant files are fdg.c and kavl.h (also see kavl.h in klab).

Therefore, for high-resolution 3D modeling, I'd recommend hickit to save time.

tarak77 commented 4 years ago

Okk, thanks!