Re: [IMP-dev] NBL cleanup and other small patches

[Ben Webb <>]

Daniel Russel wrote:
> Frido was complaining that the nbl was too slow, so I thought I would 
> check in my local changes. The big thing is that the fastest 
> implementation I have uses the CGAL library.

All patches to IMP need to be reviewed before they are checked in. 
Obviously, I am not going to do this while I'm on vacation, so unless 
somebody else with some understanding of the code volunteers to check 
through these patches, they'll have to wait until I'm back in the lab.

I don't think we can use CGAL. It is certainly available for Fedora, but 
we build on a lot of other platforms too. And my understanding is that 
large chunks of it are QPL licensed, which is certainly incompatible 
with the IMP license. If we did use it, we'd have to be very careful to 
use only the LGPL parts. So I'd rather we didn't use it at all.

Your timings suggest that the current grid nonbonded list implementation 
is not O(N). Why not? It seems like it should be from my understanding 
of the code.

	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle