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Re: [IMP-dev] Restraint::get_particles()




On Aug 18, 2008, at 10:07 PM, Ben Webb wrote:

Daniel Russel wrote:
You should read the emails on imp-dev occasionally :-)

Indeed.

Anyway, that method should definitely not be made public as it isn't
guaranteed to do anything useful. For some of the restraints
(NonbondedRestraints) it returns nothing and for others, such as the
PairListRestraint it globs together lots of particles which aren't
actually interacting.

The best solution is probably to add a new virtual method
get_interacting_pairs which returns a list of interacting particle
pairs (since I think that is what you want). Or something similar. It
would be quite easy to implement for existing restraints.

Agreed. I seem to recall that's what you suggested the last time Keren
asked this question. I think I agreed that time around too. ;)
funny !! ;)


Keren, what is your use case? If it's not "get a list of interacting
pairs" then we'll need to do something different.
Ben - as I wrote in my last reply - it is not all_pairs, since the optimization tries to find that. We get MSMS data which says a,b,c,d,e create a complex - but we do not know which interacts with which. so what DOMINO needs out of the restraint is a-e .



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