On Sep 21, 2009, at 7:30 AM, Friedrich Foerster wrote:
Depends which refiner :-) A LeavesRefiner returns the hierarchy leaves, the ChildrenRefiner returns the children... Basically it is a way of selecting a set of particles from a given one.On Sep 21, 2009, at 3:54 PM, Daniel Russel wrote:I think the problem is that the list of particles the connectivity restraint ends up with is [p0,p1...p5]. You should just give it two particles, one for each protein (with radius and center computed from a sphere cover, or with the distance computed using a particle refiner).could you give an example, please? i have no clue what a refiner does. the doc says it returns particles. no clue which ones ...
For the first month or so it allowed direct specification of the sets of particles, but not for well over a year (it was changed back when you complained about it being really slow...)I doubt the code below ever really did what you wanted (although it might have happened to agree:-)yes, it did work fine. probably going back to brad, the syntax was simply to specify each protein as a list. pretty convenient ...
at some point in the recent months, it started being ignored which particles are put into IMP.Particles. they seem to be just thrown into one basket, which they were not before. needless to say i'd prefer that simple syntax compared dealing with hyper-abstract classes etc unless someone convinces me of the necessity of those.Mostly it just keeps the interfaces uniform and simplifies the connectivity restraint a great deal (and makes is to that it can be fast when using rigid bodies). In general, if you want to refer to a particular feature, make sure there is a particle which relates to that feature.