On Sep 21, 2009, at 7:30 AM, Friedrich Foerster wrote:
> > 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 ... 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.
>> 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 ... 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...)
> 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.