On Wed, Sep 23, 2009 at 4:42 PM, Daniel Russel drussel@gmail.com wrote: > > On Sep 23, 2009, at 7:31 AM, Friedrich Foerster wrote: > >> On Wed, Sep 23, 2009 at 5:14 AM, Daniel Russel drussel@gmail.com wrote: >>> >>> On Sep 22, 2009, at 6:55 PM, Keren Lasker wrote: >>> >>>> Daniel - >>>> 1. does this solution means that f3-f5-f7 (and f0-f1-f2) are simplified >>>> to >>>> a single sphere ? >> >> so i implemented option 1, which seems to do what i want (the >> restraint acting closest two spheres). >> to check that the code actually does the right thing (score the single >> shortest distance between (f3,f5,f7) and (f0,f1,f2)) i tried to return >> the connected pairs (=ONE pair for my desired restraint, not FIVE >> restraints for the undesired behavior). sadly, >> connrest.get_connected_pairs() returns my newly generated particles, >> which specify the interacting fragments. is there any way to return >> the actually interacting LowestRefined particles? otherwise, i cannot >> check that the code does the right thing (and the information is >> useful for me)... > > Good point. The easiest way around is for me to add add a method to the > LowestRefinedPairScore that returns the actual pair given an input pair. > Makes the verification two steps, but it is just verification, so being > slightly annoying seems fine to me. I'll do that later today.
thanks. that'd be ver useful for me.
> > BTW, if you really only have an interaction between two sets of particles, > you might as well skip the connectivityrestraint and just use a > pairrestraint.
? I need the msp functionality, i.e., the restraint should only use the shortest inter-fragment distance for scoring. i thought the ConnectivityRestraint is the appropriate restraint type. if PairRestraint does the same i could also use that - however, i have sometimes >2 fragments involved, so anyways, i'll need the ConnectivityRestraint, i guess. i'd encourage another thing for the documentation: it'd be useful to have a somewhat more informative short description (one sentence) for each class/function in IMP. for example, if PairRestraint calculates the msp between input particles if they have children, it'd be nice to tell that explicitly. even better would be to link to ConnectivityRestraint and highlight similarities/differences.
thanks
frido
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