On Sep 23, 2009, at 7:31 AM, Friedrich Foerster wrote:
On Wed, Sep 23, 2009 at 5:14 AM, Daniel Russel <>
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.
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.