Re: [IMP-dev] maximum diameter restraints

On Mon, Dec 1, 2008 at 4:39 PM, Daniel Russel <">drussel@gmail.com> wrote:

I have some code for you, but the repository appears to be broken.

Here is the example:
import IMP
import IMP.core

# This example addes a restraint on bipartite nonbonded interactions
# after excluding a set of bonded interactions.

m= IMP.Model()
# The set of particles

lc= IMP.core.ListSingletonContainer(IMP.core.create_xyzr_particles(m, 20, 1.0))
ps = IMP.core.AllPairsPairContainer(lc)

# Set up the nonbonded list
h=IMP.core.HarmonicUpperBound(10,1)

d=IMP.core.DistancePairScore(h)

is that line the actual maximum distance restraint? i guess it is now a max diameter of 10?

r= IMP.core.PairsRestraint(d, ps)
m.add_restraint(r)

# Set up optimizer
o= IMP.core.ConjugateGradients()
o.set_model(m)

o.optimize(100)

for i in range(0, ps.get_number_of_particle_pairs()):

p= ps.get_particle_pair(i)
print IMP.core.distance(IMP.core.XYZDecorator(p[0]),

IMP.core.XYZDecorator(p[1]))

On Dec 1, 2008, at 12:11 AM, Friedrich Foerster wrote:

hi impians,

for the 26s project i would like to use a maximum diameter restraint
on the shape of proteins. so it'd be a restraint similar to the
connectivity restraint: all distances in a protein are evaluated and
if the largest distance is above a specified threshold, a harmonic
restraint would be applied on the respective pair.
did anybody already put something like that into imp? and if no, is
anybody familiar with the core also interested in that and willing to
code it? it'd take me ages and the code would be ugly ;)

thanks

frido

--

Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried

Tel: +49 89 8578 2651
Fax: +49 89 8578 2641

" target="_blank">foerster@biochem.mpg.de

www.tomotronic.org

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