IMP  2.0.0
The Integrative Modeling Platform
core/restrain_minimum_distance.py

This example shows how to restrain based on the minimum distance between two arbitrary sets of particles. You should also see IMP::atom::create_distance_restraint() for a related helper function.

1 ## \example core/restrain_minimum_distance.py
2 ## This example shows how to restrain based on the minimum distance between two arbitrary sets of particles. You should also see IMP::atom::create_distance_restraint() for a related helper function.
3 
4 import IMP
5 import IMP.core
6 m= IMP.Model()
7 
8 # stuff to create some XYZR particles
9 ds0= IMP.core.create_xyzr_particles(m, 10, 1, 50)
10 ds1= IMP.core.create_xyzr_particles(m, 10, 1, 50)
11 
12 # first create a table mapping a sentinenal particle to each set
14 tref.add_particle(ds0[0], ds0)
15 tref.add_particle(ds1[0], ds1)
16 
17 # create a pair score to apply to the closest pair
19 # create the pair score with this refiner telling it to use the
20 # single closest particle
21 ps= IMP.core.KClosePairsPairScore(hps, tref, 1)
22 
23 # create a restraint by binding the pair score to the sentinal particles
24 r= IMP.core.PairRestraint(ps, (ds0[0], ds1[0]), "distance")
25 
27 bm= IMP.core.BallMover(ds0+ds1, 1)
28 mc.add_mover(bm)
29 mc.set_scoring_function([r])
30 mc.optimize(1000)
31 
32 # find out which pair ended up close
33 for p0 in ds0:
34  for p1 in ds1:
35  if IMP.core.get_distance(p0, p1) <.1:
36  print p0, p1