IMP  2.0.0
The Integrative Modeling Platform
assess_dope.py
1 ## \example atom/assess_dope.py
2 ## The script shows how to assess a protein conformation using DOPE.
3 
4 import IMP
5 import IMP.atom
6 import IMP.container
7 
8 def create_representation():
9  m=IMP.Model()
10  mp0= IMP.atom.read_pdb(IMP.atom.get_example_path('1fdx.B99990001.pdb'), m, IMP.atom.NonWaterNonHydrogenPDBSelector())
11  prot=IMP.atom.get_by_type(mp0, IMP.atom.CHAIN_TYPE)[0]
12  return (m, prot)
13 
14 def add_dope(m, prot):
15  ps=IMP.atom.get_by_type(prot, IMP.atom.ATOM_TYPE)
16  for p in ps:
17  if not IMP.atom.Atom.particle_is_instance(p):
18  print "Huh?", p
19  dpc = IMP.container.ClosePairContainer(ps, 15.0, 0.0)
20 # exclude pairs of atoms belonging to the same residue
21 # for consistency with MODELLER DOPE score
22  f=IMP.atom.SameResiduePairFilter()
23  dpc.add_pair_filter(f)
24  IMP.atom.add_dope_score_data(prot)
25  dps= IMP.atom.DopePairScore(15.0)
26 # dps= IMP.membrane.DopePairScore(15.0, IMP.membrane.get_data_path("dope_scorehr.lib"))
27  d= IMP.container.PairsRestraint(dps, dpc)
28  m.add_restraint(d)
29 
30 print "creating representation"
31 (m,prot)=create_representation()
32 
33 print "creating DOPE score function"
34 add_dope(m,prot)
35 
36 IMP.base.set_check_level(IMP.base.USAGE)
37 print "DOPE SCORE ::",m.evaluate(False)