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IMP Reference Guide  2.6.1
The Integrative Modeling Platform
multiresolution.py

This example shows how to use the multiresolution support available in IMP.atom via the IMP.atom.Resolution decorator and IMP.atom.Selection

1 ## \example rmf/multiresolution.py
2 # In this example a pdb is converted into a multiresolution model,
3 # somewhat painfully.
4 
5 from __future__ import print_function, division
6 import IMP.atom
7 import sys
8 import RMF
9 import IMP.rmf
10 
11 IMP.setup_from_argv(sys.argv, "Create a multiresolution rmf file")
12 
13 pdbname = IMP.rmf.get_example_path("big.pdb")
14 
15 m = IMP.Model()
16 h = IMP.atom.read_pdb(pdbname, m)
17 IMP.atom.add_bonds(h)
18 
19 chains = IMP.atom.get_by_type(h, IMP.atom.CHAIN_TYPE)
20 
21 if IMP.get_bool_flag("run_quick_test"):
22  chains = [chains[0]]
23 
24 
25 def recursive_approximation(res):
26  print("approximating", res)
27  lr = len(res)
28  if lr <= 1:
29  return res
30  if lr > 4:
31  me = recursive_approximation(res[0:lr // 4])\
32  + recursive_approximation(res[lr // 4: lr // 2])\
33  + recursive_approximation(res[lr // 2: 3 * lr // 4])\
34  + recursive_approximation(res[3 * lr // 4: lr])
35  else:
36  me = res
37  p = IMP.Particle(m)
38  hc = IMP.atom.Hierarchy.setup_particle(p)
39  IMP.atom.setup_as_approximation(p, res)
40  nm = str(IMP.atom.Residue(res[0]).get_index()) + "-"\
41  + str(IMP.atom.Residue(res[-1]).get_index())
42  p.set_name(nm)
43  for mm in me:
44  hc.add_child(mm)
45  return [hc]
46 
47 for c in chains:
48  res = IMP.atom.get_by_type(h, IMP.atom.RESIDUE_TYPE)
49  for r in res:
50  c.remove_child(r)
51  lvs = IMP.atom.get_leaves(r)
52  IMP.atom.setup_as_approximation(r, lvs)
53  lr = len(res)
54  me = recursive_approximation(res[0:lr // 4])\
55  + recursive_approximation(res[lr // 4: lr // 2])\
56  + recursive_approximation(res[lr // 2: 3 * lr // 4])\
57  + recursive_approximation(res[3 * lr // 4: lr])
58  for mm in me:
59  c.add_child(mm)
60 
61 print("writing")
62 fn = IMP.create_temporary_file_name("multires", ".rmf")
63 rmf = RMF.create_rmf_file(fn)
64 print("adding")
65 IMP.rmf.add_hierarchies(rmf, chains)
66 
67 print("see file", fn)