RMF
alternatives.py

The RMF format supports storing alternative representations of the structure through the RMF::decorator::Alternatives decorator and associated types. Multiple versions of the hierarchy are stored, all representing the same biological entity. Different representations can be used for different purposes based on resolution or other criteria.

1 ## \example alternatives.py
2 # The RMF format supports storing alternative representations of the structure
3 # through the RMF::decorator::Alternatives decorator and associated types.
4 # Multiple versions of the hierarchy are stored, all representing the same
5 # biological entity. Different representations can be used for different
6 # purposes based on resolution or other criteria.
7 
8 import RMF
9 
10 tfn = RMF._get_temporary_file_path("alternatives.rmf3")
11 print("File is", tfn)
12 
13 f = RMF.create_rmf_file(tfn)
14 f.add_frame("frame", RMF.FRAME)
15 
16 # make a trivial set of multiple resolution represntations
17 rh = f.get_root_node()
18 
19 pf = RMF.ParticleFactory(f)
20 gpf = RMF.GaussianParticleFactory(f)
21 rff = RMF.ReferenceFrameFactory(f)
22 
23 
24 def frange(x, y, jump):
25  while x < y:
26  yield x
27  x += jump
28 
29 
30 def create_hierarchy(radius):
31  root = f.add_node(str(radius), RMF.REPRESENTATION)
32  for i in frange(0., 8, radius):
33  for j in frange(0., 8, radius):
34  for k in frange(0., 8, radius):
35  center = RMF.Vector3(
36  i + radius / 2,
37  j + radius / 2,
38  k + radius / 2)
39  n = root.add_child(
40  str(i) + "-" + str(j) + "-" + str(k),
41  RMF.REPRESENTATION)
42  d = pf.get(n)
43  d.set_static_radius(radius)
44  d.set_frame_coordinates(center)
45  d.set_static_mass(radius ** 3)
46  return root
47 
48 
49 def create_gmm(radius=1.):
50  root = f.add_node("gmm" + str(radius), RMF.REPRESENTATION)
51  for i in frange(0., 8, radius):
52  for j in frange(0., 8, radius):
53  center = RMF.Vector3(
54  i + radius / 2,
55  j + radius / 2,
56  4)
57 
58  n = root.add_child(
59  str(i) + "-" + str(j),
60  RMF.REPRESENTATION)
61  d = gpf.get(n)
62  d.set_variances(RMF.Vector3(radius / 2, radius / 2, 4))
63  d.set_static_mass(radius ** 3)
64  rf = rff.get(n)
65  rf.set_rotation(RMF.Vector4(1, 0, 0, 0))
66  rf.set_translation(center)
67  return root
68 
69 n = create_hierarchy(4)
70 rh.add_child(n)
71 
72 af = RMF.AlternativesFactory(f)
73 da = af.get(n)
74 da.add_alternative(create_hierarchy(1), RMF.PARTICLE)
75 da.add_alternative(create_hierarchy(2), RMF.PARTICLE)
76 da.add_alternative(create_hierarchy(4), RMF.PARTICLE)
77 da.add_alternative(create_gmm(), RMF.GAUSSIAN_PARTICLE)
78 
79 RMF.show_hierarchy(n)
80 
81 print("particles", RMF.get_resolutions(n, RMF.PARTICLE))
82 print("gaussian particles", RMF.get_resolutions(n, RMF.GAUSSIAN_PARTICLE))