RMF
alternatives.py
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 from __future__ import print_function
9 import RMF
10 
11 tfn = RMF._get_temporary_file_path("alternatives.rmf3")
12 print("File is", tfn)
13 
14 f = RMF.create_rmf_file(tfn)
15 f.add_frame("frame", RMF.FRAME)
16 
17 # make a trivial set of multiple resolution represntations
18 rh = f.get_root_node()
19 
20 pf = RMF.ParticleFactory(f)
21 gpf = RMF.GaussianParticleFactory(f)
22 rff = RMF.ReferenceFrameFactory(f)
23 
24 
25 def frange(x, y, jump):
26  while x < y:
27  yield x
28  x += jump
29 
30 
31 def create_hierarchy(radius):
32  root = f.add_node(str(radius), RMF.REPRESENTATION)
33  for i in frange(0., 8, radius):
34  for j in frange(0., 8, radius):
35  for k in frange(0., 8, radius):
36  center = RMF.Vector3(
37  i + radius / 2,
38  j + radius / 2,
39  k + radius / 2)
40  n = root.add_child(
41  str(i) + "-" + str(j) + "-" + str(k),
42  RMF.REPRESENTATION)
43  d = pf.get(n)
44  d.set_static_radius(radius)
45  d.set_frame_coordinates(center)
46  d.set_static_mass(radius ** 3)
47  return root
48 
49 
50 def create_gmm(radius=1.):
51  root = f.add_node("gmm" + str(radius), RMF.REPRESENTATION)
52  for i in frange(0., 8, radius):
53  for j in frange(0., 8, radius):
54  center = RMF.Vector3(
55  i + radius / 2,
56  j + radius / 2,
57  4)
58 
59  n = root.add_child(
60  str(i) + "-" + str(j),
61  RMF.REPRESENTATION)
62  d = gpf.get(n)
63  d.set_variances(RMF.Vector3(radius / 2, radius / 2, 4))
64  d.set_static_mass(radius ** 3)
65  rf = rff.get(n)
66  rf.set_rotation(RMF.Vector4(1, 0, 0, 0))
67  rf.set_translation(center)
68  return root
69 
70 n = create_hierarchy(4)
71 rh.add_child(n)
72 
73 af = RMF.AlternativesFactory(f)
74 da = af.get(n)
75 da.add_alternative(create_hierarchy(1), RMF.PARTICLE)
76 da.add_alternative(create_hierarchy(2), RMF.PARTICLE)
77 da.add_alternative(create_hierarchy(4), RMF.PARTICLE)
78 da.add_alternative(create_gmm(), RMF.GAUSSIAN_PARTICLE)
79 
80 RMF.show_hierarchy(n)
81 
82 print("particles", RMF.get_resolutions(n, RMF.PARTICLE))
83 print("gaussian particles", RMF.get_resolutions(n, RMF.GAUSSIAN_PARTICLE))
RMF::show_hierarchy
void show_hierarchy(NodeConstHandle root)
RMF::create_rmf_file
FileHandle create_rmf_file(std::string path)
Create an RMF from a file system path.