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IMP Reference Guide  develop.879b8d2544,2020/09/30
The Integrative Modeling Platform
rmf/pdb.py

Write a PDB to an RMF file.

1 ## \example rmf/pdb.py
2 # Write a PDB to an RMF file.
3 #
4 
5 from __future__ import print_function
6 import IMP.atom
7 import IMP.rmf
8 import RMF
9 import sys
10 
11 IMP.setup_from_argv(sys.argv, "pdb")
12 
13 m = IMP.Model()
14 
15 # Create a new IMP.atom.Hierarchy from the contents of the pdb file
16 h = IMP.atom.read_pdb(IMP.rmf.get_example_path("simple.pdb"), m)
17 
18 tfn = "pdb.rmf"
19 
20 print("File name is", tfn)
21 
22 # open the file, clearing any existing contents
23 rh = RMF.create_rmf_file(tfn)
24 
25 # add the hierarchy to the file
27 
28 # add the current configuration to the file as frame 0
30 
31 # change a coordinate
32 IMP.core.XYZ(IMP.atom.get_leaves(h)[0]).set_x(0)
33 
34 # add the new configuration to the file as frame 1
36 
37 # close the file
38 del rh
39 
40 # reopen it, don't clear the file when opening it
41 rh = RMF.open_rmf_file_read_only(tfn)
42 
43 # hps is a list with one element which is a copy of h
44 hps = IMP.rmf.create_hierarchies(rh, m)
45 
47 
48 # load the second configuration into hps
49 IMP.rmf.load_frame(rh, RMF.FrameID(0))
50 
51 print("Try running rmf_display or rmf_show on", tfn)