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IMP Reference Guide  2.6.2
The Integrative Modeling Platform
rmf/pdb.py

Write a PDB to an hdf5 file.

1 ## \example rmf/pdb.py
2 # Write a PDB to an hdf5 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 # find the name for a temporary file to use to for writing the hdf5 file
19 tfn = IMP.create_temporary_file_name("pdb", ".rmf")
20 
21 print("File name is", tfn)
22 
23 # open the temporary file, clearing any existing contents
24 rh = RMF.create_rmf_file(tfn)
25 
26 # add the hierarchy to the file
28 
29 # add the current configuration to the file as frame 0
31 
32 # change a coordinate
33 IMP.core.XYZ(IMP.atom.get_leaves(h)[0]).set_x(0)
34 
35 # add the new configuration to the file as frame 1
37 
38 # close the file
39 del rh
40 
41 # reopen it, don't clear the file when opening it
42 rh = RMF.open_rmf_file_read_only(tfn)
43 
44 # hps is a list with one element which is a copy of h
45 hps = IMP.rmf.create_hierarchies(rh, m)
46 
48 
49 # load the second configuration into hps
50 IMP.rmf.load_frame(rh, RMF.FrameID(0))
51 
52 print("Try running hdf5_display or hdf5_show on", tfn)