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IMP Reference Guide  2.6.1
The Integrative Modeling Platform
rmf/link.py

This example is like module/rmf/pdb.py except that instead of creating a new hierarchy from the rmf file, it simply links the existing hierarchy to the file. This mechanism can be used for loading multiple conformations for scoring or other analysis without having to set up restraints and things each time.

1 ## \example rmf/link.py
2 # This example is like module/rmf/pdb.py except that instead of creating a
3 # new hierarchy from the rmf file, it simply links the existing hierarchy
4 # to the file. This mechanism can be used for loading multiple
5 # conformations for scoring or other analysis without having to set up
6 # restraints and things each time.
7 
8 from __future__ import print_function
9 import IMP.atom
10 import IMP.rmf
11 import RMF
12 import sys
13 
14 IMP.setup_from_argv(sys.argv, "link")
15 
16 m = IMP.Model()
17 
18 # Create a new IMP.atom.Hierarchy from the contents of the pdb file
19 h = IMP.atom.read_pdb(IMP.rmf.get_example_path("simple.pdb"), m)
20 
21 # find the name for a temporary file to use to for writing the hdf5 file
22 tfn = IMP.create_temporary_file_name("link", ".rmf")
23 
24 print("File name is", tfn)
25 
26 # open the temporary file, clearing any existing contents
27 rh = RMF.create_rmf_file(tfn)
28 
29 # add the hierarchy to the file
31 
32 # add the current configuration to the file as frame 0
34 
35 # close the file
36 del rh
37 
38 # reopen it, don't clear the file when opening it
39 rh = RMF.open_rmf_file_read_only(tfn)
40 
41 # link to the existing pdb hierarchy
43 
44 # load the same coordinates in, ok, that is not very exciting
45 IMP.rmf.load_frame(rh, RMF.FrameID(0))
46 
47 print("Try running hdf5_display or hdf5_show on", tfn)