IMP  2.3.1
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 import IMP.atom
9 import IMP.rmf
10 import RMF
11 m = IMP.kernel.Model()
12 
13 # Create a new IMP.atom.Hierarchy from the contents of the pdb file
14 h = IMP.atom.read_pdb(IMP.rmf.get_example_path("simple.pdb"), m)
15 
16 # find the name for a temporary file to use to for writing the hdf5 file
17 tfn = IMP.create_temporary_file_name("link", ".rmf")
18 
19 print "File name is", tfn
20 
21 # open the temporary file, clearing any existing contents
22 rh = RMF.create_rmf_file(tfn)
23 
24 # add the hierarchy to the file
26 
27 # add the current configuration to the file as frame 0
29 
30 # close the file
31 del rh
32 
33 # reopen it, don't clear the file when opening it
34 rh = RMF.open_rmf_file_read_only(tfn)
35 
36 # link to the existing pdb hierarchy
38 
39 # load the same coordinates in, ok, that is not very exciting
40 IMP.rmf.load_frame(rh, RMF.FrameID(0))
41 
42 print "Try running hdf5_display or hdf5_show on", tfn