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.

## \example 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.

import IMP.atom
import IMP.rmf
import RMF
m= IMP.Model()

# Create a new IMP.atom.Hierarchy from the contents of the pdb file
h= IMP.atom.read_pdb(IMP.rmf.get_example_path("simple.pdb"), m)

# find the name for a temporary file to use to for writing the hdf5 file
tfn=IMP.create_temporary_file_name("link", ".rmf")

print "File name is", tfn

# open the temporary file, clearing any existing contents
rh = RMF.create_rmf_file(tfn)

# add the hierarchy to the file
IMP.rmf.add_hierarchies(rh, [h])

# add the current configuration to the file as frame 0
IMP.rmf.save_frame(rh, 0)

# close the file
del rh

# reopen it, don't clear the file when opening it
rh= RMF.open_rmf_file(tfn)

# link to the existing pdb hierarchy
IMP.rmf.link_hierarchies(rh, [h])

# load the same coordinates in, ok, that is not very exciting
IMP.rmf.load_frame(rh, 0)

print "Try running hdf5_display or hdf5_show on", tfn