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IMP Reference Guide
2.6.1
The Integrative Modeling Platform
IMP Manual
Reference Guide
Modules
Classes
Examples
version 2.6.1
rmf/pdb.py
Write a PDB to an hdf5 file.
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## \example rmf/pdb.py
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# Write a PDB to an hdf5 file.
3
#
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5
from
__future__
import
print_function
6
import
IMP.atom
7
import
IMP.rmf
8
import
RMF
9
import
sys
10
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IMP.setup_from_argv
(sys.argv,
"pdb"
)
12
13
m =
IMP.Model
()
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# 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
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# 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
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print(
"File name is"
, tfn)
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# open the temporary file, clearing any existing contents
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rh = RMF.create_rmf_file(tfn)
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# add the hierarchy to the file
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IMP.rmf.add_hierarchies
(rh, [h])
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# add the current configuration to the file as frame 0
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IMP.rmf.save_frame
(rh)
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# change a coordinate
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IMP.core.XYZ
(
IMP.atom.get_leaves
(h)[0]).set_x(0)
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# add the new configuration to the file as frame 1
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IMP.rmf.save_frame
(rh)
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# close the file
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del rh
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# reopen it, don't clear the file when opening it
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rh = RMF.open_rmf_file_read_only(tfn)
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# hps is a list with one element which is a copy of h
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hps =
IMP.rmf.create_hierarchies
(rh, m)
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IMP.atom.show_molecular_hierarchy
(hps[0])
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# load the second configuration into hps
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IMP.rmf.load_frame
(rh, RMF.FrameID(0))
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print(
"Try running hdf5_display or hdf5_show on"
, tfn)