IMP  2.0.0
The Integrative Modeling Platform
molecular_hierarchy.py
1 ## \example atom/molecular_hierarchy.py
2 ## In this example, we read a protein from a PDB file and set the center and radius of each residue to enclose the atoms in that residue.
3 ##
4 ## Then a second copy of the protein is loaded and they are both added to the same hierarchy
5 ## to define a hypothetical assembly.
6 ##
7 
8 import IMP
9 import IMP.core
10 import IMP.atom
11 
12 m = IMP.Model()
13 mp0= IMP.atom.read_pdb(IMP.atom.get_example_path('example_protein.pdb'), m)
14 # get the 16th residue of the first chain
15 hchain= IMP.atom.get_by_type(mp0, IMP.atom.CHAIN_TYPE)[0]
16 # decorate the chain particle with an IMP.atom.Chain decorator.
17 # unfortunately, our python wrapper does not handle converseions properly
18 # as a result you have to manually get the particle for that chain
19 chain=IMP.atom.Chain(hchain.get_particle())
20 r16 = IMP.atom.get_residue(chain, 16)
21 r16.show()
22 
23 # get all the atoms
24 atoms= IMP.atom.get_by_type(mp0, IMP.atom.ATOM_TYPE)
25 # I didn't really have anything interesting to do with them...
26 
27 # create a new version of the protein that is coarsened (one particle per residue)
29 
30 # we don't need mp0 any more
32 
33 # load another copy
34 mp1= IMP.atom.read_pdb(IMP.atom.get_example_path('example_protein.pdb'), m)
35 
36 # create a graph from the hierarchy
38 # process the file with dot like
39 # dot -Tpdf hierarchy.dot > hierarchy.pdf
40 mp1t.show_graphviz(open("hierarchy.dot", "w"))
41 # try to display it graphically, assuming altgraph is installed
42 try:
43  mp1t.show_with_altgraph()
44 except:
45  pass
46 
47 # make this one rigid
49 
50 # create a hierarchy which contains the two proteins
51 p = IMP.Particle(m)
53 rmp.add_child(smp0)
54 rmp.add_child(mp1)