doc/ref/atom_2molecular_hierarchy_8py-example.html

## \example atom/molecular_hierarchy.py

# 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.

#

# Then a second copy of the protein is loaded and they are both added to the

# same hierarchy to define a hypothetical assembly.

#


import IMP

import IMP.core

import IMP.atom

import sys


IMP.setup_from_argv(sys.argv, "molecular hierarchy")


m = IMP.Model()

mp0 = IMP.atom.read_pdb(IMP.atom.get_example_path('example_protein.pdb'), m)

# get the 16th residue of the first chain

hchain = IMP.atom.get_by_type(mp0, IMP.atom.CHAIN_TYPE)[0]

# decorate the chain particle with an IMP.atom.Chain decorator.

# unfortunately, our Python wrapper does not handle conversions properly

# as a result you have to manually get the particle for that chain

chain = IMP.atom.Chain(hchain.get_particle())

r16 = IMP.atom.get_residue(chain, 16)

r16.show()


# get all the atoms

atoms = IMP.atom.get_by_type(mp0, IMP.atom.ATOM_TYPE)

# I didn't really have anything interesting to do with them...


# create a new version of the protein that is coarsened (one particle per

# residue)

smp0 = IMP.atom.create_simplified_along_backbone(chain, 1)


# we don't need mp0 any more

IMP.atom.destroy(mp0)


# load another copy

mp1 = IMP.atom.read_pdb(IMP.atom.get_example_path('example_protein.pdb'), m)


# create a graph from the hierarchy

mp1t = IMP.atom.get_hierarchy_tree(mp1)

# process the file with dot like

# dot -Tpdf hierarchy.dot > hierarchy.pdf

mp1t.show_graphviz(open("hierarchy.dot", "w"))

# try to display it graphically, assuming altgraph is installed

try:

    mp1t.show_with_altgraph()

except:

    pass


# make this one rigid

IMP.atom.create_rigid_body(mp1)


# create a hierarchy which contains the two proteins

p = IMP.Particle(m)

rmp = IMP.atom.Hierarchy.setup_particle(p)

rmp.add_child(smp0)

rmp.add_child(mp1)