core/rigid_bodies.py

This example shows how to set up rigid bodies, one per residue in a protein. A score state is then used to ensure that the bodies remain rigid during the optimization process.

## \example core/rigid_bodies.py
# This example shows how to set up rigid bodies, one per residue in a protein. A score
# state is then used to ensure that the bodies remain rigid during the optimization process.
#

import IMP
import IMP.core
import IMP.atom
import IMP.container

m = IMP.kernel.Model()
# create a new IMP.atom.Hierarchy for the pdb file
mp1 = IMP.atom.read_pdb(IMP.core.get_example_path('example_protein.pdb'), m)
chains = IMP.atom.get_by_type(mp1, IMP.atom.CHAIN_TYPE)
rd = IMP.atom.Hierarchy(chains[0])
# Create a rigid body from the first chain
# note that rbs != chains[0] as the bounding volume for rbs needs to include all of the
# chain, but chains[0] might have a smaller sphere associated with it.
rbs = IMP.atom.create_rigid_body(chains[0])
print("all done")