rigid_body_and_excluded_volume_restraint.py

## \example restrainer/rigid_body_and_excluded_volume_restraint.py
# This example shows how to use IMP::core::RigidBody and IMP::core::ExcludedVolumeRestraint. We will construct a molecular hierarchy consisting of five proteins, and then apply connectivity restraint obtained from yeast two-hybrid experimental data to these proteins. We will define these proteins as rigid bodies and apply excluded volume restraint to prevent these proteins from interpenetrating.
# On the following figure, we see an XML representation of the molecular hierarchy.
#
# \include eg2_representation.xml
#
# From restrainer's point of view, a Rigid Body is a special form of restraint. Therefore, to make some parts of the hierarchy rigid, suitable rigid body declarations should be placed in the restraint XML file.
#
# \include eg2_restraint.xml
#
#

# -- File: rigid_body_and_excluded_volume_restraint.py --#

import IMP
import IMP.restrainer

# Create restrainer object
restrainer = IMP.restrainer.Main()

# Add representation and restraint to restrainer
rep = restrainer.add_representation(
    IMP.restrainer.get_example_path('input/eg2_representation.xml'))
rsr = restrainer.add_restraint(
    IMP.restrainer.get_example_path('input/eg2_restraint.xml'))

# =======================================================================###
#  At this point all data from XML files have been placed into the model.
#  Now it is possible to perform various operations on the IMP model.
# =======================================================================###

# Get the IMP model object used by restrainer
model = restrainer.get_model()

# Find the IMP data structure with the given id
protein1_hierarchy = rep.get_imp_hierarchy_by_id('Protein1')

# Get root hierarchy
root_hierarchy = rep.get_root_imp_hierarchy()

# Get the rigid body with the given id
protein1_rb = rsr.get_rigid_body_by_id("Protein1")

# Get all rigid bodies
rbs = rsr.get_all_rigid_bodies()

# Define transformation
ub = IMP.algebra.Vector3D(-50.0, -50.0, -50.0)
lb = IMP.algebra.Vector3D(50.0, 50.0, 50.0)
bb = IMP.algebra.BoundingBox3D(ub, lb)
translation = IMP.algebra.get_random_vector_in(bb)
rotation = IMP.algebra.get_random_rotation_3d()
transformation = IMP.algebra.Transformation3D(rotation, translation)

# Perform geometric transformations on the Protein1 rigid body
protein1_rb.set_reference_frame(IMP.algebra.ReferenceFrame3D(transformation))
protein1_rb.show()