atom/rigid_brownian_dynamics.py

This example shows how to run brownian dynamics with rigid bodies.

## \example atom/rigid_brownian_dynamics.py
# This example shows how to run brownian dynamics with rigid bodies.

import IMP.atom
import IMP.core
import IMP.algebra
import IMP.display
import sys

IMP.setup_from_argv(sys.argv, "rigid brownian dynamics")


def create_rigid_body(m, name):
    prb = IMP.core.RigidBody.setup_particle(
        IMP.Particle(m), IMP.algebra.ReferenceFrame3D())
    prb.set_coordinates_are_optimized(True)
    prb.set_name(name + " rb")
    ph = IMP.atom.Molecule.setup_particle(IMP.Particle(m))
    ph.set_name(name)
    for i in range(0, 2):
        for j in range(0, 2):
            for k in range(0, 2):
                d = IMP.core.XYZR.setup_particle(IMP.Particle(m),
                                                 IMP.algebra.Sphere3D(
                                                     IMP.algebra.Vector3D(
                                                         i, j, k) * 10.0,
                                                     10))
                ph.add_child(IMP.atom.Fragment.setup_particle(d))
                IMP.atom.Mass.setup_particle(d, 1000)
                prb.add_member(d)
                d.set_name(name + str(i) + str(j) + str(k))
    d = IMP.atom.RigidBodyDiffusion.setup_particle(prb)
    d.set_rotational_diffusion_coefficient(
        d.get_rotational_diffusion_coefficient() * 100)
    return prb, ph


def display(i, w, hs):
    w.set_frame(i)
    for h in hs:
        g = IMP.atom.HierarchyGeometry(h)
        w.add_geometry(g)


m = IMP.Model()
IMP.set_log_level(IMP.SILENT)

rb0, h0 = create_rigid_body(m, "first")
rb1, h1 = create_rigid_body(m, "second")
rb1.set_reference_frame(IMP.algebra.ReferenceFrame3D(
    IMP.algebra.Transformation3D(IMP.algebra.Vector3D(30, 0, 0))))

ev = IMP.core.ExcludedVolumeRestraint(
    IMP.container.ListSingletonContainer(
        m, rb0.get_rigid_members() + rb1.get_rigid_members()), 1, 3)

cr = IMP.atom.create_distance_restraint(
    IMP.atom.Selection(h0), IMP.atom.Selection(h1), 0, 1)

sf = IMP.core.RestraintsScoringFunction([ev, cr])

bd = IMP.atom.BrownianDynamics(m)
bd.set_scoring_function(sf)
bd.set_time_step(10000)

nm = IMP.create_temporary_file_name("rigid_bd", ".pym")
nm = "rigid.pym"
w = IMP.display.PymolWriter(nm)
for i in range(0, 100):
    display(i, w, [h0, h1])
    bd.optimize(10)