em2d/optimize_em2d_with_montecarlo.py

Example of optimizing an EM2D restraint using Monte Carlo.

## \example em2d/optimize_em2d_with_montecarlo.py
# Example of optimizing an EM2D restraint using Monte Carlo.
#

from __future__ import print_function
import IMP
import IMP.core
import IMP.atom
import IMP.em2d
import IMP.algebra
import IMP.container
import random
import sys

IMP.setup_from_argv(sys.argv, "optimize EM2D with MonteCarlo")


# An Optimizer score to get the values of the statistics after a given set
# of evaluations
class WriteStatisticsOptimizerScore(IMP.OptimizerState):

    def __init__(self, m, restraints):
        IMP.OptimizerState.__init__(self, m, "WriteStats")
        self.count = 0
        self.restraints = restraints

    def update(self):
        if (self.count != 10):
            self.count += 1
            return
        else:
            self.count = 0
        o = self.get_optimizer()
        m = o.get_model()
        for r in self.restraints:
            print(r.get_name(), r.get_last_score())
        # for i in range(0,m.get_number_of_restraints()):
        #    r=m.get_restraint(i)
        #    print "restraint",r.get_name(),"value",r.evaluate(False)


# Get model from PDB file
IMP.set_log_level(IMP.TERSE)
m = IMP.Model()
prot = IMP.atom.read_pdb(
    IMP.em2d.get_example_path("1z5s.pdb"), m, IMP.atom.ATOMPDBSelector())
IMP.atom.add_radii(prot)

# get the chains
chains = IMP.atom.get_by_type(prot, IMP.atom.CHAIN_TYPE)
print("there are", len(chains), "chains in 1z5s.pdb")

# set the chains as rigid bodies
native_chain_centers = []
rigid_bodies = []
for c in chains:
    atoms = IMP.core.get_leaves(c)
    rbd = IMP.core.RigidBody.setup_particle(c, atoms)
    rbd.set_coordinates_are_optimized(True)
    rigid_bodies.append(rbd)
    print("chain has", rbd.get_number_of_members(), \
        "atoms", "coordinates: ", rbd.get_coordinates())
    native_chain_centers.append(rbd.get_coordinates())

bb = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(-25, -40, -60),
                               IMP.algebra.Vector3D(25, 40, 60))
# rotate and translate the chains
for rbd in rigid_bodies:
    # rotation
    rotation = IMP.algebra.get_random_rotation_3d()
    transformation1 = IMP.algebra.get_rotation_about_point(
        rbd.get_coordinates(), rotation)
    # translation
    transformation2 = IMP.algebra.Transformation3D(
        IMP.algebra.get_random_vector_in(bb))
    # Apply
    final_transformation = IMP.algebra.compose(
        transformation1, transformation2)
    IMP.core.transform(rbd, final_transformation)
print("Writing transformed assembly")
IMP.atom.write_pdb(prot, "1z5s-transformed.pdb")

# set distance restraints measusring some distances between rigid bodies
# for the solution.
d01 = IMP.algebra.get_distance(
    native_chain_centers[0], native_chain_centers[1])
r01 = IMP.core.DistanceRestraint(m,
    IMP.core.Harmonic(d01, 1), chains[0], chains[1])
r01.set_name("distance 0-1")
d12 = IMP.algebra.get_distance(
    native_chain_centers[1], native_chain_centers[2])
r12 = IMP.core.DistanceRestraint(m,
    IMP.core.Harmonic(d12, 1), chains[1], chains[2])
r12.set_name("distance 1-2")
d23 = IMP.algebra.get_distance(
    native_chain_centers[2], native_chain_centers[3])
r23 = IMP.core.DistanceRestraint(m,
    IMP.core.Harmonic(d23, 1), chains[2], chains[3])
r23.set_name("distance 2-3")
d30 = IMP.algebra.get_distance(
    native_chain_centers[3], native_chain_centers[0])
r30 = IMP.core.DistanceRestraint(m,
    IMP.core.Harmonic(d30, 1), chains[3], chains[0])
r30.set_name("distance 3-0")
print("Distances in the solution: d01 =", \
    d01, "d12 =", d12, "d23 =", d23, "d30 =", d30)

# set em2D restraint
srw = IMP.em2d.SpiderImageReaderWriter()
selection_file = IMP.em2d.get_example_path("all-1z5s-projections.sel")
images_to_read_names = [IMP.get_relative_path(selection_file, x) for x in
                        IMP.em2d.read_selection_file(selection_file)]
em_images = IMP.em2d.read_images(images_to_read_names, srw)
print(len(em_images), "images read")

em2d_restraint = IMP.em2d.Em2DRestraint(m)
apix = 1.5  # sampling rate of the available EM images
# resolution at which you want to generate the projections of the model
# In principle you want "perfect" projections, so use the highest resolution
resolution = 1
# Number of projections to use for the initial registration
#  (coarse registration) to estimate the registration parameters
n_projections = 20
params = IMP.em2d.Em2DRestraintParameters(apix, resolution, n_projections)

# This method (recommended) uses preprocessing of the images and projections
# to speed-up the registration
params.coarse_registration_method = IMP.em2d.ALIGN2D_PREPROCESSING
# use true if you want to save the projections from the model that best
# match the Em images
params.save_match_images = False

score_function = IMP.em2d.EM2DScore()
em2d_restraint = IMP.em2d.Em2DRestraint(m)
em2d_restraint.setup(score_function, params)
em2d_restraint.set_images(em_images)
em2d_restraint.set_name("em2d restraint")
container = IMP.container.ListSingletonContainer(m, IMP.core.get_leaves(prot))
em2d_restraint.set_particles(container)
em2d_restraints_set = IMP.RestraintSet(m)

# The next two lines are commented, because the optimization of the example
# is expensive. To run the full example, uncomment them (It can take a few
# hours).
# em2d_restraints_set.add_restraint(em2d_restraint)
# em2d_restraints_set.set_weight(1000) # weight for the em2D restraint

# Create scoring function using all restraints
all_restraints = [r01, r12, r23, r30, em2d_restraints_set]
sf = IMP.core.RestraintsScoringFunction(all_restraints)

# MONTECARLO OPTIMIZATION
s = IMP.core.MonteCarlo(m)
s.set_scoring_function(sf)
# Add movers for the rigid bodies
movers = []
for rbd in rigid_bodies:
    movers.append(IMP.core.RigidBodyMover(rbd, 5, 2))
s.add_movers(movers)
print("MonteCarlo sampler has", s.get_number_of_movers(), "movers")
# Add an optimizer state to save intermediate configurations of the hierarchy
o_state = IMP.atom.WritePDBOptimizerState(chains, "intermediate-step-%1%.pdb")
o_state.set_period(10)
s.add_optimizer_state(o_state)

ostate2 = WriteStatisticsOptimizerScore(m, all_restraints)
s.add_optimizer_state(ostate2)

# Perform optimization
temperatures = [200, 100, 60, 40, 20, 5]
# 200 steps recommended for accurate optimization; a smaller number is used
# here for demonstration purposes
optimization_steps = 10
for T in temperatures:
    s.set_kt(T)
    s.optimize(optimization_steps)
IMP.atom.write_pdb(prot, "solution.pdb")


# Check that the optimization achieves distances close to the solution
print("*** End optimization ***")
new_centers = []
for rbd in rigid_bodies:
    print("chain has", rbd.get_number_of_members(), \
        "atoms", "coordinates: ", rbd.get_coordinates())
    new_centers.append(rbd.get_coordinates())

d01 = IMP.algebra.get_distance(new_centers[0], new_centers[1])
d12 = IMP.algebra.get_distance(new_centers[1], new_centers[2])
d23 = IMP.algebra.get_distance(new_centers[2], new_centers[3])
d30 = IMP.algebra.get_distance(new_centers[3], new_centers[0])
print("Distances at the end of the optimization: d01 =", \
    d01, "d12 =", d12, "d23 =", d23, "d30 =", d30)