profile_fit.py

## \example saxs/profile_fit.py
# In this example, we read a protein from a PDB file and experimental profile
# file. Next we compute the theoretical profile from the PDB file and fit it
# to the experimental one. Unlike in profile.py example, here we fit the
# profile with adjustment of the excluded volume and hydration layer density
# of the molecule.
#
# This application is available as a web service at salilab.org/foxs. It is
# also available as C++ code in IMP at modules/foxs/bin/foxs.cpp.
#
# The experimental data for lysozyme is taken from crysol program
# (www.embl-hamburg.de/ExternalInfo/Research/Sax/crysol.html)
#

from __future__ import print_function
import IMP
import IMP.atom
import IMP.core
import IMP.saxs
import sys

IMP.setup_from_argv(sys.argv, "profile fit")

m = IMP.Model()

# read PDB
mp = IMP.atom.read_pdb(IMP.saxs.get_example_path('6lyz.pdb'), m,
                       IMP.atom.NonWaterNonHydrogenPDBSelector(), True, True)

# read experimental profile
exp_profile = IMP.saxs.Profile(IMP.saxs.get_example_path('lyzexp.dat'))

print('min_q = ' + str(exp_profile.get_min_q()))
print('max_q = ' + str(exp_profile.get_max_q()))
print('delta_q = ' + str(exp_profile.get_delta_q()))

# select particles from the model
particles = IMP.atom.get_by_type(mp, IMP.atom.ATOM_TYPE)

# add radius for water layer computation
ft = IMP.saxs.get_default_form_factor_table()
for i in range(0, len(particles)):
    radius = ft.get_radius(particles[i])
    IMP.core.XYZR.setup_particle(particles[i], radius)
# compute surface accessibility
s = IMP.saxs.SolventAccessibleSurface()
surface_area = s.get_solvent_accessibility(IMP.core.XYZRs(particles))

# calculate SAXS profile
delta_q = 0.5 / 500
model_profile = IMP.saxs.Profile(0.0, 0.5, delta_q)
model_profile.calculate_profile_partial(particles, surface_area)
# model_profile.write_SAXS_file('6lyz.dat')

# calculate chi-square score (should be ~0.25 for this example)
saxs_score = IMP.saxs.ProfileFitterChi(exp_profile)
chi = saxs_score.compute_score(model_profile)
print('Chi without parameter fitting = ' + str(chi))

chi = (saxs_score.fit_profile(model_profile)).get_chi_square()
print('Chi after adjustment of excluded volume and water layer parameters = '
      + str(chi))
saxs_score.fit_profile(model_profile, 0.95, 1.05, -2.0, 4.0, False,
                       '6lyz_fitted.dat')