em/fit_restraint.py

A simple example showing how to set up a fit restraint. The number of spheres and resolution are randomly chosen and so should not be considered significant.

## \example em/fit_restraint.py
# A simple example showing how to set up a fit restraint. The number of
# spheres and resolution are randomly chosen and so should not be
# considered significant.

from __future__ import print_function
import IMP.em
import IMP.core
import IMP.atom
IMP.base.set_log_level(IMP.base.SILENT)
m = IMP.kernel.Model()
# 1. setup the input protein
# 1.1 select a selector.
sel = IMP.atom.NonWaterPDBSelector()
# 1.2 read the protein
mh = IMP.atom.read_pdb(IMP.em.get_example_path("input.pdb"), m, sel)
ps = IMP.core.get_leaves(mh)
IMP.atom.add_radii(mh)
# 2. read the density map
resolution = 8.
voxel_size = 1.5
dmap = IMP.em.read_map(
    IMP.em.get_example_path("input.mrc"), IMP.em.MRCReaderWriter())
dmap.get_header_writable().set_resolution(resolution)
# 3. calculate the cross correlation between the density and the map
print("The cross-correlation score is:", 1. - IMP.em.compute_fitting_score(ps, dmap))
# 4. add a fitting restraint
r = IMP.em.FitRestraint(ps, dmap)
m.add_restraint(r)
print("The fit of the particles in the density is:", r.evaluate(False))