15 from __future__
import print_function
33 print(
'min_q = ' + str(exp_profile.get_min_q()))
34 print(
'max_q = ' + str(exp_profile.get_max_q()))
35 print(
'delta_q = ' + str(exp_profile.get_delta_q()))
38 particles = IMP.atom.get_by_type(mp, IMP.atom.ATOM_TYPE)
42 for i
in range(0, len(particles)):
43 radius = ft.get_radius(particles[i])
47 surface_area = s.get_solvent_accessibility(
IMP.core.XYZRs(particles))
52 model_profile.calculate_profile_partial(particles, surface_area)
56 saxs_score = IMP.saxs.ProfileFitterChi(exp_profile)
57 chi = saxs_score.compute_score(model_profile)
58 print(
'Chi without parameter fitting = ' + str(chi))
60 chi = (saxs_score.fit_profile(model_profile)).get_chi_square()
61 print(
'Chi after adjustment of excluded volume and water layer parameters = '
63 saxs_score.fit_profile(model_profile, 0.95, 1.05, -2.0, 4.0,
False,
Select non water and non hydrogen atoms.
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
static XYZR setup_particle(Model *m, ParticleIndex pi)
FormFactorTable * get_default_form_factor_table()
void read_pdb(TextInput input, int model, Hierarchy h)
Class for storing model, its restraints, constraints, and particles.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Basic functionality that is expected to be used by a wide variety of IMP users.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for small angle X-ray scattering (SAXS) data.