def _test_fast_local_refinement(self):
"""test that local rigid fitting work well with rigid bodies"""
self.ps_all = [] # all the molecules together as one particle
for n in range(3):
self.ps_all += self.pss[n]
d_map = IMP.em.particles2density(self.ps_all, 8, 1.5)
d_map.calcRMS()
fnames = ["1atiB01.pdb", "1arsA01.pdb", "1ab4A02.pdb"]
self.radius_key = IMP.core.XYZR.get_radius_key()
self.weight_key = IMP.atom.Mass.get_mass_key()
self.mhs = [] # 3 molecular hierarchies
self.pss = [] # 3 particles
# 3 copies of the molecular hierarchies used later as rigid bodies
self.mhs_copy = []
sel = IMP.atom.NonWaterPDBSelector()
mh = IMP.atom.read_pdb(self.open_input_file("1atiB01.pdb"),
self.imp_model, sel)
IMP.atom.add_radii(mh)
rb = IMP.atom.setup_as_rigid_body(mh)
ps = IMP.Particles(IMP.core.get_leaves(IMP.atom.Hierarchy(mh)))
score_before = IMP.em.compute_fitting_score(ps, d_map)
rand_t = IMP.algebra.Transformation3D(
IMP.algebra.get_random_rotation_3d(),
IMP.algebra.get_random_vector_in(
IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(-5., -5., -5.),
IMP.algebra.Vector3D(5., 5., 5.))))
IMP.core.transform(self.rbs_of_copy[0], rand_t)
fs = IMP.em.local_rigid_fitting(rb, self.radius_key, self.weight_key,
d_map, None, 3, 5, 20, 2, 3, True)
score_after = IMP.em.compute_fitting_score(ps, d_map)
print("score_after:", score_after, " score_before:", score_before)
self.assertAlmostEqual(score_after, score_before, delta=0.05)
self.assertGreater(fs.get_number_of_solutions(), 0)
print(fs.get_score(0))
