def test_component_placement_score(self):
"""Testing that component placement score returns the same transformation if called twice"""
m = IMP.Model()
# read PDB
mp1_ref = atom.read_pdb(self.open_input_file("1z5s_A.pdb"),
m, atom.NonWaterPDBSelector())
mp1_mdl = atom.read_pdb(self.open_input_file("1z5s_A.pdb"),
m, atom.NonWaterPDBSelector())
mp2_ref = atom.read_pdb(self.open_input_file("1z5s_C.pdb"),
m, atom.NonWaterPDBSelector())
mp2_mdl = atom.read_pdb(self.open_input_file("1z5s_C.pdb"),
m, atom.NonWaterPDBSelector())
xyz1_ref = core.XYZs(atom.get_leaves(mp1_ref))
xyz1_mdl = core.XYZs(atom.get_leaves(mp1_mdl))
xyz2_ref = core.XYZs(atom.get_leaves(mp2_ref))
xyz2_mdl = core.XYZs(atom.get_leaves(mp2_mdl))
# create a random transformation
t = IMP.algebra.Transformation3D(IMP.algebra.get_random_rotation_3d(),
IMP.algebra.get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d()))
for d in xyz1_mdl:
core.transform(d, t)
t = IMP.algebra.Transformation3D(IMP.algebra.get_random_rotation_3d(),
IMP.algebra.get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d()))
# core.get_transformed(xyz2_mdl,t)
for d in xyz2_mdl:
core.transform(d, t)
da1 = atom.get_component_placement_score(
xyz1_ref, xyz2_ref, xyz1_mdl, xyz2_mdl)
da2 = atom.get_component_placement_score(
xyz1_ref, xyz2_ref, xyz1_mdl, xyz2_mdl)
self.assertAlmostEqual(da1[1], da2[1])
def test_placement_score(self):
"""Test placement score"""
m = IMP.kernel.Model()
# read PDB
mp = atom.read_pdb(self.open_input_file("mini.pdb"),
m, atom.NonWaterPDBSelector())
mp1 = atom.read_pdb(self.open_input_file("mini.pdb"),
m, atom.NonWaterPDBSelector())
xyz = core.XYZs(atom.get_leaves(mp))
xyz1 = core.XYZs(atom.get_leaves(mp1))
# create a random transformation
t = IMP.algebra.Transformation3D(IMP.algebra.get_random_rotation_3d(),
IMP.algebra.get_random_vector_in(IMP.algebra.get_unit_bounding_box_3d()))
for d in xyz1:
core.transform(d, t)
da = atom.get_placement_score(xyz1, xyz)
d = t.get_translation().get_magnitude()
a = IMP.algebra.get_axis_and_angle(t.get_rotation()).second
self.assertAlmostEqual(da[0], d, 2)
self.assertAlmostEqual(da[1], a, 2)