def test_random_projection_generation(self): """Generation of random projection from a PDB file with em2d images""" testfile = "opencv_test.spi" if os.path.isfile(testfile): # delete the file to check os.remove(testfile) smodel = IMP.Model() ssel = IMP.atom.ATOMPDBSelector() prot = IMP.atom.read_pdb( self.get_input_file_name("1z5s.pdb"), smodel, ssel) IMP.atom.add_radii(prot) particles = IMP.core.get_leaves(prot) rows = 80 cols = 80 resolution = 1 apix = 1.5 img = em2d.Image() img.set_size(rows, cols) srw = em2d.SpiderImageReaderWriter() rr = em2d.RegistrationResult() rr.set_random_registration(0, 5) options = em2d.ProjectingOptions(apix, resolution) options.srw = srw em2d.get_projection(img, particles, rr, options) img.write(testfile, srw) self.assertTrue(os.path.isfile(testfile), "Projection image not generated") os.remove(testfile)
def test_rigid_body_image_fit_restraint(self): """Test scoring with RigidBodiesImageFitRestraint""" m = IMP.kernel.Model() # read full complex fn = self.get_input_file_name("1z5s.pdb") prot = atom.read_pdb(fn, m, IMP.atom.ATOMPDBSelector()) # read components names = ["1z5sA", "1z5sB", "1z5sC", "1z5sD"] fn_pdbs = [self.get_input_file_name(name + ".pdb") for name in names] components = [ atom.read_pdb(fn, m, IMP.atom.ATOMPDBSelector()) for fn in fn_pdbs ] components_rbs = [atom.create_rigid_body(c) for c in components] # img R = alg.get_identity_rotation_3d() reg = em2d.RegistrationResult(R) img = em2d.Image() img.set_size(80, 80) srw = em2d.SpiderImageReaderWriter() resolution = 5 pixel_size = 1.5 options = em2d.ProjectingOptions(pixel_size, resolution) ls = core.get_leaves(prot) em2d.get_projection(img, ls, reg, options) # img.write("rbfit_test_image.spi",srw) # set restraint score_function = em2d.EM2DScore() rb_fit = em2d.RigidBodiesImageFitRestraint(score_function, components_rbs, img) pp = em2d.ProjectingParameters(pixel_size, resolution) rb_fit.set_projecting_parameters(pp) # set the trivial case: n_masks = 1 for rb in components_rbs: # set as the only possible orientation the one that the rigid # body already has rb_fit.set_orientations(rb, [ rb.get_reference_frame().get_transformation_to().get_rotation( ) ]) self.assertEqual(rb_fit.get_number_of_masks(rb), n_masks, "Incorrect number rigid body masks") # Calculate the positions of the rigid bodies respect to the centroid # of the entire molecule ls = core.get_leaves(prot) xyzs = core.XYZs(ls) centroid = core.get_centroid(xyzs) coords = [rb.get_coordinates() - centroid for rb in components_rbs] for rb, coord in zip(components_rbs, coords): rb.set_coordinates(coord) # Check that the value is a perfect registration m.add_restraint(rb_fit) score = rb_fit.evaluate(False) # print "score ...", score # It seems that projecting with the masks is slightly less accurate # I have to establish a tolerance of 0.03 self.assertAlmostEqual(score, 0, delta=0.03, msg="Wrong value for the score %f " % (score))