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))