def test_rigid_body_image_fit_restraint(self):
"""Test scoring with RigidBodiesImageFitRestraint"""
m = IMP.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
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))
def read_from_database(self, fn_database, fields=["reference_frames"],
max_number=False, orderby=False ):
"""
Read orientations and positions from a database file.
self.anchored and self.fixed overwrite
the positions and orientations read from the database
"""
db = solutions_io.ResultsDB()
db.connect(fn_database)
data = db.get_solutions(fields, max_number, orderby)
db.close()
self.transformations = [ [] for T in range(self.nc)]
# Each record contains a reference frame for each of the
# components. But here the states considered make sense as columns.
# Each rigidbody is considered to have all the states in a column.
for d in data:
texts = d[0].split("/")
for i, t in zip(range(self.nc), texts):
T = io.TextToTransformation3D(t).get_transformation()
self.transformations[i].append(T)
# Set the anchored components
for i in range(self.nc):
if self.anchored[i]:
origin = alg.Transformation3D(alg.get_identity_rotation_3d(),
alg.Vector3D(0.0, 0.0, 0.))
self.transformations[i] = [origin]
# If fixed, only the first state is kept
for i in range(self.nc):
if self.fixed[i]:
if len(self.transformations[i]) == 0:
raise ValueError("There are positions to keep fixed")
self.transformations[i] = [self.transformations[i][0]]
def __init__(self, model, rigid_bodies, anchored):
log.info("Setting MonteCarloRelativeMoves")
self.model = model
self.rbs = rigid_bodies
self.components = []
self.best_models = []
self.anchored = anchored
self.parent_rbs = []
# triplets with the information to build a relative mover using the
# results from docking with HEX
self.dock_transforms = None
self.non_relative_move_prob = 0.1
log.debug("Anchored components %s", self.anchored)
T = alg.Transformation3D(alg.get_identity_rotation_3d(),
alg.Vector3D(0., 0., 0.))
origin = alg.ReferenceFrame3D(T)
for rb in self.rbs:
rb.set_reference_frame(origin)
def __init__(self, model, rigid_bodies, anchored):
log.info("Setting MonteCarloRelativeMoves")
self.model = model
self.rbs = rigid_bodies
self.components = []
self.best_models = []
self.anchored = anchored
self.parent_rbs = []
# triplets with the information to build a relative mover using the
# results from docking with HEX
self.dock_transforms = None
self.non_relative_move_prob = 0.1
log.debug("Anchored components %s", self.anchored)
T = alg.Transformation3D(alg.get_identity_rotation_3d(),
alg.Vector3D(0., 0., 0.))
origin = alg.ReferenceFrame3D(T)
for rb in self.rbs:
rb.set_reference_frame(origin)
def get_orientations_nearby(rotation, n, f):
"""
Rotations nearby a given one. They are got intepolating with
the rotations of the uniform coverage. The parameter f
(0 <= f <= 1) must be close to 0 to get orientations
that are close to the given orientation
- Values from 0.1 (tight cluster) to 0.4 (loose)
seem to be ok
n - number of rotations requested
"""
log.debug("Computing nearby rotations around %s", rotation)
unif = alg.get_uniform_cover_rotations_3d(n)
id_rot = alg.get_identity_rotation_3d()
oris = []
for rot in unif:
r = alg.get_interpolated(rot, id_rot, f)
r = alg.compose(r, rotation )
oris.append(r)
return oris
def get_orientations_nearby(rotation, n, f):
"""
Rotations nearby a given one. They are got intepolating with
the rotations of the uniform coverage. The parameter f
(0 <= f <= 1) must be close to 0 to get orientations
that are close to the given orientation
- Values from 0.1 (tight cluster) to 0.4 (loose)
seem to be ok
n - number of rotations requested
"""
log.debug("Computing nearby rotations around %s", rotation)
unif = alg.get_uniform_cover_rotations_3d(n)
id_rot = alg.get_identity_rotation_3d()
oris = []
for rot in unif:
r = alg.get_interpolated(rot, id_rot, f)
r = alg.compose(r, rotation)
oris.append(r)
return oris
def read_from_database(self,
fn_database,
fields=["reference_frames"],
max_number=False,
orderby=False):
"""
Read orientations and positions from a database file.
self.anchored and self.fixed overwrite
the positions and orientations read from the database
"""
if not os.path.exists(fn_database):
raise IOError(
"read_from_database: Database file not found. "
"Are you perhaps trying to run the DOMINO optimization without "
"having the database yet?")
db = solutions_io.ResultsDB()
db.connect(fn_database)
data = db.get_solutions(fields, max_number, orderby)
db.close()
self.transformations = [[] for T in range(self.n_components)]
# Each record contains a reference frame for each of the
# components. But here the states considered make sense as columns.
# Each rigidbody is considered to have all the states in a column.
for d in data:
texts = d[0].split("/")
for i, t in zip(range(self.n_components), texts):
T = io.TextToTransformation3D(t).get_transformation()
self.transformations[i].append(T)
# Set the anchored components
for i in range(self.n_components):
if self.anchored[i]:
origin = alg.Transformation3D(alg.get_identity_rotation_3d(),
alg.Vector3D(0.0, 0.0, 0.))
self.transformations[i] = [origin]
# If fixed, only the first state is kept
for i in range(self.n_components):
if self.fixed[i]:
if len(self.transformations[i]) == 0:
raise ValueError("There are positions to keep fixed")
self.transformations[i] = [self.transformations[i][0]]
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))