def test__rigid_bodies_drms(self):
""" Test drms measure taking into account rigid bodies"""
m = IMP.Model()
sel = atom.CAlphaPDBSelector()
prot1 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
prot2 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
hchains1 = atom.get_by_type(prot1, atom.CHAIN_TYPE)
hchains2 = atom.get_by_type(prot2, atom.CHAIN_TYPE)
xyzs1 = core.XYZs(atom.get_leaves(prot1))
xyzs2 = core.XYZs(atom.get_leaves(prot2))
x = 0
ranges = []
for h in hchains1:
ls1 = (atom.get_leaves(h))
y = x + len(ls1)
ranges.append((x, y))
x = y
drms = atom.get_drms(xyzs1, xyzs2)
rb_drms = atom.get_rigid_bodies_drms(xyzs1, xyzs2, ranges)
self.assertAlmostEqual(rb_drms, 0)
self.assertAlmostEqual(drms, rb_drms, delta=1e-3, msg="rb_drms != drms")
# Same thing after transformation of each of the chains
for h in hchains2:
R = alg.get_random_rotation_3d()
v = alg.get_random_vector_in(alg.get_unit_bounding_box_3d())
T = alg.Transformation3D(R, v)
ls = atom.get_leaves(h)
for l in ls:
core.transform(l.get_as_xyz(), T)
drms = atom.get_drms(xyzs1, xyzs2)
rb_drms = atom.get_rigid_bodies_drms(xyzs1, xyzs2, ranges)
self.assertAlmostEqual(drms, rb_drms, delta=0.3, msg="rb_drms != drms")
def test_sampling_schema(self):
"""
Test
"""
subunits = ["subunitA", "subunitB", "subunitC", "subunitD"]
anchored = [False, False, False, False]
fixed = [False, False, False, False]
n_transformations = 50
db = database.Database2()
fn = 'temp.db'
db.create(fn, overwrite=True)
db.connect(fn)
transformations = []
table_name = "results"
db.create_table(table_name, ["reference_frames"], [str])
for i in range(n_transformations):
Ts = []
for j in range(len(subunits)):
center = alg.Vector3D(0, 0, 0)
T = alg.Transformation3D(
alg.get_random_rotation_3d(),
alg.get_random_vector_in(alg.Sphere3D(center, 34)))
Ts.append(T)
transformations.append(Ts)
data = []
for Ts in transformations:
text = [io.Transformation3DToText(T).get_text() for T in Ts]
text = "/".join(text)
data.append([
text,
])
db.store_data(table_name, data)
db.close()
sch = sampling.SamplingSchema(4, fixed, anchored)
sch.read_from_database(fn)
for i in range(len(transformations)):
for j in range(len(subunits)):
T = transformations[i][j]
t = T.get_translation()
q = T.get_rotation().get_quaternion()
pos = sch.transformations[j][i].get_translation()
ori = sch.transformations[j][i].get_rotation().get_quaternion()
for k in range(3):
self.assertAlmostEqual(pos[k], t[k])
for k in range(4):
self.assertAlmostEqual(q[k], ori[k])
os.remove(fn)
def apply_random_transform(rb, max_trans=100):
"""
Apply a random transformation to the rigid body and change the reference
frame
"""
bb = alg.BoundingBox3D(alg.Vector3D(-max_trans, -max_trans, -max_trans),
alg.Vector3D(max_trans, max_trans, max_trans))
Trand = alg.Transformation3D(alg.get_random_rotation_3d(),
alg.get_random_vector_in(bb))
ref = rb.get_reference_frame()
Tr = ref.get_transformation_to()
T = alg.compose(Trand, Tr)
rb.set_reference_frame(alg.ReferenceFrame3D(T))
def test_sampling_schema(self):
"""
Test
"""
subunits = [ "subunitA", "subunitB", "subunitC", "subunitD"]
anchored = [False, False, False, False]
fixed = [False, False, False, False]
n_transformations = 50
db = Database.Database2()
fn = 'temp.db'
db.create(fn, overwrite=True)
db.connect(fn)
transformations = []
table_name = "results"
db.create_table(table_name, ["reference_frames"], [str])
for i in range(n_transformations):
Ts = []
for j in range(len(subunits)):
center = alg.Vector3D(0, 0, 0)
T = alg.Transformation3D(alg.get_random_rotation_3d(),
alg.get_random_vector_in(alg.Sphere3D(center,34)))
Ts.append(T)
transformations.append(Ts)
data = []
for Ts in transformations:
text = [io.Transformation3DToText(T).get_text() for T in Ts]
text = "/".join(text)
data.append([text,])
db.store_data(table_name,data)
db.close()
sch = sampling.SamplingSchema(4, fixed, anchored)
sch.read_from_database(fn)
for i in range(len(transformations)):
for j in range(len(subunits)):
T = transformations[i][j]
t = T.get_translation()
q = T.get_rotation().get_quaternion()
pos = sch.transformations[j][i].get_translation()
ori = sch.transformations[j][i].get_rotation().get_quaternion()
for k in range(3):
self.assertAlmostEqual(pos[k], t[k])
for k in range(4):
self.assertAlmostEqual(q[k], ori[k])
os.remove(fn)
def test__rigid_bodies_drms(self):
""" Test drms measure taking into account rigid bodies"""
m = IMP.kernel.Model()
sel = atom.CAlphaPDBSelector()
prot1 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
prot2 = atom.read_pdb(self.open_input_file("mini.pdb"), m, sel)
hchains1 = atom.get_by_type(prot1, atom.CHAIN_TYPE)
hchains2 = atom.get_by_type(prot2, atom.CHAIN_TYPE)
xyzs1 = core.XYZs(atom.get_leaves(prot1))
xyzs2 = core.XYZs(atom.get_leaves(prot2))
x = 0
ranges = []
for h in hchains1:
ls1 = (atom.get_leaves(h))
y = x + len(ls1)
ranges.append((x, y))
x = y
drms = atom.get_drms(xyzs1, xyzs2)
rb_drms = atom.get_rigid_bodies_drms(xyzs1, xyzs2, ranges)
self.assertAlmostEqual(rb_drms, 0)
self.assertAlmostEqual(
drms,
rb_drms,
delta=1e-3,
msg="rb_drms != drms")
# Same thing after transformation of each of the chains
for h in hchains2:
R = alg.get_random_rotation_3d()
v = alg.get_random_vector_in(alg.get_unit_bounding_box_3d())
T = alg.Transformation3D(R, v)
ls = atom.get_leaves(h)
for l in ls:
core.transform(l.get_as_xyz(), T)
drms = atom.get_drms(xyzs1, xyzs2)
rb_drms = atom.get_rigid_bodies_drms(xyzs1, xyzs2, ranges)
self.assertAlmostEqual(drms, rb_drms, delta=0.3, msg="rb_drms != drms")
native_chain_centers = []
rigid_bodies= []
for c in chains:
atoms=core.get_leaves(c)
rbd=core.RigidBody.setup_particle(c,atoms)
rigid_bodies.append(rbd)
print "chain has",rbd.get_number_of_members(), \
"atoms","coordinates: ",rbd.get_coordinates()
native_chain_centers.append(rbd.get_coordinates())
bb=alg.BoundingBox3D(alg.Vector3D(-25, -40,-60),
alg.Vector3D( 25, 40, 60))
# rotate and translate the chains
for rbd in rigid_bodies:
# rotation
rotation= alg.get_random_rotation_3d()
transformation1=alg.get_rotation_about_point(rbd.get_coordinates(),rotation)
# translation
transformation2=alg.Transformation3D(alg.get_random_vector_in(bb))
# Apply
final_transformation = alg.compose(transformation1,transformation2)
core.transform(rbd,final_transformation)
print "Writing transformed assembly"
atom.write_pdb (prot,"1z5s-transformed.pdb")
# set distance restraints measusring some distances between rigid bodies
# for the solution.
d01 = alg.get_distance(native_chain_centers[0],native_chain_centers[1])
r01 = core.DistanceRestraint(core.Harmonic(d01,1),chains[0],chains[1])
r01.set_name("distance 0-1")
d12 = alg.get_distance(native_chain_centers[1],native_chain_centers[2])