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])