def test_transform_update(self):
""" Test update of rotation and translation using selection """
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_answer_0)
ncs_obj = ncs.input(hierarchy=pdb_inp.construct_hierarchy())
pdb_inp = iotbx.pdb.input(lines=pdb_answer_0, source_info=None)
nrgl = ncs_obj.get_ncs_restraints_group_list()
asu_site_cart = pdb_inp.atoms().extract_xyz()
# reference matrices
r1 = nrgl[0].copies[0].r
t1 = nrgl[0].copies[0].t
r2 = nrgl[0].copies[1].r
t2 = nrgl[0].copies[1].t
# modify matrices in the ncs group list
nrgl[0].copies[0].r = r1 + r2
nrgl[0].copies[0].t = t1 + t2
nrgl[0].copies[1].r = r1 + r2
nrgl[0].copies[1].t = t1 + t2
nu.recalculate_ncs_transforms(nrgl, asu_site_cart)
# Get the updated values
r1_n = nrgl[0].copies[0].r
t1_n = nrgl[0].copies[0].t
r2_n = nrgl[0].copies[1].r
t2_n = nrgl[0].copies[1].t
#
self.assertTrue(is_same_transform(r1, t1, r1_n, t1_n))
self.assertTrue(is_same_transform(r2, t2, r2_n, t2_n))
def test_transform_update(self): """ Test update of rotation and translation using selection """ pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_answer_0) ncs_obj = ncs.input(hierarchy=pdb_inp.construct_hierarchy()) pdb_inp = iotbx.pdb.input(lines=pdb_answer_0,source_info=None) nrgl = ncs_obj.get_ncs_restraints_group_list() asu_site_cart = pdb_inp.atoms().extract_xyz() # reference matrices r1 = nrgl[0].copies[0].r t1 = nrgl[0].copies[0].t r2 = nrgl[0].copies[1].r t2 = nrgl[0].copies[1].t # modify matrices in the ncs group list nrgl[0].copies[0].r = r1 + r2 nrgl[0].copies[0].t = t1 + t2 nrgl[0].copies[1].r = r1 + r2 nrgl[0].copies[1].t = t1 + t2 nu.recalculate_ncs_transforms(nrgl,asu_site_cart) # Get the updated values r1_n = nrgl[0].copies[0].r t1_n = nrgl[0].copies[0].t r2_n = nrgl[0].copies[1].r t2_n = nrgl[0].copies[1].t # self.assertTrue(is_same_transform(r1,t1,r1_n,t1_n)) self.assertTrue(is_same_transform(r2,t2,r2_n,t2_n))
def test_proper_biomat_application(self):
""" Test that when building bio-molecule and then finding NCS relatin
from it, we get the same rotation and translation"""
pdb_strings = [pdb_test_data7,pdb_test_data8]
methods = ['ba','cau']
for method,pdb_string in zip(methods,pdb_strings):
print "method:", method
pdb_inp = pdb.input(source_info=None, lines=pdb_string)
crystal_symmetry = pdb_inp.crystal_symmetry()
m = multimer(
pdb_str=pdb_string,
round_coordinates=False,
reconstruction_type=method,
error_handle=True,eps=1e-2)
# The exact transforms from pdb_string
r1_expected = matrix.sqr(
[0.309017, -0.951057, 0.0,0.951057, 0.309017,-0.0,0.0,0.0,1.0])
r2_expected = matrix.sqr(
[-0.809017,-0.587785,0.0,0.587785,-0.809017,-0.0,0.0,0.0,1.0])
t1_expected = matrix.col([0,0,7])
t2_expected = matrix.col([0,0,0])
# Look at biomt records retrieved from PDB file
if method == 'ba':
rec = pdb_inp.process_BIOMT_records()
else:
rec = pdb_inp.process_mtrix_records()
r1 = rec.r[1]
r2 = rec.r[2]
t1 = rec.t[1]
t2 = rec.t[2]
(the_same, transpose) = is_same_transform(r1,t1,r1_expected,t1_expected)
self.assertTrue(the_same)
(the_same, transpose)= is_same_transform(r2,t2,r2_expected,t2_expected)
self.assertTrue(the_same)
# Look at the rotation and translation found by the NCS search
s = m.assembled_multimer.as_pdb_string(crystal_symmetry=crystal_symmetry)
print "new h:", s
ncs_obj = ncs.input(pdb_string=s)
print "ncs_obj.number_of_ncs_groups", ncs_obj.number_of_ncs_groups
r1 = ncs_obj.ncs_transform['002'].r
t1 = ncs_obj.ncs_transform['002'].t
r2 = ncs_obj.ncs_transform['003'].r
t2 = ncs_obj.ncs_transform['003'].t
(the_same, transpose) = is_same_transform(r1,t1,r1_expected,t1_expected)
self.assertTrue(the_same)
(the_same, transpose)= is_same_transform(r2,t2,r2_expected,t2_expected)
self.assertTrue(the_same)
if method == 'ba':
self.assertEqual(ncs_obj.number_of_ncs_groups,1)
elif method == 'cau':
self.assertEqual(ncs_obj.number_of_ncs_groups,2)
def exercise_06():
""" Test that when building bio-molecule and then finding NCS relatin
from it, we get the same rotation and translation"""
pdb_strings = [pdb_str_4, pdb_str_5]
for method, pdb_string in enumerate(pdb_strings):
pdb_inp = pdb.input(source_info=None, lines=pdb_string)
crystal_symmetry = pdb_inp.crystal_symmetry()
# The exact transforms from pdb_string
r1_expected = matrix.sqr([
0.309017, -0.951057, 0.0, 0.951057, 0.309017, -0.0, 0.0, 0.0, 1.0
])
r2_expected = matrix.sqr([
-0.809017, -0.587785, 0.0, 0.587785, -0.809017, -0.0, 0.0, 0.0, 1.0
])
t1_expected = matrix.col([0, 0, 7])
t2_expected = matrix.col([0, 0, 0])
# Look at biomt records retrieved from PDB file
if method == 0:
rec = pdb_inp.process_BIOMT_records()
h = pdb_inp.construct_hierarchy_BIOMT_expanded()
else:
rec = pdb_inp.process_MTRIX_records()
h = pdb_inp.construct_hierarchy_MTRIX_expanded()
r1 = rec.r[1]
r2 = rec.r[2]
t1 = rec.t[1]
t2 = rec.t[2]
(the_same, transpose) = is_same_transform(r1, t1, r1_expected,
t1_expected)
assert the_same
(the_same, transpose) = is_same_transform(r2, t2, r2_expected,
t2_expected)
assert the_same
# Look at the rotation and translation found by the NCS search
s = h.as_pdb_string(crystal_symmetry=crystal_symmetry)
ncs_obj = ncs.input(hierarchy=pdb.input(source_info=None,
lines=s).construct_hierarchy())
r1 = ncs_obj.ncs_transform['0000000002'].r
t1 = ncs_obj.ncs_transform['0000000002'].t
r2 = ncs_obj.ncs_transform['0000000003'].r
t2 = ncs_obj.ncs_transform['0000000003'].t
(the_same, transpose) = is_same_transform(r1, t1, r1_expected,
t1_expected)
assert the_same
(the_same, transpose) = is_same_transform(r2, t2, r2_expected,
t2_expected)
assert the_same
if method == 0:
assert ncs_obj.number_of_ncs_groups == 1
elif method == 1:
assert ncs_obj.number_of_ncs_groups == 2