def test_update_x(self):
""" Verify that transforms are getting updated """
# print sys._getframe().f_code.co_name
x1 = nu.concatenate_rot_tran(self.tr_obj1)
x2 = nu.shake_transformations(x=x1,
shake_angles_sigma=0.035,
shake_translation_sigma=0.5)
# update with shaken parameters
self.tr_obj1 = nu.update_rot_tran(x=x2, transforms_obj=self.tr_obj1)
self.ncs_restraints_group_list = nu.update_rot_tran(
x=x2, ncs_restraints_group_list=self.ncs_restraints_group_list)
x3 = nu.concatenate_rot_tran(
ncs_restraints_group_list=self.ncs_restraints_group_list)
x4 = nu.concatenate_rot_tran(transforms_obj=self.tr_obj1)
assert abs(sum(list(x3 - x4))) < 1.0e-3
the, psi, phi = x2[6:9]
rot = scitbx.rigid_body.rb_mat_xyz(the=the,
psi=psi,
phi=phi,
deg=False)
a3 = rot.rot_mat()
the, psi, phi = x4[6:9]
rot = scitbx.rigid_body.rb_mat_xyz(the=the,
psi=psi,
phi=phi,
deg=False)
a4 = rot.rot_mat()
assert abs(sum(list(a3 - a4))) < 1.0e-3
# test that update_rot_tran dose not unintentionally change x
round_val = 3
r_elems = []
for rec in self.ncs_restraints_group_list:
for c in rec.copies:
r = c.r.round(round_val)
r_elems.append(r.elems)
def test_update_x(self):
""" Verify that transforms are getting updated """
# print sys._getframe().f_code.co_name
x1 = nu.concatenate_rot_tran(self.tr_obj1)
x2 = nu.shake_transformations(
x = x1,
shake_angles_sigma=0.035,
shake_translation_sigma=0.5)
# update with shaken parameters
self.tr_obj1 = nu.update_rot_tran(
x=x2, transforms_obj=self.tr_obj1)
self.ncs_restraints_group_list = nu.update_rot_tran(
x=x2, ncs_restraints_group_list=self.ncs_restraints_group_list)
x3 = nu.concatenate_rot_tran(
ncs_restraints_group_list=self.ncs_restraints_group_list)
x4 = nu.concatenate_rot_tran(
transforms_obj=self.tr_obj1)
assert abs(sum(list(x3-x4))) < 1.0e-3
the,psi,phi =x2[6:9]
rot = scitbx.rigid_body.rb_mat_xyz(
the=the, psi=psi, phi=phi, deg=False)
a3 = rot.rot_mat()
the,psi,phi =x4[6:9]
rot = scitbx.rigid_body.rb_mat_xyz(
the=the, psi=psi, phi=phi, deg=False)
a4 = rot.rot_mat()
assert abs(sum(list(a3-a4))) < 1.0e-3
# test that update_rot_tran dose not unintentionally change x
round_val = 3
r_elems = []
for rec in self.ncs_restraints_group_list:
for c in rec.copies:
r = c.r.round(round_val)
r_elems.append(r.elems)
def run(prefix="tst", d_min=1.0):
"""
NCS constraints: xyz, adp, and operators.
"""
pdb_file_name_answer = "%s_answer.pdb" % prefix
of = open(pdb_file_name_answer, "w")
print >> of, pdb_str_answer
of.close()
#
pdb_file_name_poor = "%s_poor.pdb" % prefix
of = open(pdb_file_name_poor, "w")
print >> of, pdb_str_poor
of.close()
#
pdb_inp_answer = iotbx.pdb.input(file_name=pdb_file_name_answer)
ph_answer = pdb_inp_answer.construct_hierarchy()
ph_answer.atoms().reset_i_seq()
xrs_answer = pdb_inp_answer.xray_structure_simple()
#
pdb_inp_poor = iotbx.pdb.input(file_name=pdb_file_name_poor)
ph_poor = pdb_inp_poor.construct_hierarchy()
ph_poor_obj = iotbx.pdb.input(source_info=None, lines=pdb_str_poor2)
ph_poor.atoms().reset_i_seq()
xrs_poor = pdb_inp_poor.xray_structure_simple()
#
ppf = mmtbx.utils.process_pdb_file_srv(log=False).process_pdb_files(
raw_records=pdb_str_poor.splitlines())[0]
mmtbx.utils.assert_xray_structures_equal(
x1=ppf.xray_structure(show_summary=False), x2=xrs_poor)
restraints_manager = mmtbx.restraints.manager(
geometry=ppf.geometry_restraints_manager(show_energies=False),
normalization=True)
#
fc = xrs_answer.structure_factors(d_min=d_min).f_calc()
fft_map = fc.fft_map(resolution_factor=0.25)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
#
ncs_obj_poor = mmtbx.ncs.asu_ncs_converter(pdb_hierarchy=ph_answer,
add_identity=True)
ncs_obj_poor.write_pdb_file(file_name="asu.pdb",
crystal_symmetry=xrs_poor.crystal_symmetry(),
mode="asu")
# create transformation object
transforms_obj = ncs.input(hierarchy=ph_answer)
x = transforms_obj.get_ncs_restraints_group_list().concatenate_rot_tran()
x = nu.shake_transformations(x=x,
shake_angles_sigma=1 * math.pi / 180,
shake_translation_sigma=0.1)
nrgl = transforms_obj.get_ncs_restraints_group_list()
nrgl.update_rot_tran(x=x)
rm, tv = nrgl.get_rotation_translation_as_list()
# just to see how result of shaking looks like
rm_ = [rm[0]] + rm
tv_ = [tv[0]] + tv
ncs_obj_poor.back_rotation_matrices = rm_
ncs_obj_poor.back_translation_vectors = tv_
ncs_obj_poor.update_sites_cart(sites_cart_master_ncs_copy=ncs_obj_poor.
ph_first_chain.atoms().extract_xyz())
ncs_obj_poor.write_pdb_file(file_name="asu2.pdb",
crystal_symmetry=xrs_poor.crystal_symmetry(),
mode="asu")
ncs_restraints_group_list = transforms_obj.get_ncs_restraints_group_list()
refine_selection = flex.size_t(
xrange(transforms_obj.truncated_hierarchy.atoms_size()))
for i in xrange(5):
data_weight = 1
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_real_space(
map_data = map_data,
xray_structure = xrs_poor,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = refine_selection,
real_space_gradients_delta = d_min/4,
restraints_manager = restraints_manager,
data_weight = data_weight,
refine_sites = True)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object=tfg_obj,
xray_structure=xrs_poor,
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=refine_selection,
finite_grad_differences_test=False,
max_iterations=60,
refine_sites=True)
xrs_poor = tfg_obj.xray_structure
ph_poor.adopt_xray_structure(tfg_obj.xray_structure)
#
ncs_obj_poor = mmtbx.ncs.asu_ncs_converter(pdb_hierarchy=ph_poor,
add_identity=False)
rm, tv = ncs_restraints_group_list.get_rotation_translation_as_list()
#
ph_poor.write_pdb_file(file_name="refined.pdb")
def run(prefix="tst", d_min=1.0):
"""
NCS constraints: xyz, adp, and operators.
"""
pdb_file_name_answer = "%s_answer.pdb" % prefix
of = open(pdb_file_name_answer, "w")
print(pdb_str_answer, file=of)
of.close()
#
pdb_file_name_poor = "%s_poor.pdb" % prefix
of = open(pdb_file_name_poor, "w")
print(pdb_str_poor, file=of)
of.close()
#
pdb_inp_answer = iotbx.pdb.input(file_name=pdb_file_name_answer)
ph_answer = pdb_inp_answer.construct_hierarchy()
ph_answer.atoms().reset_i_seq()
xrs_answer = pdb_inp_answer.xray_structure_simple()
#
pdb_inp_poor = iotbx.pdb.input(file_name=pdb_file_name_poor)
ph_poor = pdb_inp_poor.construct_hierarchy()
ph_poor_obj = iotbx.pdb.input(source_info=None, lines=pdb_str_poor2)
ph_poor.atoms().reset_i_seq()
xrs_poor = pdb_inp_poor.xray_structure_simple()
#
ppf = mmtbx.utils.process_pdb_file_srv(log=False).process_pdb_files(
raw_records=pdb_str_poor.splitlines())[0]
mmtbx.utils.assert_xray_structures_equal(
x1=ppf.xray_structure(show_summary=False), x2=xrs_poor)
restraints_manager = mmtbx.restraints.manager(
geometry=ppf.geometry_restraints_manager(show_energies=False),
normalization=True)
#
fc = xrs_answer.structure_factors(d_min=d_min).f_calc()
fft_map = fc.fft_map(resolution_factor=0.25)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
#
transforms_obj = ncs.input(hierarchy=ph_answer)
x = transforms_obj.get_ncs_restraints_group_list().concatenate_rot_tran()
x = nu.shake_transformations(x=x,
shake_angles_sigma=1 * math.pi / 180,
shake_translation_sigma=0.1)
nrgl = transforms_obj.get_ncs_restraints_group_list()
nrgl.update_rot_tran(x=x)
ncs_restraints_group_list = transforms_obj.get_ncs_restraints_group_list()
refine_selection = flex.size_t(
range(transforms_obj.truncated_hierarchy.atoms_size()))
for i in range(5):
data_weight = 1
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_real_space(
map_data = map_data,
xray_structure = xrs_poor,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = refine_selection,
real_space_gradients_delta = d_min/4,
restraints_manager = restraints_manager,
data_weight = data_weight,
refine_sites = True)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object=tfg_obj,
xray_structure=xrs_poor,
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=refine_selection,
finite_grad_differences_test=False,
max_iterations=60,
refine_sites=True)
xrs_poor = tfg_obj.xray_structure
ph_poor.adopt_xray_structure(tfg_obj.xray_structure)
ph_poor.write_pdb_file(file_name="refined.pdb")
def __init__(self,
n_macro_cycle,
sites,
u_iso,
transformations,
finite_grad_differences_test,
use_geometry_restraints,
shake_site_mean_distance = 1.5,
d_min = 2,
shake_angles_sigma = 0.035,
shake_translation_sigma = 0.5):
""" create temp test files and data for tests """
adopt_init_args(self, locals())
self.test_files_names = [] # collect names of files for cleanup
# 1 NCS copy: starting template to generate whole asu; place into P1 box
pdb_inp = iotbx.pdb.input(source_info=None, lines=ncs_1_copy)
pdb_obj = iotbx.pdb.hierarchy.input(pdb_string=ncs_1_copy)
mtrix_object = pdb_inp.process_mtrix_records()
ph = pdb_inp.construct_hierarchy()
xrs = pdb_inp.xray_structure_simple()
xrs_one_ncs = xrs.orthorhombic_unit_cell_around_centered_scatterers(
buffer_size=8)
ph.adopt_xray_structure(xrs_one_ncs)
of = open("one_ncs_in_asu.pdb", "w")
print >> of, mtrix_object.as_pdb_string()
print >> of, ph.as_pdb_string(crystal_symmetry=xrs_one_ncs.crystal_symmetry())
of.close()
# 1 NCS copy -> full asu (expand NCS). This is the answer-structure
m = multimer(file_name="one_ncs_in_asu.pdb",
round_coordinates=False,
reconstruction_type='cau',error_handle=True,eps=1e-2)
assert m.number_of_transforms == 2, m.number_of_transforms
xrs_asu = m.assembled_multimer.extract_xray_structure(
crystal_symmetry = xrs_one_ncs.crystal_symmetry())
m.write("full_asu.pdb")
# force ASU none-rounded coordinates into xray structure
xrs_asu.set_sites_cart(m.sites_cart())
assert xrs_asu.crystal_symmetry().is_similar_symmetry(
xrs_one_ncs.crystal_symmetry())
# Generate Fobs from answer structure
f_obs = abs(xrs_asu.structure_factors(d_min=d_min, algorithm="direct").f_calc())
r_free_flags = f_obs.generate_r_free_flags()
mtz_dataset = f_obs.as_mtz_dataset(column_root_label="F-obs")
mtz_dataset.add_miller_array(
miller_array=r_free_flags,
column_root_label="R-free-flags")
mtz_object = mtz_dataset.mtz_object()
mtz_object.write(file_name = "data.mtz")
# Shake structure - subject to refinement input
xrs_shaken = xrs_one_ncs.deep_copy_scatterers()
if sites: xrs_shaken.shake_sites_in_place(
mean_distance=shake_site_mean_distance)
if self.u_iso:
u_random = flex.random_double(xrs_shaken.scatterers().size())
xrs_shaken = xrs_shaken.set_u_iso(values=u_random)
if self.transformations:
transforms_obj = ncs.input(
transform_info = mtrix_object,
pdb_hierarchy_inp = pdb_obj)
x = nu.concatenate_rot_tran(transforms_obj=transforms_obj)
x = nu.shake_transformations(
x = x,
shake_angles_sigma=self.shake_angles_sigma,
shake_translation_sigma=self.shake_translation_sigma)
transforms_obj = nu.update_rot_tran(x=x,transforms_obj=transforms_obj)
mtrix_object = transforms_obj.build_MTRIX_object()
ph.adopt_xray_structure(xrs_shaken)
of = open("one_ncs_in_asu_shaken.pdb", "w")
print >> of, mtrix_object.as_pdb_string()
print >> of, ph.as_pdb_string(crystal_symmetry=xrs.crystal_symmetry())
of.close()
self.f_obs = f_obs
self.r_free_flags = r_free_flags
self.xrs_one_ncs = xrs_one_ncs
# Get restraints manager
self.grm = None
pdb_str = m.assembled_multimer.as_pdb_string(
crystal_symmetry=xrs_one_ncs.crystal_symmetry())
self.iso_restraints = None
if(self.use_geometry_restraints):
self.grm = nu.get_restraints_manager(pdb_string=pdb_str)
if(self.u_iso):
temp = mmtbx.refinement.adp_refinement.adp_restraints_master_params
self.iso_restraints = temp.extract().iso
def run(prefix="tst", d_min=1.0):
"""
NCS constraints: xyz, adp, and operators.
"""
pdb_file_name_answer = "%s_answer.pdb"%prefix
of=open(pdb_file_name_answer, "w")
print >> of, pdb_str_answer
of.close()
#
pdb_file_name_poor = "%s_poor.pdb"%prefix
of=open(pdb_file_name_poor, "w")
print >> of, pdb_str_poor
of.close()
#
pdb_inp_answer = iotbx.pdb.input(file_name=pdb_file_name_answer)
ph_answer = pdb_inp_answer.construct_hierarchy()
ph_answer.atoms().reset_i_seq()
xrs_answer = pdb_inp_answer.xray_structure_simple()
#
pdb_inp_poor = iotbx.pdb.input(file_name=pdb_file_name_poor)
ph_poor = pdb_inp_poor.construct_hierarchy()
ph_poor_obj = iotbx.pdb.hierarchy.input(pdb_string=pdb_str_poor2)
ph_poor.atoms().reset_i_seq()
xrs_poor = pdb_inp_poor.xray_structure_simple()
#
ppf = mmtbx.utils.process_pdb_file_srv(log=False).process_pdb_files(
raw_records=pdb_str_poor.splitlines())[0]
mmtbx.utils.assert_xray_structures_equal(
x1=ppf.xray_structure(show_summary = False),
x2=xrs_poor)
restraints_manager = mmtbx.restraints.manager(
geometry = ppf.geometry_restraints_manager(show_energies = False),
normalization = True)
#
fc = xrs_answer.structure_factors(d_min=d_min).f_calc()
fft_map = fc.fft_map(resolution_factor = 0.25)
fft_map.apply_sigma_scaling()
map_data = fft_map.real_map_unpadded()
#
ncs_obj_poor = mmtbx.ncs.asu_ncs_converter(pdb_hierarchy = ph_answer,
add_identity=True)
ncs_obj_poor.write_pdb_file(file_name="asu.pdb",
crystal_symmetry=xrs_poor.crystal_symmetry(), mode="asu")
rm = ncs_obj_poor.back_rotation_matrices
tv = ncs_obj_poor.back_translation_vectors
ir = [rm[0]]
it = [tv[0]]
# create transformation object
transforms_obj = ncs.input(
pdb_hierarchy_inp = ph_poor_obj,
rotations=rm,
translations=tv)
x = nu.concatenate_rot_tran(transforms_obj=transforms_obj)
x = nu.shake_transformations(
x = x,
shake_angles_sigma=1*math.pi/180,
shake_translation_sigma=0.1)
transforms_obj = nu.update_rot_tran(x=x, transforms_obj=transforms_obj)
rm,tv = nu.get_rotation_translation_as_list(transforms_obj=transforms_obj)
# just to see how result of shaking looks like
rm_ = ir+rm
tv_ = it+tv
ncs_obj_poor.back_rotation_matrices=rm_
ncs_obj_poor.back_translation_vectors=tv_
ncs_obj_poor.update_sites_cart(
sites_cart_master_ncs_copy=ncs_obj_poor.ph_first_chain.atoms().extract_xyz())
ncs_obj_poor.write_pdb_file(file_name="asu2.pdb",
crystal_symmetry=xrs_poor.crystal_symmetry(), mode="asu")
transforms_obj = nu.update_transforms(transforms_obj,rm,tv)
ncs_restraints_group_list = transforms_obj.get_ncs_restraints_group_list()
refine_selection = flex.size_t(xrange(transforms_obj.total_asu_length))
for i in xrange(5):
data_weight = 1
for action in [[False, True], [True, False]]:
refine_sites, refine_transformations = action
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_real_space(
map_data = map_data,
xray_structure = xrs_poor,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = refine_selection,
real_space_gradients_delta = d_min/4,
restraints_manager = restraints_manager,
data_weight = data_weight,
refine_sites = refine_sites,
refine_transformations = refine_transformations)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object = tfg_obj,
xray_structure = xrs_poor,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = refine_selection,
finite_grad_differences_test = False,
max_iterations = 60,
refine_sites = refine_sites,
refine_transformations = refine_transformations)
xrs_poor = tfg_obj.xray_structure
ph_poor.adopt_xray_structure(tfg_obj.xray_structure)
#
ncs_obj_poor = mmtbx.ncs.asu_ncs_converter(pdb_hierarchy = ph_poor,
add_identity=False)
rm,tv = nu.get_rotation_translation_as_list(
ncs_restraints_group_list= ncs_restraints_group_list)
#
ph_poor.write_pdb_file(file_name="refined.pdb")
