def test_2(fmodel,
convention,
phi=0.0,
psi=0.0,
the=0.0,
trans=[0.0, 0.0, 0.0]):
rot_obj = scitbx.rigid_body.euler(phi=phi,
psi=psi,
the=the,
convention=convention)
size = fmodel.xray_structure.scatterers().size()
fmodel.xray_structure.apply_rigid_body_shift(rot=rot_obj.rot_mat(),
trans=trans)
fmodel.update_xray_structure(update_f_calc=True)
assert approx_equal(fmodel.r_work(), 0.0)
params = mmtbx.refinement.rigid_body.master_params.extract()
params.refine_rotation = True
params.refine_translation = True
params.target = "ls_wunit_k1"
rb = mmtbx.refinement.rigid_body.manager(
fmodel=fmodel,
selections=[flex.bool(size, True).iselection()],
params=params)
assert approx_equal(rb.translation()[0], [0.0, 0.0, 0.0])
assert approx_equal(rb.rotation()[0], [0.0, 0.0, 0.0])
assert approx_equal(fmodel.r_work(), 0.0)
def test_3(fmodel, convention, phi=1, psi=2, the=3, trans=[0, 0, 0]):
rot_obj = scitbx.rigid_body.euler(phi=phi,
psi=psi,
the=the,
convention=convention)
size = fmodel.xray_structure.scatterers().size()
fmodel.xray_structure.apply_rigid_body_shift(rot=rot_obj.rot_mat(),
trans=trans)
fmodel.update_xray_structure(update_f_calc=True)
assert fmodel.r_work() > 0.15
params = mmtbx.refinement.rigid_body.master_params.extract()
params.refine_rotation = True
params.refine_translation = False
params.high_resolution = 1.0
params.max_iterations = 50
params.lbfgs_line_search_max_function_evaluations = 50
params.target = "ls_wunit_k1"
rb = mmtbx.refinement.rigid_body.manager(
fmodel=fmodel,
selections=[flex.bool(size, True).iselection()],
params=params)
if (convention == "xyz"):
assert approx_equal(rb.rotation()[0], [-1.0, -2.0, -3.0], 0.2) # XXX
assert approx_equal(rb.translation()[0], [0.0, 0.0, 0.0])
assert approx_equal(fmodel.r_work(), 0.0)
def test_5(fmodel, convention):
size = fmodel.xray_structure.scatterers().size()
sel1 = flex.bool()
sel2 = flex.bool()
for i in xrange(size):
if (i < 500):
sel1.append(True)
sel2.append(False)
else:
sel1.append(False)
sel2.append(True)
selections = [sel1.iselection(), sel2.iselection()]
rot_obj_1 = scitbx.rigid_body.euler(phi=1,
psi=2,
the=3,
convention=convention)
rot_obj_2 = scitbx.rigid_body.euler(phi=3,
psi=2,
the=1,
convention=convention)
fmodel.xray_structure.apply_rigid_body_shift(rot=rot_obj_1.rot_mat(),
trans=[0.5, 1.0, 1.5],
selection=sel1.iselection())
fmodel.xray_structure.apply_rigid_body_shift(rot=rot_obj_2.rot_mat(),
trans=[1.5, 0.5, 1.0],
selection=sel2.iselection())
fmodel.update_xray_structure(update_f_calc=True)
assert fmodel.r_work() > 0.35
params = mmtbx.refinement.rigid_body.master_params.extract()
params.refine_rotation = True
params.refine_translation = True
params.high_resolution = 1.0
params.target = "ls_wunit_k1"
rb = mmtbx.refinement.rigid_body.manager(fmodel=fmodel,
selections=selections,
params=params)
if (convention == "xyz"):
assert approx_equal(rb.rotation()[0], [-1, -2, -3], 0.2)
assert approx_equal(rb.rotation()[1], [-3, -2, -1], 0.2)
assert approx_equal(rb.translation()[0], [-0.5, -1.0, -1.5], 1.e-4)
assert approx_equal(rb.translation()[1], [-1.5, -0.5, -1.0], 1.e-4)
assert approx_equal(fmodel.r_work(), 0.0, 0.0005)
assert approx_equal(fmodel.r_free(), 0.0, 0.0005)
def test_5(fmodel, convention):
size = fmodel.xray_structure.scatterers().size()
sel1 = flex.bool()
sel2 = flex.bool()
for i in xrange(size):
if(i<500):
sel1.append(True)
sel2.append(False)
else:
sel1.append(False)
sel2.append(True)
selections = [sel1.iselection(), sel2.iselection()]
rot_obj_1 = scitbx.rigid_body.euler(
phi = 1, psi = 2, the = 3, convention = convention)
rot_obj_2 = scitbx.rigid_body.euler(
phi = 3, psi = 2, the = 1, convention = convention)
fmodel.xray_structure.apply_rigid_body_shift(
rot = rot_obj_1.rot_mat(),
trans = [0.5,1.0,1.5],
selection = sel1.iselection())
fmodel.xray_structure.apply_rigid_body_shift(
rot = rot_obj_2.rot_mat(),
trans = [1.5,0.5,1.0],
selection = sel2.iselection())
fmodel.update_xray_structure(update_f_calc = True)
assert fmodel.r_work() > 0.35
params = mmtbx.refinement.rigid_body.master_params.extract()
params.refine_rotation = True
params.refine_translation = True
params.high_resolution = 1.0
params.target="ls_wunit_k1"
rb = mmtbx.refinement.rigid_body.manager(fmodel = fmodel,
selections = selections,
params = params)
if(convention == "xyz"):
assert approx_equal(rb.rotation()[0], [-1,-2,-3], 0.2)
assert approx_equal(rb.rotation()[1], [-3,-2,-1], 0.2)
assert approx_equal(rb.translation()[0], [-0.5,-1.0,-1.5], 1.e-4)
assert approx_equal(rb.translation()[1], [-1.5,-0.5,-1.0], 1.e-4)
assert approx_equal(fmodel.r_work(), 0.0, 0.0005)
assert approx_equal(fmodel.r_free(), 0.0, 0.0005)
def test_2(fmodel, convention, phi = 0.0, psi = 0.0, the = 0.0,
trans = [0.0,0.0,0.0]):
rot_obj = scitbx.rigid_body.euler(
phi = phi, psi = psi, the = the, convention = convention)
size = fmodel.xray_structure.scatterers().size()
fmodel.xray_structure.apply_rigid_body_shift(
rot = rot_obj.rot_mat(),
trans = trans)
fmodel.update_xray_structure(update_f_calc = True)
assert approx_equal(fmodel.r_work(), 0.0)
params = mmtbx.refinement.rigid_body.master_params.extract()
params.refine_rotation = True
params.refine_translation = True
params.target="ls_wunit_k1"
rb = mmtbx.refinement.rigid_body.manager(
fmodel = fmodel,
selections = [flex.bool(size,True).iselection()],
params = params)
assert approx_equal(rb.translation()[0], [0.0,0.0,0.0])
assert approx_equal(rb.rotation()[0], [0.0,0.0,0.0])
assert approx_equal(fmodel.r_work(), 0.0)
def test_4(fmodel, convention, phi =1, psi =2, the =3, trans =[0.5,1.0,1.5]):
rot_obj = scitbx.rigid_body.euler(
phi = phi, psi = psi, the = the, convention = convention)
size = fmodel.xray_structure.scatterers().size()
fmodel.xray_structure.apply_rigid_body_shift(
rot = rot_obj.rot_mat(),
trans = trans)
fmodel.update_xray_structure(update_f_calc = True)
assert fmodel.r_work() > 0.15
params = mmtbx.refinement.rigid_body.master_params.extract()
params.refine_rotation = True
params.refine_translation = True
params.high_resolution = 1.0
params.target="ls_wunit_k1"
rb = mmtbx.refinement.rigid_body.manager(
fmodel = fmodel,
selections = [flex.bool(size,True).iselection()],
params = params)
if(convention == "xyz"):
assert approx_equal(rb.rotation()[0], [-1.0,-2.0,-3.0], 0.2) # XXX
assert approx_equal(rb.translation()[0], [-0.5,-1.0,-1.5], 1.e-3)
assert approx_equal(fmodel.r_work(), 0.0, 1.e-3)
def finite_differences_test():
print "finite_differences_test: "
fmodel = get_fmodel_from_pdb(pdb_file_name="enk_rbr.pdb",
algorithm="direct",
d_min=2.0,
target="ls_wunit_k1")
xray.set_scatterer_grad_flags(
scatterers=fmodel.xray_structure.scatterers(), site=True)
for convention in ["zyz", "xyz"]:
rot_obj = scitbx.rigid_body.euler(phi=0,
psi=0,
the=0,
convention=convention)
size = fmodel.xray_structure.scatterers().size()
selections = [flex.bool(size, True).iselection()]
fmodel.xray_structure.apply_rigid_body_shift(rot=rot_obj.rot_mat(),
trans=[1, 2, 3])
fmodel.update_xray_structure(update_f_calc=True)
fmodel_copy = fmodel.deep_copy()
centers_of_mass = []
for s in selections:
xrs = fmodel_copy.xray_structure.select(s)
centers_of_mass.append(xrs.center_of_mass())
tg_obj = mmtbx.refinement.rigid_body.target_and_grads(
centers_of_mass=centers_of_mass,
sites_cart=fmodel_copy.xray_structure.sites_cart(),
target_functor=fmodel_copy.target_functor(),
rot_objs=[rot_obj],
selections=selections,
suppress_gradients=False)
assert approx_equal(tg_obj.target(), fmodel_copy.target_w())
g_rot, g_transl = tg_obj.gradients_wrt_r(), tg_obj.gradients_wrt_t()
fd_transl = fd_translation(fmodel_copy, e=0.0001)
assert approx_equal(list(g_transl[0]), fd_transl)
fd_rot = fd_rotation(fmodel=fmodel_copy,
e=0.0001,
convention=convention)
assert approx_equal(list(g_rot[0]), fd_rot)
def finite_differences_test():
print "finite_differences_test: "
fmodel = get_fmodel_from_pdb(pdb_file_name = "enk_rbr.pdb",
algorithm = "direct",
d_min = 2.0,
target = "ls_wunit_k1")
xray.set_scatterer_grad_flags(
scatterers = fmodel.xray_structure.scatterers(),
site = True)
for convention in ["zyz","xyz"]:
rot_obj = scitbx.rigid_body.euler(
phi = 0, psi = 0, the = 0, convention = convention)
size = fmodel.xray_structure.scatterers().size()
selections = [flex.bool(size, True).iselection()]
fmodel.xray_structure.apply_rigid_body_shift(
rot = rot_obj.rot_mat(), trans = [1,2,3])
fmodel.update_xray_structure(update_f_calc = True)
fmodel_copy = fmodel.deep_copy()
centers_of_mass = []
for s in selections:
xrs = fmodel_copy.xray_structure.select(s)
centers_of_mass.append(xrs.center_of_mass())
tg_obj = mmtbx.refinement.rigid_body.target_and_grads(
centers_of_mass = centers_of_mass,
sites_cart = fmodel_copy.xray_structure.sites_cart(),
target_functor = fmodel_copy.target_functor(),
rot_objs = [rot_obj],
selections = selections,
suppress_gradients = False)
assert approx_equal(tg_obj.target(),fmodel_copy.target_w())
g_rot, g_transl = tg_obj.gradients_wrt_r(), tg_obj.gradients_wrt_t()
fd_transl = fd_translation(fmodel_copy, e = 0.0001)
assert approx_equal(list(g_transl[0]), fd_transl)
fd_rot = fd_rotation(fmodel = fmodel_copy,
e = 0.0001,
convention = convention)
assert approx_equal(list(g_rot[0]), fd_rot)