def fd_rotation(fmodel, e, convention):
grads = []
for shift in [[e, 0, 0], [0, e, 0], [0, 0, e]]:
xrs1 = fmodel.xray_structure.deep_copy_scatterers()
xrs2 = fmodel.xray_structure.deep_copy_scatterers()
fm = fmodel.deep_copy()
#
rot_obj = scitbx.rigid_body.euler(phi=shift[0],
psi=shift[1],
the=shift[2],
convention=convention)
selections = [flex.bool(xrs1.scatterers().size(), True)]
xrs_g1_1 = mmtbx.refinement.rigid_body.apply_transformation(
xray_structure=xrs1,
rotation_matrices=[rot_obj.rot_mat()],
translation_vectors=[(0.0, 0.0, 0.0)],
selections=selections)
#
rot_obj = scitbx.rigid_body.euler(phi=-shift[0],
psi=-shift[1],
the=-shift[2],
convention=convention)
selections = [flex.bool(xrs1.scatterers().size(), True)]
xrs_g1_2 = mmtbx.refinement.rigid_body.apply_transformation(
xray_structure=xrs2,
rotation_matrices=[rot_obj.rot_mat()],
translation_vectors=[(0.0, 0.0, 0.0)],
selections=selections)
fm.update_xray_structure(xray_structure=xrs_g1_1, update_f_calc=True)
t1 = fm.target_functor()().target_work()
fm.update_xray_structure(xray_structure=xrs_g1_2, update_f_calc=True)
t2 = fm.target_functor()().target_work()
grads.append((t1 - t2) / (2 * e * math.pi / 180))
return grads
def fd_translation(fmodel, e):
grads = []
for shift in [[e, 0, 0], [0, e, 0], [0, 0, e]]:
xrs1 = fmodel.xray_structure.deep_copy_scatterers()
xrs2 = fmodel.xray_structure.deep_copy_scatterers()
fm = fmodel.deep_copy()
xrs_g1_1 = xrs1.translate(x=shift[0], y=shift[1], z=shift[2])
xrs_g1_2 = xrs2.translate(x=-shift[0], y=-shift[1], z=-shift[2])
fm.update_xray_structure(xray_structure=xrs_g1_1, update_f_calc=True)
t1 = fm.target_functor()().target_work()
fm.update_xray_structure(xray_structure=xrs_g1_2, update_f_calc=True)
t2 = fm.target_functor()().target_work()
grads.append((t1 - t2) / (2 * e))
return grads
def fd_translation(fmodel, e):
grads = []
for shift in [[e,0,0],[0,e,0],[0,0,e]]:
xrs1 = fmodel.xray_structure.deep_copy_scatterers()
xrs2 = fmodel.xray_structure.deep_copy_scatterers()
fm = fmodel.deep_copy()
xrs_g1_1 = xrs1.translate(x = shift[0], y = shift[1], z = shift[2])
xrs_g1_2 = xrs2.translate(x =-shift[0], y =-shift[1], z =-shift[2])
fm.update_xray_structure(xray_structure = xrs_g1_1,
update_f_calc = True)
t1 = fm.target_functor()().target_work()
fm.update_xray_structure(xray_structure = xrs_g1_2,
update_f_calc = True)
t2 = fm.target_functor()().target_work()
grads.append( (t1-t2)/(2*e) )
return grads
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)
def fd_rotation(fmodel, e, convention):
grads = []
for shift in [[e,0,0],[0,e,0],[0,0,e]]:
xrs1 = fmodel.xray_structure.deep_copy_scatterers()
xrs2 = fmodel.xray_structure.deep_copy_scatterers()
fm = fmodel.deep_copy()
#
rot_obj = scitbx.rigid_body.euler(phi = shift[0],
psi = shift[1],
the = shift[2],
convention = convention)
selections = [flex.bool(xrs1.scatterers().size(), True)]
xrs_g1_1 = mmtbx.refinement.rigid_body.apply_transformation(
xray_structure = xrs1,
rotation_matrices = [rot_obj.rot_mat()],
translation_vectors = [(0.0,0.0,0.0)],
selections = selections)
#
rot_obj = scitbx.rigid_body.euler(phi = -shift[0],
psi = -shift[1],
the = -shift[2],
convention = convention)
selections = [flex.bool(xrs1.scatterers().size(), True)]
xrs_g1_2 = mmtbx.refinement.rigid_body.apply_transformation(
xray_structure = xrs2,
rotation_matrices = [rot_obj.rot_mat()],
translation_vectors = [(0.0,0.0,0.0)],
selections = selections)
fm.update_xray_structure(xray_structure = xrs_g1_1,
update_f_calc = True)
t1 = fm.target_functor()().target_work()
fm.update_xray_structure(xray_structure = xrs_g1_2,
update_f_calc = True)
t2 = fm.target_functor()().target_work()
grads.append( (t1-t2)/(2*e*math.pi/180) )
return grads
