def uij_from_tls_vector_and_origin(xyz, tls_vector, origin):
assert tls_vector.shape == (21, )
tls_obj = tlso(t=tls_vector[0:6],
l=tls_vector[6:12],
s=tls_vector[12:21],
origin=origin)
return uij_from_tls_object(xyz=xyz, tls_obj=tls_obj)
def exercise_00(pdb_str, formula):
"""
TLS group 6 of 4muy.
"""
pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str)
pdb_hierarchy = pdb_inp.construct_hierarchy()
asc = pdb_hierarchy.atom_selection_cache()
cs = pdb_inp.crystal_symmetry_from_cryst1()
tls_extract = mmtbx.tls.tools.tls_from_pdb_inp(
remark_3_records = pdb_inp.extract_remark_iii_records(3),
pdb_hierarchy = pdb_hierarchy)
#
deg_to_rad_scale = math.pi/180
tls_params_one_group = tls_extract.tls_params[0]
T = matrix.sym(sym_mat3=tls_params_one_group.t)
L = matrix.sym(sym_mat3=tls_params_one_group.l)
S = matrix.sqr(tls_params_one_group.s)
origin = tls_params_one_group.origin
tlso = tools.tlso(
t = T.as_sym_mat3(),
l = L.as_sym_mat3(),
s = S,
origin = origin)
log = open("analysis.log","w")
r = analysis.run(T=T, L=L*(deg_to_rad_scale**2), S=S*deg_to_rad_scale,
log=log, find_t_S_using_formula=formula).self_check(show=False)
log.close()
#
rs = flex.double()
for trial in xrange(10):
o = tools.u_tls_vs_u_ens(pdb_str=pdb_str,
dx = r.dx,
dy = r.dy,
dz = r.dz,
sx = r.sx,
sy = r.sy,
sz = r.sz,
lx = r.l_x,
ly = r.l_y,
lz = r.l_z,
tx = r.tx,
ty = r.ty,
tz = r.tz,
vx = r.v_x,
vy = r.v_y,
vz = r.v_z,
w_M_lx = r.w_M_lx,
w_M_ly = r.w_M_ly,
w_M_lz = r.w_M_lz,
origin = origin,
n_models = 10000,
assert_similarity=False)
rs.append(o.r)
return flex.mean(rs)
def run(pdb_file_name, n_models, log, output_file_name_prefix, eps=1.e-7):
pdb_inp = iotbx.pdb.input(file_name=pdb_file_name)
pdb_hierarchy = pdb_inp.construct_hierarchy()
asc = pdb_hierarchy.atom_selection_cache()
cs = pdb_inp.crystal_symmetry_from_cryst1()
tls_extract = mmtbx.tls.tools.tls_from_pdb_inp(
remark_3_records=pdb_inp.extract_remark_iii_records(3),
pdb_hierarchy=pdb_hierarchy)
for i_group, tls_params_one_group in enumerate(tls_extract.tls_params):
selection = asc.selection(tls_params_one_group.selection_string)
pdb_hierarchy_sel = pdb_hierarchy.select(selection)
xrs = pdb_hierarchy_sel.extract_xray_structure(crystal_symmetry=cs)
deg_to_rad_scale = math.pi / 180
# Units: T[A], L[deg**2], S[A*deg]
T = matrix.sym(sym_mat3=tls_params_one_group.t)
L = matrix.sym(sym_mat3=tls_params_one_group.l)
S = matrix.sqr(tls_params_one_group.s)
origin = tls_params_one_group.origin
tlso = tools.tlso(t=T.as_sym_mat3(),
l=L.as_sym_mat3(),
s=S,
origin=origin)
# sanity check
if (not adptbx.is_positive_definite(tls_params_one_group.t, eps)):
raise Sorry("T matrix is not positive definite.")
if (not adptbx.is_positive_definite(tls_params_one_group.l, eps)):
raise Sorry("L matrix is not positive definite.")
r = analysis.run(T=T,
L=L * (deg_to_rad_scale**2),
S=S * deg_to_rad_scale,
log=log).self_check()
ensemble_generator_obj = ensemble_generator(
tls_from_motions_object=r,
pdb_hierarchy=pdb_hierarchy_sel,
xray_structure=xrs,
n_models=n_models,
origin=origin,
log=log)
ensemble_generator_obj.write_pdb_file(
file_name=output_file_name_prefix +
"_ensemble_%s.pdb" % str(i_group))
# get U from TLS
u_from_tls = tools.uaniso_from_tls_one_group(
tlso=tlso, sites_cart=xrs.sites_cart(), zeroize_trace=False)
# get U from ensemble
pdb_hierarchy_from_tls = pdb_hierarchy_sel.deep_copy()
pdb_hierarchy_from_ens = pdb_hierarchy_sel.deep_copy()
u_from_ens = tools.u_cart_from_ensemble(
models=ensemble_generator_obj.states.root.models())
for i in xrange(xrs.sites_cart().size()):
print "atom %d:" % i
print " Ucart(from TLS):", ["%8.5f" % u for u in u_from_tls[i]]
print " Ucart(from ens):", ["%8.5f" % u for u in u_from_ens[i]]
#
u1, u2 = u_from_tls.as_double(), u_from_ens.as_double()
cc = flex.linear_correlation(x=u1, y=u2).coefficient()
r = flex.sum(flex.abs(u1-u2))/\
flex.sum(flex.abs(flex.abs(u1)+flex.abs(u2)))*2
print "%6.4f %6.4f" % (cc, r)
#
pdb_hierarchy_from_tls.atoms().set_uij(u_from_tls)
pdb_hierarchy_from_ens.atoms().set_uij(u_from_ens)
pdb_hierarchy_from_tls.write_pdb_file(
file_name=output_file_name_prefix +
"_u_from_tls_%s.pdb" % str(i_group),
crystal_symmetry=cs)
pdb_hierarchy_from_ens.write_pdb_file(
file_name=output_file_name_prefix +
"_u_from_ensemble_%s.pdb" % str(i_group),
crystal_symmetry=cs)
return ensemble_generator_obj
def uaniso_from_tls_and_back():
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/1OC2_tst.pdb",
test=os.path.isfile)
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
file_name = pdb_file,
raw_records = None,
force_symmetry = True)
xray_structure = processed_pdb_file.xray_structure()
selections = []
for string in ["chain A", "chain B"]:
selections.append(processed_pdb_file.all_chain_proxies.selection(
string = string))
input_tls_data = iotbx.pdb.remark_3_interpretation.extract_tls_parameters(
remark_3_records=processed_pdb_file.all_chain_proxies.pdb_inp
.extract_remark_iii_records(iii=3),
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy,
chain_ids=[]).tls_params
tls_params = []
for item in input_tls_data:
tls_params.append(tools.tlso(t = item.t,
l = item.l,
s = item.s,
origin = item.origin))
tools.show_tls(tlsos = tls_params)
u_cart_from_tls = tools.u_cart_from_tls(
sites_cart = xray_structure.sites_cart(),
selections = selections,
tlsos = tls_params)
i = 0
for utls,atom in zip(u_cart_from_tls,
processed_pdb_file.all_chain_proxies.pdb_atoms):
updb = atom.uij
#i += 1
#print " ", i
#print "%6.4f %6.4f %6.4f %6.4f %6.4f %6.4f "% \
# (utls[0],utls[1],utls[2],utls[3],utls[4],utls[5])
#print "%6.4f %6.4f %6.4f %6.4f %6.4f %6.4f "% \
# (updb[0],updb[1],updb[2],updb[3],updb[4],updb[5])
assert approx_equal(utls,updb, 1.e-4)
tlsos_initial = []
for input_tls_data_ in input_tls_data:
tlsos_initial.append(tools.tlso(
t = ([0.0,0.0,0.0,0.0,0.0,0.0]),
l = ([0.0,0.0,0.0,0.0,0.0,0.0]),
s = ([0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0]),
origin = input_tls_data_.origin))
tls_from_uanisos = tools.tls_from_uanisos(
number_of_macro_cycles = 300,
max_iterations = 1000,
xray_structure = xray_structure,
selections = selections,
tlsos_initial = tlsos_initial)
print("\nTLS from Uaniso:\n")
tools.show_tls(tlsos = tls_from_uanisos)
for input_tls_data_,tls_from_uanisos_ in zip(tls_params,tls_from_uanisos):
assert approx_equal(input_tls_data_.t, tls_from_uanisos_.t, 1.e-4)
assert approx_equal(input_tls_data_.l, tls_from_uanisos_.l, 1.e-4)
assert approx_equal(input_tls_data_.s, tls_from_uanisos_.s, 1.e-4)
assert approx_equal(input_tls_data_.origin, tls_from_uanisos_.origin, 1.e-3)
#
print(format_cpu_times())
def run(pdb_file_name,
n_models,
log,
output_file_name_prefix,
eps=1.e-7):
pdb_inp = iotbx.pdb.input(file_name = pdb_file_name)
pdb_hierarchy = pdb_inp.construct_hierarchy()
asc = pdb_hierarchy.atom_selection_cache()
cs = pdb_inp.crystal_symmetry_from_cryst1()
tls_extract = mmtbx.tls.tools.tls_from_pdb_inp(
remark_3_records = pdb_inp.extract_remark_iii_records(3),
pdb_hierarchy = pdb_hierarchy)
for i_group, tls_params_one_group in enumerate(tls_extract.tls_params):
selection = asc.selection(tls_params_one_group.selection_string)
pdb_hierarchy_sel = pdb_hierarchy.select(selection)
xrs = pdb_hierarchy_sel.extract_xray_structure(crystal_symmetry=cs)
deg_to_rad_scale = math.pi/180
# Units: T[A], L[deg**2], S[A*deg]
T = matrix.sym(sym_mat3=tls_params_one_group.t)
L = matrix.sym(sym_mat3=tls_params_one_group.l)
S = matrix.sqr(tls_params_one_group.s)
origin = tls_params_one_group.origin
tlso = tools.tlso(
t = T.as_sym_mat3(),
l = L.as_sym_mat3(),
s = S,
origin = origin)
# sanity check
if(not adptbx.is_positive_definite(tls_params_one_group.t, eps)):
raise Sorry("T matrix is not positive definite.")
if(not adptbx.is_positive_definite(tls_params_one_group.l, eps)):
raise Sorry("L matrix is not positive definite.")
r = analysis.run(T=T, L=L*(deg_to_rad_scale**2), S=S*deg_to_rad_scale,
log=log).self_check()
ensemble_generator_obj = ensemble_generator(
tls_from_motions_object = r,
pdb_hierarchy = pdb_hierarchy_sel,
xray_structure = xrs,
n_models = n_models,
origin = origin,
log = log)
ensemble_generator_obj.write_pdb_file(
file_name=output_file_name_prefix+"_ensemble_%s.pdb"%str(i_group))
# get U from TLS
u_from_tls = tools.uaniso_from_tls_one_group(
tlso = tlso,
sites_cart = xrs.sites_cart(),
zeroize_trace = False)
# get U from ensemble
pdb_hierarchy_from_tls = pdb_hierarchy_sel.deep_copy()
pdb_hierarchy_from_ens = pdb_hierarchy_sel.deep_copy()
u_from_ens = tools.u_cart_from_ensemble(
models = ensemble_generator_obj.states.root.models())
for i in xrange(xrs.sites_cart().size()):
print "atom %d:"%i
print " Ucart(from TLS):", ["%8.5f"%u for u in u_from_tls[i]]
print " Ucart(from ens):", ["%8.5f"%u for u in u_from_ens[i]]
#
u1, u2 = u_from_tls.as_double(), u_from_ens.as_double()
cc = flex.linear_correlation(x=u1, y=u2).coefficient()
r = flex.sum(flex.abs(u1-u2))/\
flex.sum(flex.abs(flex.abs(u1)+flex.abs(u2)))*2
print "%6.4f %6.4f"%(cc, r)
#
pdb_hierarchy_from_tls.atoms().set_uij(u_from_tls)
pdb_hierarchy_from_ens.atoms().set_uij(u_from_ens)
pdb_hierarchy_from_tls.write_pdb_file(
file_name = output_file_name_prefix+"_u_from_tls_%s.pdb"%str(i_group),
crystal_symmetry = cs)
pdb_hierarchy_from_ens.write_pdb_file(
file_name = output_file_name_prefix+"_u_from_ensemble_%s.pdb"%str(i_group),
crystal_symmetry = cs)
return ensemble_generator_obj
def uaniso_from_tls_and_back():
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
pdb_file = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/1OC2_tst.pdb",
test=os.path.isfile)
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
file_name = pdb_file,
raw_records = None,
force_symmetry = True)
xray_structure = processed_pdb_file.xray_structure()
selections = []
for string in ["chain A", "chain B"]:
selections.append(processed_pdb_file.all_chain_proxies.selection(
string = string))
input_tls_data = iotbx.pdb.remark_3_interpretation.extract_tls_parameters(
remark_3_records=processed_pdb_file.all_chain_proxies.pdb_inp
.extract_remark_iii_records(iii=3),
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy,
chain_ids=[]).tls_params
tls_params = []
for item in input_tls_data:
tls_params.append(tools.tlso(t = item.t,
l = item.l,
s = item.s,
origin = item.origin))
tools.show_tls(tlsos = tls_params)
u_cart_from_tls = tools.u_cart_from_tls(
sites_cart = xray_structure.sites_cart(),
selections = selections,
tlsos = tls_params)
i = 0
for utls,atom in zip(u_cart_from_tls,
processed_pdb_file.all_chain_proxies.pdb_atoms):
updb = atom.uij
#i += 1
#print " ", i
#print "%6.4f %6.4f %6.4f %6.4f %6.4f %6.4f "% \
# (utls[0],utls[1],utls[2],utls[3],utls[4],utls[5])
#print "%6.4f %6.4f %6.4f %6.4f %6.4f %6.4f "% \
# (updb[0],updb[1],updb[2],updb[3],updb[4],updb[5])
assert approx_equal(utls,updb, 1.e-4)
tlsos_initial = []
for input_tls_data_ in input_tls_data:
tlsos_initial.append(tools.tlso(
t = ([0.0,0.0,0.0,0.0,0.0,0.0]),
l = ([0.0,0.0,0.0,0.0,0.0,0.0]),
s = ([0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0]),
origin = input_tls_data_.origin))
tls_from_uanisos = tools.tls_from_uanisos(
number_of_macro_cycles = 300,
max_iterations = 1000,
xray_structure = xray_structure,
selections = selections,
tlsos_initial = tlsos_initial)
print "\nTLS from Uaniso:\n"
tools.show_tls(tlsos = tls_from_uanisos)
for input_tls_data_,tls_from_uanisos_ in zip(tls_params,tls_from_uanisos):
assert approx_equal(input_tls_data_.t, tls_from_uanisos_.t, 1.e-4)
assert approx_equal(input_tls_data_.l, tls_from_uanisos_.l, 1.e-4)
assert approx_equal(input_tls_data_.s, tls_from_uanisos_.s, 1.e-4)
assert approx_equal(input_tls_data_.origin, tls_from_uanisos_.origin, 1.e-3)
#
print format_cpu_times()
