def get_pdb_inputs(pdb_str):
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str.split('\n'))
model = mmtbx.model.manager(model_input=pdb_inp)
model.process(make_restraints=True)
return group_args(ph=model.get_hierarchy(),
grm=model.get_restraints_manager(),
xrs=model.get_xray_structure())
def run(args):
assert len(args) == 1
# Read file into pdb_input class
inp = iotbx.pdb.input(file_name=args[0])
# create a model manager
model = mmtbx.model.manager(model_input=inp)
# get number of atoms in the input model
n_atoms = model.get_number_of_atoms()
# extract atom coordinates
old_sites_cart = model.get_sites_cart()
# generate random additions
random_addition = flex.vec3_double(
flex.random_double(size=n_atoms * 3) - 0.5)
# actually add them to old coordinates
new_xyz = old_sites_cart + random_addition
# Update coordinates in model manager
model.set_sites_cart(sites_cart=new_xyz)
# get xray structure
xrs = model.get_xray_structure()
# reset B-factors (min=1, max=20)
# generate array of new B-factors
new_b = flex.random_double(size=n_atoms, factor=19) + 1
# set them in xray structure
xrs.set_b_iso(values=new_b)
# update model manager with this xray structure
model.set_xray_structure(xrs)
# output result in PDB format to the screen
print model.model_as_pdb()
print "END"
def exercise(pdb_str, use_ideal_bonds_angles):
# --------------------------------------------------------------
# code to switch off CDL
# --------------------------------------------------------------
#params_line = grand_master_phil_str
#params = iotbx.phil.parse(
# input_string=params_line, process_includes=True).extract()
#params.pdb_interpretation.restraints_library.cdl=False
# ---------------------------------------------------------------
pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=True)
pdb_hierarchy = model.get_hierarchy()
geometry_restraints = model.get_restraints_manager().geometry
xray_structure = model.get_xray_structure()
sites_cart = model.get_sites_cart()
grf = cctbx.geometry_restraints.flags.flags(default=True)
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart=sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=geometry_restraints,
geometry_restraints_flags=grf,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=500))
xray_structure.set_sites_cart(sites_cart)
pdb_hierarchy.adopt_xray_structure(xray_structure)
atoms = pdb_hierarchy.atoms()
sites_cart = xray_structure.sites_cart()
riding_h_manager = riding.manager(
pdb_hierarchy=pdb_hierarchy,
geometry_restraints=geometry_restraints,
use_ideal_bonds_angles=use_ideal_bonds_angles)
h_parameterization = riding_h_manager.h_parameterization
diagnostics = riding_h_manager.diagnostics(sites_cart=sites_cart,
threshold=0.05)
h_distances = diagnostics.h_distances
number_h = model.get_hd_selection().count(True)
number_h_para = len(h_parameterization) - h_parameterization.count(None)
assert (number_h_para == number_h), 'Not all H atoms are parameterized'
for ih in h_distances:
labels = atoms[ih].fetch_labels()
if use_ideal_bonds_angles:
assert (h_distances[ih] < 0.03), \
'distance too large: %s atom: %s (%s) residue: %s ' \
% (h_parameterization[ih].htype, atoms[ih].name, ih, labels.resseq.strip())
else:
assert (h_distances[ih] < 1e-7), \
'distance too large: %s atom: %s (%s) residue: %s distance %s' \
% (h_parameterization[ih].htype, atoms[ih].name, ih, labels.resseq.strip(), h_distances[ih])
def get_pdb_inputs(pdb_str):
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
model = mmtbx.model.manager(model_input = pdb_inp, log = null_out(), build_grm=True)
return group_args(
ph = model.get_hierarchy(),
grm = model.get_restraints_manager(),
xrs = model.get_xray_structure())
def exercise_02():
for file_name, input_model in [("m_good.pdb", model_good),
("m_bad.pdb", model_bad)]:
tmp_f = open(file_name, "w")
tmp_f.write(input_model)
tmp_f.close()
xrs_exact = iotbx.pdb.pdb_input(
file_name="m_good.pdb").xray_structure_simple()
model = mmtbx.model.manager(model_input=iotbx.pdb.input(
file_name="m_bad.pdb"))
xrs_part = model.get_xray_structure()
miller_set = miller.build_set(
crystal_symmetry=xrs_exact.crystal_symmetry(),
anomalous_flag=False,
d_min=0.6)
f_obs = abs(
miller_set.structure_factors_from_scatterers(
xray_structure=xrs_exact, algorithm="direct",
cos_sin_table=False).f_calc())
sf_par = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract()
sf_par.algorithm = "direct"
sf_par.cos_sin_table = False
fmodel = mmtbx.f_model.manager(xray_structure=xrs_part,
sf_and_grads_accuracy_params=sf_par,
target_name="ls_wunit_k1",
f_obs=f_obs)
#
out = StringIO()
params = find_hydrogens.all_master_params().extract()
params.map_cutoff = 6.5
find_hydrogens.run(fmodel=fmodel, model=model, log=out, params=params)
def test_addition_scatterers():
'''
Test overlaps when adding and moving scatterers
Test water scatterers with and without labels
'''
clashes = get_clashes_result(raw_records=raw_records_3)
results = clashes.get_results()
assert(results.n_clashes == 3)
assert approx_equal(results.clashscore, 1000, eps=0.1)
# Add water scatterers
model = clashes.model
xrs = model.get_xray_structure()
new_scatterers = flex.xray_scatterer(
xrs.scatterers().size(),
xray.scatterer(occupancy = 1, b = 10, scattering_type = "O"))
new_sites_frac = xrs.unit_cell().fractionalize(xrs.sites_cart()+[0.5,0,0])
new_scatterers.set_sites(new_sites_frac)
new_xrs = xray.structure(
special_position_settings = xrs,
scatterers = new_scatterers)
model.add_solvent(
solvent_xray_structure = new_xrs,
refine_occupancies = False,
refine_adp = "isotropic")
pnps = pnp.manager(model = model)
clashes = pnps.get_clashes()
results = clashes.get_results()
assert(results.n_clashes == 15)
assert approx_equal(results.clashscore, 2500, eps=5)
def exercise_biomt():
inp = iotbx.pdb.input(lines=biomt_txt+ss_txt+atoms_txt, source_info=None)
model = mmtbx.model.manager(
model_input = inp)
assert model.get_number_of_atoms() == 300, model.get_number_of_atoms()
assert model.get_hierarchy().atoms_size() == 300
assert model.get_xray_structure().scatterers().size() == 300
ss_ann = model.get_ss_annotation()
assert ss_ann.get_n_helices() == 2
assert ss_ann.get_n_sheets() == 1
model.expand_with_BIOMT_records()
assert model.get_number_of_atoms() == 900, model.get_number_of_atoms()
assert model.get_hierarchy().atoms_size() == 900
assert model.get_xray_structure().scatterers().size() == 900, model.get_xray_structure().scatterers().size()
ss_ann = model.get_ss_annotation()
assert ss_ann.get_n_helices() == 6
assert ss_ann.get_n_sheets() == 3
def run(args, out=sys.stdout):
if (len(args) == 0) or ("--help" in args):
raise Usage("mmtbx.rigid_bond_test model.pdb")
import mmtbx.restraints
import mmtbx.model
import iotbx.phil
cmdline = iotbx.phil.process_command_line_with_files(
args=args,
master_phil=master_phil,
pdb_file_def="model",
cif_file_def="restraints")
params = cmdline.work.extract()
validate_params(params)
model = mmtbx.model.manager(
model_input=iotbx.pdb.input(file_name=params.model), build_grm=True)
model.get_xray_structure()
model.show_rigid_bond_test(out=out, use_id_str=True, prefix=" ")
def exercise_bond_over_symmetry(mon_lib_srv, ener_lib):
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records9)
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.restraints_library.mcl = False
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (29, 0)
h = model.get_hierarchy()
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(32, 4),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
proxy2 = geometry_restraints.bond_simple_proxy(
i_seqs=(32, 24),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
grm.add_new_bond_restraints_in_place(proxies=[proxy, proxy2],
sites_cart=h.atoms().extract_xyz())
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (30, 2)
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="")
outtxt = out.getvalue()
# print(outtxt)
#
# Not clear why ZN-NE2 bond adds as 2 bonds.
assert_lines_in_text(
outtxt, """\
bond pdb="ZN ZN A 8 "
pdb=" NE2 HIS B 304 "
ideal model delta sigma weight residual sym.op.
2.900 2.969 -0.069 5.00e-02 4.00e+02 1.92e+00 -x-1/2,y+1/2,-z+3/4
""")
assert_lines_in_text(
outtxt, """\
bond pdb=" NE2 HIS B 304 "
pdb="ZN ZN A 8 "
ideal model delta sigma weight residual sym.op.
2.900 2.969 -0.069 5.00e-02 4.00e+02 1.92e+00 -x-1/2,y-1/2,-z+3/4
""")
def calculate_cc(map_data, model, resolution):
xrs = model.get_xray_structure()
fc = xrs.structure_factors(d_min = resolution).f_calc()
f_map = fc.structure_factors_from_map(
map = map_data,
use_scale = True,
anomalous_flag = False,
use_sg = False)
return fc.map_correlation(other = f_map)
def exercise(pdb_str, eps):
pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None)
model = mmtbx.model.manager(
model_input = pdb_inp,
build_grm = True,
log = null_out())
geometry_restraints = model.restraints_manager.geometry
xray_structure = model.get_xray_structure()
model.setup_riding_h_manager()
riding_h_manager = model.get_riding_h_manager()
riding_h_manager.idealize(xray_structure = xray_structure)
sites_cart = xray_structure.sites_cart()
g_analytical = geometry_restraints.energies_sites(
sites_cart = sites_cart,
compute_gradients = True).gradients
hd_selection = xray_structure.hd_selection()
g_analytical_reduced = riding_h_manager.gradients_reduced_cpp(
gradients = g_analytical,
sites_cart = sites_cart,
hd_selection = hd_selection)
#
ex = [eps,0,0]
ey = [0,eps,0]
ez = [0,0,eps]
g_fd = flex.vec3_double()
for i_site in xrange(sites_cart.size()):
g_fd_i = []
for e in [ex,ey,ez]:
ts = []
for sign in [-1,1]:
sites_cart_ = sites_cart.deep_copy()
xray_structure_ = xray_structure.deep_copy_scatterers()
sites_cart_[i_site] = [
sites_cart_[i_site][j]+e[j]*sign for j in xrange(3)]
xray_structure_.set_sites_cart(sites_cart_)
# after shift, recalculate H position
riding_h_manager.idealize(
xray_structure=xray_structure_)
sites_cart_ = xray_structure_.sites_cart()
ts.append(geometry_restraints.energies_sites(
sites_cart = sites_cart_,
compute_gradients = False).target)
g_fd_i.append((ts[1]-ts[0])/(2*eps))
g_fd.append(g_fd_i)
g_fd_reduced = g_fd.select(~hd_selection)
for g1, g2 in zip(g_analytical_reduced, g_fd_reduced):
assert approx_equal(g1,g2, 1.e-4)
def exercise_bond_near_symmetry3(mon_lib_srv, ener_lib):
""" Since neighbors_fast_pair_generator for non-symmetry interactions
provides only (i,j) pair and not (j,i), and there's no sorting involved
(no way to guess what to check), there was a bug where non-symmetry interaction
was missed in add_new_bond_restraints_in_place.
Actually testing that both bonds are added without symmetry operators.
"""
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records8)
model = mmtbx.model.manager(model_input=pdb_inp,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
h = model.get_hierarchy()
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(64, 37),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
proxy2 = geometry_restraints.bond_simple_proxy(
i_seqs=(72, 37),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
grm.add_new_hbond_restraints_in_place(
proxies=[proxy, proxy2],
sites_cart=h.atoms().extract_xyz(),
max_distance_between_connecting_atoms=10)
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="",
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
outtxt = out.getvalue()
assert not show_diff(
outtxt, """\
Bond restraints: 2
Sorted by residual:
bond pdb=" O ARG A 25 "
pdb=" N AASN A 29 "
ideal model delta sigma weight residual
2.900 2.934 -0.034 5.00e-02 4.00e+02 4.53e-01
bond pdb=" O ARG A 25 "
pdb=" N BASN A 29 "
ideal model delta sigma weight residual
2.900 2.888 0.012 5.00e-02 4.00e+02 5.59e-02
""")
def exercise_mtrix():
inp = iotbx.pdb.input(lines=mtrix_txt+ss_txt+atoms_txt, source_info=None)
model = mmtbx.model.manager(
model_input = inp)
assert model.get_number_of_atoms() == 900, model.get_number_of_atoms()
assert model.get_hierarchy().atoms_size() == 900
assert model.get_xray_structure().scatterers().size() == 900
ss_ann = model.get_ss_annotation()
# print ss_ann.as_pdb_str()
assert ss_ann.get_n_helices() == 6
assert ss_ann.get_n_sheets() == 3
def check_scattering_type_registry():
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
model = mmtbx.model.manager(model_input=pdb_inp, log=null_out())
model.process(make_restraints=True)
xrs1 = model.get_xray_structure()
xrs2 = model.get_hierarchy().extract_xray_structure(
crystal_symmetry=model.crystal_symmetry())
xrs1.scattering_type_registry(table="electron")
xrs2.scattering_type_registry(table="electron")
xrs1.scattering_type_registry().show()
xrs2.scattering_type_registry().show()
# TODO: Assert to the same value once added
assert (xrs1.scattering_type_registry().gaussian("O1-") is None)
assert (xrs2.scattering_type_registry().gaussian("O1-") is None)
def tst_1(prefix="gm_ncs_constr_tst1"):
log = sys.stdout
pdb_in = iotbx.pdb.input(source_info=None, lines=pdb_string1.split('\n'))
# print dir(pdb_in)
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params(
)
pdb_int_params.pdb_interpretation.ncs_search.enabled = True
model = mmtbx.model.manager(model_input=pdb_in,
pdb_interpretation_params=pdb_int_params,
build_grm=True)
ncs_obj = iotbx.ncs.input(hierarchy=model.get_hierarchy())
original_ncs_transform = ncs_obj.ncs_transform
ncs_restraints_group_list = ncs_obj.get_ncs_restraints_group_list()
ncs_obj.show(format='phil')
grm = model.get_restraints_manager()
tmp_xrs = model.get_xray_structure().deep_copy_scatterers()
refine_selection = flex.size_t(xrange(model.get_number_of_atoms()))
# print "refining sites"
cycle = 0
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_geometry_minimization(
xray_structure=tmp_xrs,
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=refine_selection,
restraints_manager=grm.geometry,
refine_sites=True,
refine_transformations=False,
)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object=tfg_obj,
xray_structure=tmp_xrs,
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=refine_selection,
finite_grad_differences_test=False,
max_iterations=100,
refine_sites=True,
refine_transformations=False)
refined_pdb_h = model.get_hierarchy().deep_copy()
refined_pdb_h.adopt_xray_structure(tmp_xrs)
refined_pdb_h.write_pdb_file("refined_%d.pdb" % cycle)
new_ncs_obj = iotbx.ncs.input(hierarchy=refined_pdb_h)
new_ncs_transform = new_ncs_obj.ncs_transform
spec = new_ncs_obj.get_ncs_info_as_spec()
for k, v in original_ncs_transform.iteritems():
assert approx_equal(v.r.elems, new_ncs_transform[k].r.elems)
assert approx_equal(v.t, new_ncs_transform[k].t)
overall_rmsd_after = spec.overall_rmsd()
assert overall_rmsd_after < 1e-6
def run(args):
if (len(args) != 2):
raise RuntimeError("Please specify two file names.")
fn_1 = args[0]
fn_2 = args[1]
model_filename, reflection_filename = None, None
for fn in (fn_1, fn_2):
if os.path.splitext(fn)[1] == '.mtz' and reflection_filename is None:
reflection_filename = fn
elif os.path.splitext(fn)[1] == '.pdb' and model_filename is None:
model_filename = fn
else:
raise RuntimeError("Please specify one model file and one reflection file.")
print('Model file name: ', model_filename)
print('Reflection file name: ', reflection_filename)
pdb_inp = iotbx.pdb.input(file_name=model_filename)
model = mmtbx.model.manager(model_input = pdb_inp)
miller_arrays = reflection_file_reader.any_reflection_file(
file_name = reflection_filename).as_miller_arrays()
for ma in miller_arrays:
if (ma.info().label_string()=="FOBS,SIGFOBS"):
f_obs = ma
if (ma.info().label_string() in ['R-free-flags','FreeR_flag']):
r_free = ma
f_obs, r_free = f_obs.common_sets(r_free)
r_free_flags = r_free.array(data = r_free.data()==0)
xray_structure = model.get_xray_structure()
f_model = mmtbx.f_model.manager(
f_obs = f_obs,
r_free_flags = r_free_flags,
xray_structure = xray_structure)
f_model.update_all_scales()
print('\nRwork: ', f_model.r_work())
print('\nRfree:', f_model.r_free())
def run_tst_xrs_and_hierarchy():
# Check if scatterers in xrs are neutral after calling function
pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str)
model = mmtbx.model.manager(model_input=pdb_inp, log=null_out())
model.neutralize_scatterers()
xrs = model.get_xray_structure()
for scatterer in xrs.scatterers():
assert (scatterer.scattering_type in neutral_atoms_list)
# Check if pdb_hierarchy has neutral atoms as well
pdb_str_neutralized = model.model_as_pdb()
pdb_inp_neutralized = iotbx.pdb.input(source_info=None,
lines=pdb_str_neutralized)
model_neutralized = mmtbx.model.manager(model_input=pdb_inp_neutralized,
log=null_out())
xrs_neutralized = model_neutralized.get_xray_structure()
for scatterer in xrs_neutralized.scatterers():
assert (scatterer.scattering_type in neutral_atoms_list)
def exercise_1():
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1)
model = mmtbx.model.manager(
model_input = inp,
log = null_out())
assert model.get_number_of_atoms() == 21
assert model.get_hierarchy().atoms_size() == 21
assert model.get_xray_structure().scatterers().size() == 21
ss = model.get_ss_annotation()
# print ss.as_pdb_str()
# STOP()
assert ss.get_n_helices() == 3
# because the second strand contains chain B which is not in ATOM records
# whole sheet got discarded.
assert ss.get_n_sheets() == 0
rm = model.get_restraints_manager()
assert rm.geometry.pair_proxies().bond_proxies.simple.size() == 6
# since No NCS was set, these functions return the whole thing and no
# master selection
assert model.get_master_hierarchy().atoms_size() == 21
assert model.get_master_selection().size() == 0
# print model.model_as_pdb()
# print "="*40
# Here we set NCS constraints
inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1)
pdb_int_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
pdb_int_params.pdb_interpretation.ncs_search.enabled=True
model = mmtbx.model.manager(
model_input = inp,
pdb_interpretation_params = pdb_int_params,
process_input=True,
log = null_out())
# model.get_xray_structure()
assert not model.ncs_constraints_present()
assert model.get_ncs_obj() is not None
model.setup_ncs_constraints_groups()
# print model.get_ncs_obj()
assert model.ncs_constraints_present()
assert model.get_master_hierarchy().atoms_size() == 7
# print model.get_master_hierarchy().as_pdb_string()
# print list(model.get_master_selection())
assert list(model.get_master_selection()).count(True) == 7
def get_fsc(map_data, model, params):
result = None
if (params.compute.fsc):
mtriage_params = mtriage.master_params().extract()
mtriage_params.scattering_table = params.scattering_table
mtriage_params.compute.map_counts = False
mtriage_params.compute.fsc_curve_model = True
mtriage_params.compute.d_fsc_model_05 = False
mtriage_params.compute.d_fsc_model_0 = False
mtriage_params.compute.d_fsc_model_0143 = False
mtriage_params.compute.d_model = False
mtriage_params.compute.d_model_b0 = False
mtriage_params.compute.d99 = False
mtriage_params.mask_maps = True
#mtriage_params.radius_smooth = self.atom_radius
mtriage_params.resolution = params.resolution
result = mtriage.mtriage(
map_data=map_data,
xray_structure=model.get_xray_structure(),
params=mtriage_params).get_results().masked.fsc_curve_model
return result
def neutralize(self, model):
'''
Neutralize scatterers if necessary
'''
xrs = model.get_xray_structure()
neutralized = False
for scatterer in xrs.scatterers():
type_neutralized = filter(lambda x: x.isalpha(), scatterer.scattering_type)
if (type_neutralized != scatterer.scattering_type):
neutralized = True
scatterer.scattering_type = type_neutralized
if neutralized:
print('Model was neutralized.', file=self.logger)
model.set_xray_structure(xray_structure = xrs)
new_pdb_fn = os.path.join(self.dest_dir, self.prefix + '_neut.pdb')
#model.get_hierarchy().write_pdb_file(new_pdb_file)
pdb_str = model.model_as_pdb()
with open(new_pdb_fn, 'w') as fp:
fp.write(pdb_str)
self.json_data['pdb_file_updated'] = new_pdb_fn
return model
def run(args, log=sys.stdout):
if (len(args) == 0):
parsed = defaults(log=log)
parsed.show(prefix=" ", out=log)
return
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(
args=args, log=sys.stdout, master_params=parsed)
processed_args.params.show()
params = processed_args.params.extract()
if (len(processed_args.pdb_file_names) == 0):
raise Sorry("No PDB file found.")
if (len(processed_args.pdb_file_names) > 1):
raise Sorry("More than one PDB file found.")
pdb_file_name = processed_args.pdb_file_names[0]
if (params.f_obs.f_calc.atomic_model.add_hydrogens):
pdb_file_name_r = os.path.basename(pdb_file_name) + "_reduce"
# easy_run.go("phenix.reduce %s > %s"% (pdb_file_name, pdb_file_name_r))
run_reduce_with_timeout(file_name=pdb_file_name,
parameters=" > %s" % pdb_file_name_r)
pdb_file_name = pdb_file_name_r
pdbi_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
if (params.f_obs.f_calc.atomic_model.use_ramachandran_plot_restraints):
pdbi_params.pdb_interpretation.ramachandran_plot_restraints.enabled = True
model = mmtbx.model.manager(model_input=iotbx.pdb.input(
file_name=pdb_file_name))
model.process(make_restraints=True, pdb_interpretation_params=pdbi_params)
root = iotbx.pdb.hierarchy.root()
loop_1(params=params,
root=root,
xray_structure=model.get_xray_structure(),
pdb_hierarchy=model.get_hierarchy(),
restraints_manager=model.get_restraints_manager())
root.write_pdb_file(
file_name=params.f_obs.f_calc.atomic_model.output_file_name,
crystal_symmetry=model.crystal_symmetry())
simulate_f_obs(root=root,
crystal_symmetry=model.crystal_symmetry(),
params=params)
def run(args):
# processing command-line stuff, out of the object
log = multi_out()
log.register("stdout", sys.stdout)
if len(args) == 0:
format_usage_message(log)
return
input_objects = process_command_line_with_files(
args=args,
master_phil=master_params(),
pdb_file_def="model_file_name",
map_file_def="map_file_name",
reflection_file_def="hkl_file_name",
cif_file_def="ligands_file_name")
work_params = input_objects.work.extract()
if [work_params.map_file_name, work_params.hkl_file_name].count(None) < 1:
raise Sorry("Only one source of map could be supplied.")
input_objects.work.show(prefix=" ", out=log)
if len(work_params.model_file_name) == 0:
raise Sorry("No PDB file specified")
if work_params.output_prefix is None:
work_params.output_prefix = os.path.basename(
work_params.model_file_name[0])
log_file_name = "%s.log" % work_params.output_prefix
logfile = open(log_file_name, "w")
log.register("logfile", logfile)
err_log = multi_out()
err_log.register(label="log", file_object=log)
# err_log.register(label="stderr", file_object=sys.stderr)
sys.stderr = err_log
if work_params.loop_idealization.output_prefix is None:
work_params.loop_idealization.output_prefix = "%s_rama_fixed" % work_params.output_prefix
# Here we start opening files provided,
# collect crystal symmetries
pdb_combined = iotbx.pdb.combine_unique_pdb_files(
file_names=work_params.model_file_name)
pdb_input = iotbx.pdb.input(source_info=None,
lines=flex.std_string(
pdb_combined.raw_records))
pdb_cs = pdb_input.crystal_symmetry()
crystal_symmetry = None
map_cs = None
map_content = input_objects.get_file(work_params.map_file_name)
if map_content is not None:
try:
map_cs = map_content.crystal_symmetry()
except NotImplementedError as e:
pass
try:
crystal_symmetry = crystal.select_crystal_symmetry(
from_command_line=None,
from_parameter_file=None,
from_coordinate_files=[pdb_cs],
from_reflection_files=[map_cs],
enforce_similarity=True)
except AssertionError as e:
if len(e.args) > 0 and e.args[0].startswith(
"No unit cell and symmetry information supplied"):
pass
else:
raise e
model = mmtbx.model.manager(model_input=pdb_input,
restraint_objects=input_objects.cif_objects,
crystal_symmetry=crystal_symmetry,
process_input=False,
log=log)
map_data = None
shift_manager = None
if map_content is not None:
map_data, map_cs, shift_manager = get_map_from_map(
map_content, work_params, xrs=model.get_xray_structure(), log=log)
model.shift_model_and_set_crystal_symmetry(
shift_cart=shift_manager.shift_cart)
# model.get_hierarchy().write_pdb_file("junk_shift.pdb")
hkl_content = input_objects.get_file(work_params.hkl_file_name)
if hkl_content is not None:
map_data, map_cs = get_map_from_hkl(
hkl_content,
work_params,
xrs=model.get_xray_structure(
), # here we don't care about atom order
log=log)
mi_object = model_idealization(model=model,
map_data=map_data,
params=work_params,
log=log,
verbose=False)
mi_object.run()
mi_object.print_stat_comparison()
print("RMSD from starting model (backbone, all): %.4f, %.4f" %
(mi_object.get_rmsd_from_start(), mi_object.get_rmsd_from_start2()),
file=log)
mi_object.print_runtime()
# add hydrogens if needed ?
print("All done.", file=log)
log.flush()
sys.stderr = sys.__stderr__
log.close()
def find_ligands_and_get_cif(self):
if self.json_data['success_composition'] is False:
# ready set did not fail, so don't store as failed
return
make_sub_header('Search for ligands', out=self.logger)
self.save_json()
fn = self.json_data['pdb_file']
pdb_inp = iotbx.pdb.input(file_name = fn)
try:
model = mmtbx.model.manager(
model_input = pdb_inp,
log = null_out())
except Exception as e:
self.json_data['success_readyset'] = False
msg = traceback.format_exc()
print(msg, file=self.logger)
self.write_log(
step='Model class without restraints from initial pdb ', msg=msg)
self.save_json()
return
model = self.neutralize(model = model)
sctr_keys = model.get_xray_structure().scattering_type_registry().type_count_dict()
has_hd = "H" in sctr_keys or "D" in sctr_keys
#exclude = ["common_amino_acid", "modified_amino_acid", "common_rna_dna",
# "modified_rna_dna", "ccp4_mon_lib_rna_dna", "common_water",
# "common_element", "common_small_molecule"]
exclude = ["common_amino_acid", "common_rna_dna",
"ccp4_mon_lib_rna_dna", "common_water",
"common_element"]
ph = model.get_hierarchy()
self.pickle_data.chain_dict = ph.overall_counts().chain_ids
ligands = []
needs_cif = False
get_class = iotbx.pdb.common_residue_names_get_class
n_removed = 0
n_removed_total = 0
for chain in ph.chains():
for rg in chain.residue_groups():
for resname in rg.unique_resnames():
if (not get_class(name=resname) in exclude):
if has_hd and not self.params.add_hydrogen:
n_removed = self.remove_hd_on_ligands(residue_group = rg)
if n_removed > 0:
print('Ligand %s has H atoms. %s were removed.' % (resname, n_removed),
file=self.logger)
if (resname == 'UNK'): continue
if (resname == 'UNL'): continue
if (resname == 'UNX'): continue
# if (resname == 'IOD'): continue
# if (resname == ' I'): continue
# if (resname == 'NCO'): continue
if resname not in ligands:
ligands.append(resname)
needs_cif = True
n_removed_total = n_removed_total + n_removed
# save new model if ligands have H atoms
if n_removed_total > 0:
print('Model has ligands with H atoms. Removed %s H atoms in total.' % n_removed_total, file=self.logger)
new_fn = os.path.splitext(os.path.basename(self.json_data['pdb_file_updated']))[0] + '_trim.pdb'
new_pdb_fn = os.path.join(self.dest_dir, new_fn)
pdb_str = model.model_as_pdb()
with open(new_pdb_fn, 'w') as fp:
fp.write(pdb_str)
#ph.write_pdb_file(new_pdb_fn)
self.json_data['pdb_file_updated'] = new_pdb_fn
print('New model (ligands without H atoms) saved to %s' % new_fn, file=self.logger)
# Use the neutralized file where ligand H have been removed (if present)
fn = self.json_data['pdb_file_updated']
if needs_cif:
print('Ligands found in the input model:', file=self.logger)
for ligand in ligands:
print(ligand, file=self.logger)
print('Run ready_set using %s ...' % os.path.basename(fn), file=self.logger)
self.run_ready_set()
else:
print('No ligands found', file=self.logger)
if self.params.add_hydrogen:
print('Add hydrogens.', file=self.logger)
print('Run ready_set using %s ...' % os.path.basename(fn), file=self.logger)
self.run_ready_set()
else:
self.json_data['success_readyset'] = True
def exercise_2(eps = 1.e-6):
###> Get started from PDB
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/phe_abc_tlsanl_out_geometry_minimized.pdb",
test=os.path.isfile)
model = mmtbx.model.manager(
model_input=iotbx.pdb.input(file_name=pdb_file),
build_grm=True)
model.setup_scattering_dictionaries(scattering_table="wk1995")
model.get_xray_structure().convert_to_isotropic()
u_iso_start = model.get_xray_structure().extract_u_iso_or_u_equiv()
model.get_xray_structure().convert_to_anisotropic()
selections = []
selection_strings = ["chain A", "chain B", "chain C"]
for string in selection_strings:
selections.append(model.selection(string = string))
################
selection = flex.bool(model.get_number_of_atoms(), True)
class refinement_flags: pass
refinement_flags.adp_tls = selections
model.set_refinement_flags(refinement_flags)
model.determine_tls_groups(selection_strings=selections, generate_tlsos=selections)
model.set_refinement_flags(refinement_flags)
xray_structure = model.get_xray_structure()
################
###> Get TLS <-> Ucart
T_initial = []
L_initial = []
S_initial = []
T_initial.append([0.11,0.22,0.33,0.12,0.13,0.23])
L_initial.append([1.11,1.22,1.33,1.12,1.13,1.23])
S_initial.append([0.11,0.12,0.13,0.21,0.22,0.23,0.31,0.32,-0.33])
T_initial.append([0.22,0.44,0.66,0.24,0.26,0.46])
L_initial.append([2.22,2.44,2.66,2.24,2.26,2.46])
S_initial.append([0.22,0.24,0.26,0.42,0.44,0.46,0.62,0.64,-0.66])
T_initial.append([0.33,0.66,0.99,0.36,0.39,0.69])
L_initial.append([2.33,2.66,2.99,2.36,2.39,2.69])
S_initial.append([0.22,0.24,0.26,0.42,0.44,0.46,0.62,0.64,-0.66])
tlsosA = tools.generate_tlsos(selections = selections,
xray_structure = xray_structure,
T = T_initial,
L = L_initial,
S = S_initial)
tlsos = tools.generate_tlsos(selections = selections,
xray_structure = xray_structure,
T = T_initial,
L = L_initial,
S = S_initial)
tlsos = tools.make_tlso_compatible_with_u_positive_definite(
tlsos = tlsos,
xray_structure = xray_structure.deep_copy_scatterers(),
selections = selections,
max_iterations = 50,
number_of_u_nonpositive_definite = 0,
eps = eps,
number_of_macro_cycles_for_tls_from_uanisos = 30)
u_cart_answer = tools.u_cart_from_tls(sites_cart = xray_structure.sites_cart(),
selections = selections,
tlsos = tlsos)
xray_structure.scatterers().set_u_cart(xray_structure.unit_cell(),
u_cart_answer)
assert approx_equal(u_cart_answer,
xray_structure.scatterers().extract_u_cart(xray_structure.unit_cell()))
tools.show_tls(tlsos = tlsos, text = "ANSWER")
###> Set up fmodel
sfg_params = mmtbx.f_model.sf_and_grads_accuracy_master_params.extract()
sfg_params.algorithm = "direct"
sfg_params.cos_sin_table = False
dummy = xray_structure.structure_factors(algorithm = sfg_params.algorithm,
d_min = 2.0).f_calc()
f_obs = abs(dummy.structure_factors_from_scatterers(
xray_structure = xray_structure,
algorithm = sfg_params.algorithm,
cos_sin_table = sfg_params.cos_sin_table).f_calc())
flags = f_obs.generate_r_free_flags(fraction=0.01, max_free=2000)
fmodel = mmtbx.f_model.manager(xray_structure = xray_structure,
f_obs = f_obs,
r_free_flags = flags,
target_name = "ls_wunit_k1",
sf_and_grads_accuracy_params = sfg_params)
fmodel.info(free_reflections_per_bin=250, max_number_of_bins=30).show_all()
xray_structure.convert_to_isotropic()
xray_structure.set_b_iso(value = 25.0)
fmodel.update_xray_structure(xray_structure = xray_structure,
update_f_calc = True)
fmodel.info(free_reflections_per_bin=250, max_number_of_bins=30).show_all()
print("*"*80)
###> TLS refinement against xray data
if (not "--comprehensive" in sys.argv[1:]):
number_of_macro_cycles = 1
max_number_of_iterations = 3
else:
number_of_macro_cycles = 100
max_number_of_iterations = 50
for start_tls_value in [None]:#[0.0, tlsosA, None]:
#for start_tls_value in [None]:
print(" \n "+str(start_tls_value) + " \n ")
fmodel_cp = fmodel.deep_copy()
#for sc in fmodel_cp.xray_structure.scatterers():
# sc.flags.set_use_u_aniso(True)
fmodel_cp.xray_structure.convert_to_anisotropic()
if(start_tls_value is None):
run_finite_differences_test = True
else: run_finite_differences_test = False
model.set_xray_structure(fmodel_cp.xray_structure)
tls_refinement_manager = tools.tls_refinement(
fmodel = fmodel_cp,
model = model,
selections = selections,
selections_1d = None,
refine_T = 1,
refine_L = 1,
refine_S = 1,
number_of_macro_cycles = number_of_macro_cycles,
max_number_of_iterations = max_number_of_iterations,
start_tls_value = start_tls_value,
run_finite_differences_test = run_finite_differences_test,
eps = eps)
u_cart = tls_refinement_manager.fmodel.xray_structure.scatterers().extract_u_cart(
xray_structure.unit_cell())
if("--comprehensive" in sys.argv[1:]):
format = "%10.6f %10.6f %10.6f %10.6f %10.6f %10.6f"
counter = 0
if(start_tls_value == tlsosA): tolerance = 1.e-6
else: tolerance = 0.02
for m1,m2 in zip(u_cart_answer, u_cart):
counter += 1
if(counter < 10):
print("1=" + format % (m1[0],m1[1],m1[2],m1[3],m1[4],m1[5]))
print("2=" + format % (m2[0],m2[1],m2[2],m2[3],m2[4],m2[5]))
assert approx_equal(m1,m2, tolerance)
def run(args, out=None, log=sys.stdout):
if (len(args) == 0) or (args == ["--help"]):
print(msg, file=log)
defaults(log=log, silent=False)
return
parsed = defaults(log=log, silent=True)
#
processed_args = utils.process_command_line_args(args=args,
log=log,
master_params=parsed)
params = processed_args.params.extract()
#
reflection_files = processed_args.reflection_files
if (len(reflection_files) == 0):
raise Sorry("No reflection file found.")
crystal_symmetry = processed_args.crystal_symmetry
if (crystal_symmetry is None):
raise Sorry("No crystal symmetry found.")
if (len(processed_args.pdb_file_names) == 0):
raise Sorry("No PDB file found.")
pdb_file_names = processed_args.pdb_file_names
#
rfs = reflection_file_server(crystal_symmetry=crystal_symmetry,
reflection_files=reflection_files)
parameters = extract_xtal_data.data_and_flags_master_params().extract()
if (params.f_obs_label is not None):
parameters.labels = params.f_obs_label
if (params.r_free_flags_label is not None):
parameters.r_free_flags.label = params.r_free_flags_label
if (params.high_resolution is not None):
parameters.high_resolution = params.high_resolution
determine_data_and_flags_result = extract_xtal_data.run(
reflection_file_server=rfs,
parameters=parameters,
data_parameter_scope="refinement.input.xray_data",
flags_parameter_scope="refinement.input.xray_data.r_free_flags",
data_description="X-ray data",
keep_going=True,
log=StringIO())
f_obs = determine_data_and_flags_result.f_obs
# Data
show_header(l="Data:", log=log)
f_obs.show_comprehensive_summary(prefix=" ", f=log)
# R-free-flags
show_header(l="R-free-flags:", log=log)
r_free_flags = determine_data_and_flags_result.r_free_flags
test_flag_value = determine_data_and_flags_result.test_flag_value
if (r_free_flags is None):
r_free_flags = f_obs.array(data=flex.bool(f_obs.data().size(), False))
test_flag_value = None
print(" not available", file=log)
else:
print(" flag value:", test_flag_value, file=log)
# Model
pdb_combined = iotbx.pdb.combine_unique_pdb_files(
file_names=processed_args.pdb_file_names)
pdb_combined.report_non_unique(out=log)
if (len(pdb_combined.unique_file_names) == 0):
raise Sorry("No coordinate file given.")
raw_records = pdb_combined.raw_records
try:
pdb_inp = iotbx.pdb.input(source_info=None,
lines=flex.std_string(raw_records))
except ValueError as e:
raise Sorry("Model format (PDB or mmCIF) error:\n%s" % str(e))
model = mmtbx.model.manager(model_input=pdb_inp,
crystal_symmetry=crystal_symmetry,
log=StringIO())
#
scattering_table = params.scattering_table
exptl_method = pdb_inp.get_experiment_type()
if (exptl_method is not None) and ("NEUTRON" in exptl_method):
scattering_table = "neutron"
model.setup_scattering_dictionaries(scattering_table=scattering_table,
d_min=f_obs.d_min())
#
# Model vs data
#
show_header(l="Model vs Data:", log=log)
fmodel = mmtbx.f_model.manager(xray_structure=model.get_xray_structure(),
f_obs=f_obs,
r_free_flags=r_free_flags,
twin_law=params.twin_law)
fmodel.update_all_scales(update_f_part1=True)
fmodel.show(log=log, show_header=False, show_approx=False)
print(" r_work: %6.4f" % fmodel.r_work(), file=log)
if (test_flag_value is not None):
print(" r_free: %6.4f" % fmodel.r_free(), file=log)
else:
print(" r_free: None", file=log)
print(file=log)
n_outl = f_obs.data().size() - fmodel.f_obs().data().size()
print(" Number of F-obs outliers:", n_outl, file=log)
#
# Extract information from PDB file header and output (if any)
#
pub_r_work = None
pub_r_free = None
pub_high = None
pub_low = None
pub_sigma = None
pub_program_name = None
pub_solv_cont = None
pub_matthews = None
published_results = pdb_inp.get_r_rfree_sigma(file_name=pdb_file_names[0])
if (published_results is not None):
pub_r_work = published_results.r_work
pub_r_free = published_results.r_free
pub_high = published_results.high
pub_low = published_results.low
pub_sigma = published_results.sigma
pub_program_name = pdb_inp.get_program_name()
pub_solv_cont = pdb_inp.get_solvent_content()
pub_matthews = pdb_inp.get_matthews_coeff()
#
show_header(l="Information extracted from PDB file header:", log=log)
print(" program_name : %-s" % format_value("%s", pub_program_name),
file=log)
print(" year : %-s" %
format_value("%s", pdb_inp.extract_header_year()),
file=log)
print(" r_work : %-s" % format_value("%s", pub_r_work), file=log)
print(" r_free : %-s" % format_value("%s", pub_r_free), file=log)
print(" high_resolution : %-s" % format_value("%s", pub_high), file=log)
print(" low_resolution : %-s" % format_value("%s", pub_low), file=log)
print(" sigma_cutoff : %-s" % format_value("%s", pub_sigma), file=log)
print(" matthews_coeff : %-s" % format_value("%s", pub_matthews),
file=log)
print(" solvent_cont : %-s" % format_value("%s", pub_solv_cont),
file=log)
if (exptl_method is not None):
print(" exptl_method : %-s" % format_value("%s", exptl_method),
file=log)
#
# Recompute R-factors using published cutoffs
fmodel_cut = fmodel
tmp_sel = flex.bool(fmodel.f_obs().data().size(), True)
if (pub_sigma is not None and fmodel.f_obs().sigmas() is not None):
tmp_sel &= fmodel.f_obs().data() > fmodel.f_obs().sigmas() * pub_sigma
if (pub_high is not None
and abs(pub_high - fmodel.f_obs().d_min()) > 0.03):
tmp_sel &= fmodel.f_obs().d_spacings().data() > pub_high
if (pub_low is not None
and abs(pub_low - fmodel.f_obs().d_max_min()[0]) > 0.03):
tmp_sel &= fmodel.f_obs().d_spacings().data() < pub_low
if (tmp_sel.count(True) != tmp_sel.size() and tmp_sel.count(True) > 0):
show_header(l="After applying resolution and sigma cutoffs:", log=log)
fmodel = mmtbx.f_model.manager(
xray_structure=model.get_xray_structure(),
f_obs=fmodel.f_obs().select(tmp_sel),
r_free_flags=fmodel.r_free_flags().select(tmp_sel),
twin_law=params.twin_law)
fmodel.update_all_scales(update_f_part1=True)
fmodel.show(log=log, show_header=False, show_approx=False)
print(" r_work: %6.4f" % fmodel.r_work(), file=log)
if (test_flag_value is not None):
print(" r_free: %6.4f" % fmodel.r_free(), file=log)
else:
print(" r_free: None", file=log)
print(file=log)
n_outl = f_obs.data().size() - fmodel.f_obs().data().size()
print(" Number of F-obs outliers:", n_outl, file=log)
def run(args, log=sys.stdout):
if (len(args) == 0):
print >> log, legend
defaults(log=log)
return
#
parsed = defaults(log=log)
processed_args = mmtbx.utils.process_command_line_args(
args=args, log=sys.stdout, master_params=parsed)
params = processed_args.params.extract()
reflection_files = processed_args.reflection_files
if (len(reflection_files) == 0):
if (params.hkl_file is None):
raise Sorry("No reflection file found.")
else:
hkl_in = file_reader.any_file(params.hkl_file, force_type="hkl")
hkl_in.assert_file_type("hkl")
reflection_files = [hkl_in.file_object]
crystal_symmetry = processed_args.crystal_symmetry
if (crystal_symmetry is None):
if (params.space_group is not None) and (params.unit_cell is not None):
from cctbx import crystal
crystal_symmetry = crystal.symmetry(
space_group_info=params.space_group,
unit_cell=params.unit_cell)
else:
raise Sorry("No crystal symmetry found.")
if (len(processed_args.pdb_file_names) == 0):
if (params.pdb_file is None):
raise Sorry("No model file found.")
else:
pdb_file_names = [params.pdb_file]
else:
pdb_file_names = processed_args.pdb_file_names
#
rfs = reflection_file_utils.reflection_file_server(
crystal_symmetry=crystal_symmetry,
force_symmetry=True,
reflection_files=reflection_files,
err=StringIO())
parameters = mmtbx.utils.data_and_flags_master_params().extract()
parameters.labels = params.f_obs_label
parameters.r_free_flags.label = params.r_free_flags_label
determine_data_and_flags_result = mmtbx.utils.determine_data_and_flags(
reflection_file_server=rfs,
parameters=parameters,
keep_going=True,
log=StringIO())
f_obs = determine_data_and_flags_result.f_obs
print "Input data:"
print " Iobs or Fobs:", f_obs.info().labels
r_free_flags = determine_data_and_flags_result.r_free_flags
print " Free-R flags:", r_free_flags.info().labels
#
parameters = mmtbx.utils.experimental_phases_params.extract()
parameters.labels = params.hendrickson_lattman_coefficients_label
experimental_phases_result = mmtbx.utils.determine_experimental_phases(
reflection_file_server=rfs,
parameters=parameters,
log=StringIO(),
parameter_scope="",
working_point_group=None,
symmetry_safety_check=True,
ignore_all_zeros=True)
if (experimental_phases_result is not None):
print " HL coefficients:", experimental_phases_result.info().labels
experimental_phases = extract_experimental_phases(
experimental_phases=experimental_phases_result, f_obs=f_obs)
#
if (r_free_flags is None):
r_free_flags = f_obs.array(data=flex.bool(f_obs.data().size(), False))
#
pdb_inp = mmtbx.utils.pdb_inp_from_multiple_files(pdb_file_names,
log=sys.stdout)
model = mmtbx.model.manager(model_input=pdb_inp,
process_input=False,
crystal_symmetry=crystal_symmetry,
log=sys.stdout)
if (model.get_number_of_models() > 1): #XXX support multi-models
raise Sorry("Multiple model file not supported in this tool.")
# XXX Twining not supported
xray_structure = model.get_xray_structure()
if (not xray_structure.unit_cell().is_similar_to(f_obs.unit_cell())):
raise Sorry(
"The unit cells in the model and reflections files are not " +
"isomorphous.")
print "Input model:"
print " number of atoms:", xray_structure.scatterers().size()
fmodel = mmtbx.f_model.manager(xray_structure=xray_structure,
r_free_flags=r_free_flags,
f_obs=f_obs,
abcd=experimental_phases)
fmodel.update_all_scales(
update_f_part1=True,
remove_outliers=params.remove_f_obs_outliers,
bulk_solvent_and_scaling=params.bulk_solvent_and_scaling)
print "Overall statistics:"
fmodel.info().show_all()
#
print "Output data:"
if (params.output_file_name is not None):
output_file_name = params.output_file_name
else:
pdb_file_bn = os.path.basename(pdb_file_names[0])
hkl_file_bn = os.path.basename(reflection_files[0].file_name())
try:
pdb_file_prefix = pdb_file_bn[:pdb_file_bn.index(".")]
except ValueError:
pdb_file_prefix = pdb_file_bn
try:
hkl_file_prefix = hkl_file_bn[:hkl_file_bn.index(".")]
except ValueError:
hkl_file_prefix = hkl_file_bn
output_file_name = "%s_%s.mtz" % (pdb_file_prefix, hkl_file_prefix)
print " file name:", output_file_name
print " to see the contnt of %s:" % output_file_name
print " phenix.mtz.dump %s" % output_file_name
out = open(output_file_name, "w")
fmodel.export(out=out)
out.close()
print "All done."
return output_file_name
def run(args, command_name="phenix.tls"):
if (len(args) == 0): args = ["--help"]
usage_fmt = "%s pdb_file [parameters: file or command line string]"
des_fmt = "Example: %s model.pdb fit_tls_to.selection='%s' fit_tls_to.selection='%s'"
command_line = (iotbx_option_parser(
usage=usage_fmt % command_name, description=banner).option(
"--show_defaults",
action="store_true",
help="Do not output to the screen (except errors).").option(
"--silent",
action="store_true",
help="Suppress output to the screen.")).process(args=args)
#
log = sys.stdout
if (not command_line.options.silent):
utils.print_header("TLS tools", out=log)
if (command_line.options.show_defaults):
master_params.show(out=log)
print(file=log)
return
if (not command_line.options.silent):
print(banner, file=log)
#
processed_args = utils.process_command_line_args(
args=command_line.args, master_params=master_params, log=log)
reflection_files = processed_args.reflection_files
if (processed_args.crystal_symmetry is None):
raise Sorry("No crystal symmetry found.")
if (len(processed_args.pdb_file_names) == 0):
raise Sorry("No PDB file found.")
params = processed_args.params
if (not command_line.options.silent):
utils.print_header("Input parameters", out=log)
params.show(out=log)
params = params.extract()
#
if (processed_args.crystal_symmetry.unit_cell() is None
or processed_args.crystal_symmetry.space_group() is None):
raise Sorry("No CRYST1 record found.")
pdb_combined = iotbx.pdb.combine_unique_pdb_files(
file_names=processed_args.pdb_file_names)
pdb_combined.report_non_unique(out=log)
if (len(pdb_combined.unique_file_names) == 0):
raise Sorry("No coordinate file given.")
raw_records = pdb_combined.raw_records
try:
pdb_inp = iotbx.pdb.input(source_info=None,
lines=flex.std_string(raw_records))
except ValueError as e:
raise Sorry("Model format (PDB or mmCIF) error:\n%s" % str(e))
model = mmtbx.model.manager(
model_input=pdb_inp,
restraint_objects=processed_args.cif_objects,
crystal_symmetry=processed_args.crystal_symmetry,
log=log)
if (not command_line.options.silent):
utils.print_header("TLS groups from PDB file header", out=log)
pdb_inp_tls = mmtbx.tls.tools.tls_from_pdb_inp(
remark_3_records=model._model_input.extract_remark_iii_records(3),
pdb_hierarchy=model.get_hierarchy())
#
tls_groups = []
if (pdb_inp_tls.tls_present):
if (pdb_inp_tls.error_string is not None):
raise Sorry(pdb_inp_tls.error_string)
pdb_tls = mmtbx.tls.tools.extract_tls_from_pdb(pdb_inp_tls=pdb_inp_tls,
model=model)
tls_groups = pdb_tls.pdb_inp_tls.tls_params
#
tls_selections_strings = []
#
if (len(tls_groups) == 0 and not command_line.options.silent):
print("No TLS groups found in PDB file header.", file=log)
else:
for i_seq, tls_group in enumerate(tls_groups):
tls_selections_strings.append(tls_group.selection_string)
if (not command_line.options.silent):
print("TLS group %d: %s" %
(i_seq + 1, tls_group.selection_string),
file=log)
mmtbx.tls.tools.show_tls_one_group(tlso=tls_group, out=log)
print(file=log)
#
if (len(tls_selections_strings) > 0 and len(params.selection) > 0):
raise Sorry(
"Two TLS selection sources found: PDB file header and parameters.")
if (len(params.selection) > 0):
tls_selections_strings = params.selection
if ([params.combine_tls, params.extract_tls].count(True) > 1):
raise Sorry(
"Cannot simultaneously pereform: combine_tls and extract_tls")
if ([params.combine_tls, params.extract_tls].count(True) > 0):
if (len(tls_selections_strings) == 0):
raise Sorry("No TLS selections found.")
#
if (len(tls_selections_strings)):
if (not command_line.options.silent):
utils.print_header("TLS groups selections", out=log)
selections = utils.get_atom_selections(
model=model, selection_strings=tls_selections_strings)
if (not command_line.options.silent):
print("Number of TLS groups: ", len(selections), file=log)
print("Number of atoms: %d" % model.get_number_of_atoms(),
file=log)
n_atoms_in_tls = 0
for sel_a in selections:
n_atoms_in_tls += sel_a.size()
if (not command_line.options.silent):
print("Number of atoms in TLS groups: %d" % n_atoms_in_tls,
file=log)
print(file=log)
assert len(tls_selections_strings) == len(selections)
if (not command_line.options.silent):
for sel_a, sel_s in zip(selections, tls_selections_strings):
print("Selection string:\n%s" % sel_s, file=log)
print("selects %d atoms." % sel_a.size(), file=log)
print(file=log)
print("Ready-to-use in phenix.refine:\n", file=log)
for sel_a, sel_s in zip(selections, tls_selections_strings):
print(sel_s, file=log)
#
ofn = params.output_file_name
if (ofn is None):
ofn = os.path.splitext(
os.path.basename(processed_args.pdb_file_names[0]))[0]
if (len(processed_args.pdb_file_names) > 1):
ofn = ofn + "_el_al"
if (params.combine_tls):
ofn = ofn + "_combine_tls.pdb"
elif (params.extract_tls):
ofn = ofn + "_extract_tls.pdb"
else:
ofn = None
if (ofn is not None):
ofo = open(ofn, "w")
#
if (params.extract_tls):
utils.print_header(
"Fit TLS matrices to B-factors of selected sets of atoms", out=log)
tlsos = mmtbx.tls.tools.generate_tlsos(
selections=selections,
xray_structure=model.get_xray_structure(),
value=0.0)
for rt, rl, rs in [[1, 0, 1], [1, 1, 1], [0, 1, 1], [1, 0, 0],
[0, 1, 0], [0, 0, 1], [1, 1, 1], [0, 0, 1]] * 10:
tlsos = mmtbx.tls.tools.tls_from_uanisos(
xray_structure=model.get_xray_structure(),
selections=selections,
tlsos_initial=tlsos,
number_of_macro_cycles=10,
max_iterations=100,
refine_T=rt,
refine_L=rl,
refine_S=rs,
enforce_positive_definite_TL=params.
enforce_positive_definite_TL,
verbose=-1,
out=log)
mmtbx.tls.tools.show_tls(tlsos=tlsos, out=log)
u_cart_from_tls = mmtbx.tls.tools.u_cart_from_tls(
sites_cart=model.get_sites_cart(),
selections=selections,
tlsos=tlsos)
unit_cell = model.get_xray_structure().unit_cell()
for i_seq, sc in enumerate(model.get_xray_structure().scatterers()):
if (u_cart_from_tls[i_seq] != (0, 0, 0, 0, 0, 0)):
u_star_tls = adptbx.u_cart_as_u_star(
unit_cell, tuple(u_cart_from_tls[i_seq]))
sc.u_star = tuple(
flex.double(sc.u_star) - flex.double(u_star_tls))
for sel in selections:
model.get_xray_structure().convert_to_isotropic(selection=sel)
mmtbx.tls.tools.remark_3_tls(tlsos=tlsos,
selection_strings=tls_selections_strings,
out=ofo)
#
if (params.combine_tls):
utils.print_header("Combine B_tls with B_residual", out=log)
mmtbx.tls.tools.combine_tls_and_u_local(
xray_structure=model.get_xray_structure(),
tls_selections=selections,
tls_groups=tls_groups)
print("All done.", file=log)
#
if (ofn is not None):
utils.print_header("Write output PDB file %s" % ofn, out=log)
model.set_sites_cart_from_xrs()
pdb_str = model.model_as_pdb()
ofo.write(pdb_str)
ofo.close()
print("All done.", file=log)
def __init__(self,
model,
target_map,
refine_ncs_operators=False,
number_of_cycles=1,
cycles_to_converge=2,
log=None):
# completely new way of doing this. using RSR macro-cycle
# for test compatibility:
print("Minimizing using reference map...", file=log)
if model.ncs_constraints_present():
print(" Minimizing... (NCS)", file=log)
else:
print(" Minimizing...", file=log)
from phenix.refinement.macro_cycle_real_space import run as rsr_mc_run
import scitbx.math
from phenix.command_line.real_space_refine import extract_rigid_body_selections
from phenix.command_line.real_space_refine import master_params as rsr_master_params
from mmtbx.refinement.real_space.utils import target_map as rsr_target_map
import mmtbx.idealized_aa_residues.rotamer_manager
sin_cos_table = scitbx.math.sin_cos_table(n=10000)
params = rsr_master_params().extract()
params.pdb_interpretation = model._pdb_interpretation_params.pdb_interpretation
params.refinement.run = "minimization_global+local_grid_search"
params.refine_ncs_operators = False
params.output.write_all_states = True
rotamer_manager = mmtbx.idealized_aa_residues.rotamer_manager.load(
rotamers="favored")
rigid_body_selections = extract_rigid_body_selections(
params=params,
ncs_groups=model.get_ncs_groups(),
pdb_hierarchy=model.get_hierarchy())
rsr_tm = rsr_target_map(map_data=target_map,
xray_structure=model.get_xray_structure(),
d_min=3.8,
atom_radius=params.refinement.atom_radius)
res = rsr_mc_run(params=params,
model=model,
target_map=rsr_tm,
log=log,
ncs_groups=model.get_ncs_groups(),
rotamer_manager=rotamer_manager,
sin_cos_table=sin_cos_table,
rigid_body_selections=rigid_body_selections)
model.set_sites_cart_from_hierarchy(res.model.get_hierarchy())
res.structure_monitor.states_collector.write(
file_name="rsr_all_states.pdb")
return
# end ===================================================
from mmtbx.refinement.geometry_minimization import add_rotamer_restraints
from mmtbx.refinement.minimization_monitor import minimization_monitor
self.model = model
self.log = log
print("Minimizing using reference map...", file=self.log)
self.log.flush()
# copy-paste from cctbx_project/mmtbx/refinement/geometry_minimization.py:
# minimize_wrapper_for_ramachandran
self.model.get_restraints_manager().geometry.pair_proxies(
sites_cart=self.model.get_sites_cart())
ncs_restraints_group_list = self.model.get_ncs_groups()
if ncs_restraints_group_list is None:
ncs_restraints_group_list = []
ncs_groups = None
if len(ncs_restraints_group_list) > 0:
ncs_groups = ncs_restraints_group_list
min_monitor = minimization_monitor(
number_of_cycles=number_of_cycles,
max_number_of_cycles=20,
cycles_to_converge=cycles_to_converge,
mode="no_outliers")
selection_real_space = None
import mmtbx.refinement.real_space.weight
self.w = 1
print("number_of_cycles", number_of_cycles, file=log)
print("Stats before minimization:", file=log)
ms = self.model.geometry_statistics()
ms.show(log=log)
while min_monitor.need_more_cycles():
print("Cycle number",
min_monitor.get_current_cycle_n(),
file=self.log)
self.model.get_restraints_manager().geometry.\
update_ramachandran_restraints_phi_psi_targets(
hierarchy=self.model.get_hierarchy())
print(" Updating rotamer restraints...", file=self.log)
add_rotamer_restraints(
pdb_hierarchy=self.model.get_hierarchy(),
restraints_manager=self.model.get_restraints_manager(),
selection=None,
sigma=5,
mode="fix_outliers",
accept_allowed=False,
mon_lib_srv=self.model.get_mon_lib_srv(),
rotamer_manager=self.model.get_rotamer_manager())
self.model.set_sites_cart_from_hierarchy()
if min_monitor.need_weight_optimization():
# if self.w is None:
print(" Determining weight...", file=self.log)
self.log.flush()
self.weight = mmtbx.refinement.real_space.weight.run(
map_data=target_map,
xray_structure=self.model.get_xray_structure(),
pdb_hierarchy=self.model.get_hierarchy(),
geometry_restraints_manager=self.model.
get_restraints_manager(),
rms_bonds_limit=0.015,
rms_angles_limit=1.0,
ncs_groups=ncs_groups)
# division is to put more weight onto restraints. Checked. Works.
self.w = self.weight.weight / 3.0
# self.w = self.weight.weight/15.0
# self.w = 0
# self.w = self.weight.weight
for s in self.weight.msg_strings:
print(s, file=self.log)
if ncs_restraints_group_list is None or len(
ncs_restraints_group_list) == 0:
#No NCS
print(" Minimizing...", file=self.log)
print(" with weight %f" % self.w, file=self.log)
self.log.flush()
refine_object = simple(
target_map=target_map,
selection=None,
max_iterations=150,
geometry_restraints_manager=self.model.
get_restraints_manager().geometry,
selection_real_space=selection_real_space,
states_accumulator=None,
ncs_groups=ncs_groups)
refine_object.refine(
weight=self.w,
xray_structure=self.model.get_xray_structure())
self.rmsd_bonds_final, self.rmsd_angles_final = refine_object.rmsds(
)
print("RMSDS:",
self.rmsd_bonds_final,
self.rmsd_angles_final,
file=log)
# print >> log, "sizes:", len(refine_object.sites_cart()), len(self.xrs.scatterers())
self.model.set_sites_cart(refine_object.sites_cart(),
update_grm=True)
# print >> log, "sizes", self.xrs.scatterers()
else:
# Yes NCS
# copy-paste from macro_cycle_real_space.py
# !!! Don't rearrange NCS groups here because master was just fixed!
# import mmtbx.ncs.ncs_utils as nu
# nu.get_list_of_best_ncs_copy_map_correlation(
# ncs_groups = ncs_restraints_group_list,
# xray_structure = self.model.get_xray_structure(),
# map_data = target_map,
# d_min = 3)
print(" Minimizing... (NCS)", file=self.log)
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_real_space(
map_data = target_map,
xray_structure = self.model.get_xray_structure(),
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = None,
real_space_gradients_delta = 1,
restraints_manager = self.model.get_restraints_manager(),
data_weight = self.w,
refine_sites = True)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object=tfg_obj,
xray_structure=self.model.get_xray_structure(),
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=None,
finite_grad_differences_test=False,
max_iterations=100,
refine_sites=True)
self.model.set_sites_cart(tfg_obj.xray_structure.sites_cart())
ncs_restraints_group_list.recalculate_ncs_transforms(
self.model.get_sites_cart())
ms = self.model.geometry_statistics()
min_monitor.save_cycle_results(geometry=ms)
ms.show(log=log)
def exercise_bond_over_symmetry_2(mon_lib_srv, ener_lib):
""" This test is to illustrate that bond over symmetry actually
adds 2 proxies.
"""
from cctbx.geometry_restraints.linking_class import linking_class
origin_ids = linking_class()
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records10)
params = mmtbx.model.manager.get_default_pdb_interpretation_params()
params.pdb_interpretation.restraints_library.mcl = False
model = mmtbx.model.manager(model_input=pdb_inp,
pdb_interpretation_params=params,
log=null_out(),
build_grm=True)
grm = model.get_restraints_manager().geometry
simple, asu = grm.get_all_bond_proxies()
assert (simple.size(), asu.size()) == (0, 0)
h = model.get_hierarchy()
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="")
outtxt = out.getvalue()
# print(outtxt)
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=(0, 1),
distance_ideal=2.9,
weight=400,
origin_id=origin_ids.get_origin_id('hydrogen bonds'))
grm.add_new_bond_restraints_in_place(proxies=[proxy],
sites_cart=h.atoms().extract_xyz())
simple, asu = grm.get_all_bond_proxies()
# print(simple.size(), asu.size())
assert (simple.size(), asu.size()) == (0, 2)
sites_cart = h.atoms().extract_xyz()
site_labels = model.get_xray_structure().scatterers().extract_labels()
pair_proxies = grm.pair_proxies(flags=None, sites_cart=sites_cart)
out = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
f=out,
prefix="")
outtxt = out.getvalue()
# print(outtxt)
assert_lines_in_text(
outtxt, """\
bond pdb=" CA HIS A 2 "
pdb=" N MET A 1 "
ideal model delta sigma weight residual sym.op.
2.900 1.998 0.902 5.00e-02 4.00e+02 3.25e+02 x,y+1,z
bond pdb=" N MET A 1 "
pdb=" CA HIS A 2 "
ideal model delta sigma weight residual sym.op.
2.900 1.998 0.902 5.00e-02 4.00e+02 3.25e+02 x,y-1,z
""")
es = grm.energies_sites(sites_cart=sites_cart, compute_gradients=True)
out = StringIO()
es.show(f=out)
outtxt = out.getvalue()
# print(outtxt)
# do for x coordinate
# ATOM 1 N MET A 1 9.821 1.568 5.000 1.00 66.07 N
# ATOM 2 CA HIS A 2 9.946 12.171 5.357 1.00 66.55 C
# calculation is from geometry_restraints/bond.h: gradient_0()
# weight * 2 * delta_slack * d_distance_d_site_0(epsilon);
# print("X gradient:", 400*2*0.902*(9.946-9.821)) # 90
# Note that n=2 but residual sum is 325.349. 349 is chopped off in rounding in
# cctbx/geometry_restraints/__init__py, def _bond_show_sorted_impl(...)
# where %6.2e is used. in cctbx/geometry_restraints/energies.py: def show()
# %.6g is used which is showing more numbers.
assert_lines_in_text(outtxt, """\
bond_residual_sum (n=2): 325.349""")
# print("Gradients:", list(es.gradients))
# Seems that gradients were splitted in half (note the X gradient is 90 8 lines above)
assert approx_equal(
list(es.gradients),
[(45.135801792665134, -708.451544937652, 128.90784991984805),
(-45.13580179266516, 708.4515449376522, -128.90784991984813)])
def run(
pdb_filename=None,
raw_records=None,
return_formal_charges=False,
verbose=False,
):
if pdb_filename:
# Read file into pdb_input class
inp = iotbx.pdb.input(file_name=pdb_filename)
elif raw_records:
inp = iotbx.pdb.input(lines=raw_records, source_info='lines from PDB')
else:
assert 0
# create a model manager
from io import StringIO
log = StringIO()
default_scope = mmtbx.model.manager.get_default_pdb_interpretation_scope()
working_params = default_scope.extract()
# optional???
working_params.pdb_interpretation.automatic_linking.link_metals = True
model = mmtbx.model.manager(
model_input=inp,
log=log,
)
model.process(make_restraints=True,
pdb_interpretation_params=working_params)
# get xray structure
xrs = model.get_xray_structure()
grm = model.get_restraints_manager()
t0 = time.time()
atom_valences = electron_distribution(
model.get_hierarchy(), # needs to be altloc free
model.get_restraints_manager().geometry,
verbose=verbose,
)
if verbose: print(atom_valences)
total_charge = atom_valences.get_total_charge()
#print 'total_charge',total_charge
#print 'time %0.1f' % (time.time()-t0)
rc = atom_valences.validate_atomic_formal_charges()
if return_formal_charges: return atom_valences
return total_charge
# get number of atoms in the input model
n_atoms = model.get_number_of_atoms()
# extract atom coordinates
old_sites_cart = model.get_sites_cart()
# generate random additions
random_addition = flex.vec3_double(
flex.random_double(size=n_atoms * 3) - 0.5)
# actually add them to old coordinates
new_xyz = old_sites_cart + random_addition
# Update coordinates in model manager
model.set_sites_cart(sites_cart=new_xyz)
# reset B-factors (min=1, max=20)
# generate array of new B-factors
new_b = flex.random_double(size=n_atoms, factor=19) + 1
# set them in xray structure
xrs.set_b_iso(values=new_b)
# update model manager with this xray structure
model.set_xray_structure(xrs)
# output result in PDB format to the screen
print(model.model_as_pdb())
print("END")