def minimize(self):
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_xray().xray_structure,
x2 = self.model.xray_structure)
self.model.set_refine_individual_adp()
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = self.individual_adp_params.iso.max_number_of_iterations)
is_neutron_scat_table = False
if(self.all_params.main.scattering_table == "neutron"):
is_neutron_scat_table = True
minimized = minimization.lbfgs(
restraints_manager = self.model.restraints_manager,
fmodels = self.fmodels,
model = self.model,
refine_adp = True,
is_neutron_scat_table = is_neutron_scat_table,
lbfgs_termination_params = lbfgs_termination_params,
iso_restraints = self.adp_restraints_params.iso,
verbose = 0,
target_weights = self.target_weights,
h_params = self.h_params)
self.model.xray_structure = self.fmodels.fmodel_xray().xray_structure
assert minimized.xray_structure is self.model.xray_structure
utils.assert_xray_structures_equal(
x1 = minimized.xray_structure,
x2 = self.model.xray_structure)
return minimized
def collect(
self,
step,
fmodels = None,
model = None,
rigid_body_shift_accumulator = None):
from mmtbx import utils
if(model is not None): self.model = model
if(fmodels is not None): self.fmodels = fmodels
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_xray().xray_structure,
x2 = self.model.xray_structure)
self.monitor_xray.collect(
model = self.model,
fmodel = self.fmodels.fmodel_xray(),
step = step,
wilson_b = self.model.wilson_b,
rigid_body_shift_accumulator = rigid_body_shift_accumulator)
if(self.monitor_neutron is not None):
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_neutron().xray_structure,
x2 = self.model.xray_structure)
self.monitor_neutron.collect(
model = self.model,
fmodel = self.fmodels.fmodel_neutron(),
step = step,
wilson_b = self.model.wilson_b,
rigid_body_shift_accumulator = rigid_body_shift_accumulator)
def minimize(self):
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_xray().xray_structure,
x2 = self.model.xray_structure)
self.model.set_refine_individual_adp()
self.run_lbfgs()
self.model.xray_structure = self.fmodels.fmodel_xray().xray_structure
def minimize(self, ca_only=False):
pdb_hierarchy = self.model.pdb_hierarchy(sync_with_xray_structure=True)
if ca_only:
ca_selection = pdb_hierarchy.get_peptide_c_alpha_selection()
restraint_sites_cart = self.model.xray_structure.sites_cart().\
deep_copy().select(ca_selection)
restraint_selection = ca_selection
else:
restraint_sites_cart = self.model.xray_structure.sites_cart().deep_copy()
restraint_selection = pdb_hierarchy.atoms().extract_i_seq()
self.model.restraints_manager.geometry.\
add_reference_coordinate_restraints_in_place(
pdb_hierarchy=pdb_hierarchy,
selection=restraint_selection)
##### sanity check #####
assert(self.model.restraints_manager.geometry.
get_n_reference_coordinate_proxies() >= len(restraint_sites_cart))
########################
selection = self.model.selection_moving
minimized = self.model.geometry_minimization(
max_number_of_iterations = 500,
correct_special_position_tolerance=1.0,
number_of_macro_cycles = 1,
selection = selection,
bond = True,
nonbonded = True,
angle = True,
dihedral = True,
chirality = True,
planarity = True)
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_xray().xray_structure,
x2 = self.model.xray_structure)
self.model.restraints_manager.geometry.\
remove_reference_coordinate_restraints_in_place()
def try_den_weight_cartesian(self, grid_pair):
local_seed = int(self.random_seed+grid_pair[1])
flex.set_random_seed(value=local_seed)
random.seed(local_seed)
self.fmodels.fmodel_xray().xray_structure.replace_scatterers(
self.save_scatterers_local.deep_copy())
self.fmodels.update_xray_structure(
xray_structure = self.fmodels.fmodel_xray().xray_structure,
update_f_calc = True)
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_xray().xray_structure,
x2 = self.model.xray_structure)
gamma_local = grid_pair[0]
weight_local = grid_pair[1]
self.model.restraints_manager.geometry.\
den_manager.gamma = gamma_local
self.model.restraints_manager.geometry.\
den_manager.weight = weight_local
cycle = 0
self.model.restraints_manager.geometry.\
den_manager.current_cycle = cycle+1
num_den_cycles = self.model.restraints_manager.geometry.\
den_manager.num_cycles
if self.params.den.optimize and \
self.nproc != Auto and \
self.nproc > 1:
local_log = sys.stdout
elif self.params.den.optimize and \
self.nproc == 1:
if self.verbose:
local_log = self.log
else:
local_log = StringIO()
else:
local_log = self.log
print >> self.log, " ...trying gamma %f, weight %f" % (
gamma_local, weight_local)
while cycle < num_den_cycles:
print >> local_log, "DEN cycle %s" % (cycle+1)
r_free = self.fmodels.fmodel_xray().r_free()
print >> local_log, "rfree at start of SA cycle: %f" % r_free
simulated_annealing.manager(
params = self.params.simulated_annealing,
target_weights = self.target_weights,
macro_cycle = self.macro_cycle,
h_params = self.params.hydrogens,
fmodels = self.fmodels,
model = self.model,
all_params = self.params,
out = local_log)
if self.params.den.bulk_solvent_and_scale:
self.bulk_solvent_and_scale(log=local_log)
if self.params.den.refine_adp:
self.adp_refinement(log=local_log)
self.model.restraints_manager.geometry.update_dihedral_ncs_restraints(
sites_cart=self.model.xray_structure.sites_cart(),
pdb_hierarchy=self.model.pdb_hierarchy(sync_with_xray_structure=True),
log=local_log)
cycle += 1
self.model.restraints_manager.geometry.\
den_manager.current_cycle += 1
r_free = self.fmodels.fmodel_xray().r_free()
print >> local_log, "rfree at end of SA cycle: %f" % r_free
r_free = self.fmodels.fmodel_xray().r_free()
step_xray_structure = self.fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
step_eq_distances = self.model.restraints_manager.geometry.\
den_manager.get_current_eq_distances()
return (gamma_local,
weight_local,
r_free,
step_xray_structure,
step_eq_distances)
def try_den_weight_torsion(self, grid_pair):
#backup_k_rep = self.params.tardy.\
# prolsq_repulsion_function_changes.k_rep
local_seed = int(self.random_seed+grid_pair[1])
flex.set_random_seed(value=local_seed)
random.seed(local_seed)
self.fmodels.fmodel_xray().xray_structure.replace_scatterers(
self.save_scatterers_local.deep_copy())
self.fmodels.update_xray_structure(
xray_structure = self.fmodels.fmodel_xray().xray_structure,
update_f_calc = True)
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_xray().xray_structure,
x2 = self.model.xray_structure)
gamma_local = grid_pair[0]
weight_local = grid_pair[1]
self.model.restraints_manager.geometry.\
den_manager.gamma = gamma_local
self.model.restraints_manager.geometry.\
den_manager.weight = weight_local
cycle = 0
self.model.restraints_manager.geometry.\
den_manager.current_cycle = cycle+1
num_den_cycles = self.model.restraints_manager.geometry.\
den_manager.num_cycles
if self.params.den.optimize and \
self.nproc != Auto and \
self.nproc > 1:
local_log = sys.stdout
elif self.params.den.optimize and \
self.nproc == 1:
if self.verbose:
local_log = self.log
else:
local_log = StringIO()
else:
local_log = self.log
print >> self.log, " ...trying gamma %.1f, weight %.1f" % (
gamma_local, weight_local)
while cycle < num_den_cycles:
#if self.model.restraints_manager.geometry.\
# generic_restraints_manager.den_manager.current_cycle == \
# self.model.restraints_manager.geometry.\
# generic_restraints_manager.den_manager.torsion_mid_point+1:
# self.params.tardy.\
# prolsq_repulsion_function_changes.k_rep = 1.0
print >> local_log, "DEN cycle %d" % (cycle+1)
#print >> local_log, "Random seed: %d" % flex.get_random_seed()
r_free = self.fmodels.fmodel_xray().r_free()
print >> local_log, "rfree at start of SA cycle: %.4f" % r_free
print >> local_log, "k_rep = %.2f" % \
self.params.tardy.\
prolsq_repulsion_function_changes.k_rep
tardy.run(
fmodels=self.fmodels,
model=self.model,
target_weights=self.target_weights,
params=self.params.tardy,
log=local_log,
format_for_phenix_refine=True,
call_back_after_step=False)
if self.params.den.bulk_solvent_and_scale:
self.bulk_solvent_and_scale(log=local_log)
self.fmodels.fmodel_xray().xray_structure = self.model.xray_structure
if self.params.den.refine_adp:
self.adp_refinement(log=local_log)
self.model.restraints_manager.geometry.update_dihedral_ncs_restraints(
sites_cart=self.model.xray_structure.sites_cart(),
pdb_hierarchy=self.model.pdb_hierarchy(sync_with_xray_structure=True),
log=local_log)
cycle += 1
self.model.restraints_manager.geometry.\
den_manager.current_cycle += 1
r_free = self.fmodels.fmodel_xray().r_free()
print >> local_log, "rfree at end of SA cycle: %f" % r_free
r_free = self.fmodels.fmodel_xray().r_free()
step_xray_structure = self.fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
step_eq_distances = self.model.restraints_manager.geometry.\
den_manager.get_current_eq_distances()
return (gamma_local,
weight_local,
r_free,
step_xray_structure,
step_eq_distances)
def __init__(
self,
fmodels,
model,
params,
target_weights,
macro_cycle,
ncs_manager=None,
log=None):
if log is None:
log = sys.stdout
# self.ncs_manager = ncs_manager
self.nproc = params.main.nproc
if self.nproc is Auto:
self.nproc = 1
self.verbose = params.den.verbose
self.log = log
self.fmodels = fmodels
self.model = model
self.params = params
self.target_weights = target_weights
self.adp_refinement_manager = None
self.macro_cycle = macro_cycle
self.tan_b_iso_max = 0
self.random_seed = params.main.random_seed
den_manager = model.restraints_manager. \
geometry.den_manager
print_statistics.make_header("DEN refinement", out=self.log)
pdb_hierarchy = self.model.pdb_hierarchy(sync_with_xray_structure=True)
if den_manager.get_n_proxies() == 0:
print_statistics.make_sub_header(
"DEN restraint nework", out = self.log)
den_manager.build_den_proxies(pdb_hierarchy=pdb_hierarchy)
den_manager.build_den_restraints()
den_manager.show_den_summary(
sites_cart=self.model.xray_structure.sites_cart())
if den_manager.params.output_kinemage:
den_manager.output_kinemage(
self.model.xray_structure.sites_cart())
print_statistics.make_sub_header(
"coordinate minimization before annealing", out=self.log)
self.minimize(ca_only=self.params.den.minimize_c_alpha_only)
self.save_scatterers_local = fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
#DEN refinement start, turn on
if params.den.optimize:
grid = den_manager.get_optimization_grid()
print >> log, \
"Running DEN torsion optimization on %d processors..." % \
params.main.nproc
else:
grid = [(params.den.gamma, params.den.weight)]
grid_results = []
grid_so = []
if "torsion" in params.den.annealing_type:
print >> self.log, "Running torsion simulated annealing"
if ( (params.den.optimize) and
( (self.nproc is Auto) or (self.nproc > 1) )):
stdout_and_results = easy_mp.pool_map(
processes=params.main.nproc,
fixed_func=self.try_den_weight_torsion,
args=grid,
func_wrapper="buffer_stdout_stderr")
for so, r in stdout_and_results:
if (r is None):
raise RuntimeError(("DEN weight optimization failed:"+
"\n%s\nThis is a "+
"serious error; please contact [email protected].") % so)
grid_so.append(so)
grid_results.append(r)
else:
for grid_pair in grid:
result = self.try_den_weight_torsion(
grid_pair=grid_pair)
grid_results.append(result)
self.show_den_opt_summary_torsion(grid_results)
elif "cartesian" in params.den.annealing_type:
print >> self.log, "Running Cartesian simulated annealing"
if ( (params.den.optimize) and
( (self.nproc is Auto) or (self.nproc > 1) )):
stdout_and_results = easy_mp.pool_map(
processes=params.main.nproc,
fixed_func=self.try_den_weight_cartesian,
args=grid,
func_wrapper="buffer_stdout_stderr")
for so, r in stdout_and_results:
if (r is None):
raise RuntimeError(("DEN weight optimization failed:"+
"\n%s\nThis is a "+
"serious error; please contact [email protected].") % so)
grid_so.append(so)
grid_results.append(r)
else:
for grid_pair in grid:
result = self.try_den_weight_cartesian(
grid_pair=grid_pair)
grid_results.append(result)
self.show_den_opt_summary_cartesian(grid_results)
else:
raise "error in DEN annealing type"
low_r_free = 1.0
best_xray_structure = None
best_eq_distances = None
best_gamma = None
best_weight = None
best_so_i = None
for i, result in enumerate(grid_results):
cur_r_free = result[2]
if cur_r_free < low_r_free:
low_r_free = cur_r_free
best_gamma = result[0]
best_weight = result[1]
best_xray_structure = result[3]
best_eq_distances = result[4]
best_so_i = i
assert best_xray_structure is not None
if params.den.optimize:
print >> self.log, "\nbest gamma: %.1f" % best_gamma
print >> self.log, "best weight: %.1f\n" % best_weight
if params.den.verbose:
if len(grid_so) >= (best_so_i+1):
print >> self.log, "\nBest annealing results:\n"
print >> self.log, grid_so[best_so_i]
fmodels.fmodel_xray().xray_structure.replace_scatterers(
best_xray_structure.deep_copy())
fmodels.update_xray_structure(
xray_structure = fmodels.fmodel_xray().xray_structure,
update_f_calc = True)
utils.assert_xray_structures_equal(
x1 = fmodels.fmodel_xray().xray_structure,
x2 = model.xray_structure)
model.restraints_manager.geometry.\
den_manager.import_eq_distances(eq_distances=best_eq_distances)
self.model.restraints_manager.geometry.update_dihedral_ncs_restraints(
sites_cart=self.model.xray_structure.sites_cart(),
pdb_hierarchy=self.model.pdb_hierarchy(sync_with_xray_structure=True),
log=self.log)
def show_geometry(
xray_structures,
processed_pdb_file,
scattering_table,
hierarchy,
model_selections,
show_geometry_statistics,
mvd_obj,
atom_selections):
if(len(xray_structures)>1):
tmp = xray_structures[0]
for xi in xray_structures[1:]:
tmp = tmp.concatenate(xi)
xray_structures = tmp
else:
xray_structures = xray_structures[0]
##
utils.assert_xray_structures_equal(
x1 = xray_structures,
x2 = processed_pdb_file.xray_structure(),
sites = True,
adp = False,
occupancies = True)
##
hd_sel_all = xray_structures.hd_selection()
if(show_geometry_statistics):
sctr_keys = \
xray_structures.scattering_type_registry().type_count_dict().keys()
has_hd = "H" in sctr_keys or "D" in sctr_keys
geometry = processed_pdb_file.geometry_restraints_manager(
show_energies = False,
plain_pairs_radius = 5.0,
assume_hydrogens_all_missing = not has_hd)
restraints_manager_all = mmtbx.restraints.manager(
geometry = geometry,
normalization = True)
models = hierarchy.models()
geometry_statistics = []
n_residues_in_altlocs = None
for i_seq, model_selection in enumerate(model_selections):
hierarchy_i_seq = pdb.hierarchy.root()
hierarchy_i_seq.append_model(models[i_seq].detached_copy())
#
overall_counts_i_seq = hierarchy_i_seq.overall_counts()
n_residues_in_altlocs = \
overall_counts_i_seq.n_alt_conf_pure + \
overall_counts_i_seq.n_alt_conf_proper + \
overall_counts_i_seq.n_alt_conf_improper
#
resname_classes = []
for k,v in zip(overall_counts_i_seq.resname_classes.keys(),
overall_counts_i_seq.resname_classes.values()):
resname_classes.append(" ".join([k.replace("common_",""), str(v)]))
#
xray_structure = xray_structures.select(model_selection)
assert hierarchy_i_seq.atoms().size() == xray_structure.scatterers().size()
hd_sel = xray_structure.hd_selection()
def select_atom_selections(selection = model_selection,
atom_selections = atom_selections):
result = group_args()
result.all = atom_selections.all .select(selection)
result.macromolecule = atom_selections.macromolecule.select(selection)
result.solvent = atom_selections.solvent .select(selection)
result.ligand = atom_selections.ligand .select(selection)
result.backbone = atom_selections.backbone .select(selection)
result.sidechain = atom_selections.sidechain .select(selection)
return result
atom_selections_i_model = select_atom_selections(
selection = model_selection,
atom_selections = atom_selections)
if(hd_sel.count(True) > 0 and scattering_table != "neutron"):
xray_structure_stat = show_xray_structure_statistics(
xray_structure = xray_structure,
hd_sel = hd_sel,
atom_selections = atom_selections_i_model)
else:
xray_structure_stat = show_xray_structure_statistics(
xray_structure = xray_structure,
atom_selections=atom_selections_i_model)
model_statistics_geometry_macromolecule = None
model_statistics_geometry_solvent = None
model_statistics_geometry_ligand = None
model_statistics_geometry_all = None
molprobity_stats_i_seq = None
rms_b_iso_or_b_equiv_bonded = None
if(show_geometry_statistics):
# exclude hydrogens
if(hd_sel.count(True) > 0 and scattering_table != "neutron"):
xray_structure = xray_structure.select(~hd_sel)
model_selection = model_selection.select(~hd_sel)
hierarchy_i_seq = hierarchy_i_seq.select(~hd_sel)
geometry = restraints_manager_all.geometry.select(selection=~hd_sel_all)
atom_selections_i_model = select_atom_selections(selection =~hd_sel_all,
atom_selections = atom_selections_i_model)
model_selection_as_bool = flex.bool(xray_structures.scatterers().size(),
model_selection)
geometry = restraints_manager_all.geometry.select(selection =
model_selection_as_bool)
restraints_manager = mmtbx.restraints.manager(
geometry = geometry,
normalization = True)
restraints_manager.geometry.pair_proxies(sites_cart =
xray_structure.sites_cart())
###
model_statistics_geometry_all = model_statistics.geometry(
pdb_hierarchy = hierarchy_i_seq,
molprobity_scores = True,
restraints_manager = restraints_manager)
#
if(atom_selections.macromolecule.count(True)>0):
mac_sel = atom_selections_i_model.macromolecule
model_statistics_geometry_macromolecule = model_statistics.geometry(
pdb_hierarchy = hierarchy_i_seq.select(mac_sel),
molprobity_scores = True,
restraints_manager = restraints_manager.select(mac_sel))
#
if(atom_selections.solvent.count(True)>0):
sol_sel = atom_selections_i_model.solvent
model_statistics_geometry_solvent = model_statistics.geometry(
pdb_hierarchy = hierarchy_i_seq.select(sol_sel),
molprobity_scores = True,
restraints_manager = restraints_manager.select(sol_sel))
#
if(atom_selections.ligand.count(True)>0):
lig_sel = atom_selections_i_model.ligand
model_statistics_geometry_ligand = model_statistics.geometry(
pdb_hierarchy = hierarchy_i_seq.select(lig_sel),
molprobity_scores = True,
restraints_manager = restraints_manager.select(lig_sel))
###
rms_b_iso_or_b_equiv_bonded = utils.rms_b_iso_or_b_equiv_bonded(
restraints_manager = restraints_manager,
xray_structure = xray_structure)
#
molprobity_stats_i_seq = molprobity_stats(
model_statistics_geometry = model_statistics_geometry_all,
resname_classes = overall_counts_i_seq.resname_classes)
geometry_statistics.append(group_args(
n_residues_in_altlocs = n_residues_in_altlocs,
resname_classes = resname_classes,
xray_structure_stat = xray_structure_stat,
rms_b_iso_or_b_equiv_bonded = rms_b_iso_or_b_equiv_bonded,
geometry_all = model_statistics_geometry_all,
geometry_macromolecule = model_statistics_geometry_macromolecule,
geometry_solvent = model_statistics_geometry_solvent,
geometry_ligand = model_statistics_geometry_ligand,
molprobity = molprobity_stats_i_seq))
mvd_obj.collect(models = geometry_statistics)
return geometry_statistics
def try_den_weight_torsion(self, grid_pair):
#backup_k_rep = self.params.tardy.\
# prolsq_repulsion_function_changes.k_rep
local_seed = int(self.random_seed + grid_pair[1])
flex.set_random_seed(value=local_seed)
random.seed(local_seed)
self.fmodels.fmodel_xray().xray_structure.replace_scatterers(
self.save_scatterers_local.deep_copy())
self.fmodels.update_xray_structure(
xray_structure=self.fmodels.fmodel_xray().xray_structure,
update_f_calc=True)
utils.assert_xray_structures_equal(
x1=self.fmodels.fmodel_xray().xray_structure,
x2=self.model.get_xray_structure())
gamma_local = grid_pair[0]
weight_local = grid_pair[1]
self.model.restraints_manager.geometry.\
den_manager.gamma = gamma_local
self.model.restraints_manager.geometry.\
den_manager.weight = weight_local
cycle = 0
self.model.restraints_manager.geometry.\
den_manager.current_cycle = cycle+1
num_den_cycles = self.model.restraints_manager.geometry.\
den_manager.num_cycles
if self.params.den.optimize and \
self.nproc != Auto and \
self.nproc > 1:
local_log = sys.stdout
elif self.params.den.optimize and \
self.nproc == 1:
if self.verbose:
local_log = self.log
else:
local_log = StringIO()
else:
local_log = self.log
print >> self.log, " ...trying gamma %.1f, weight %.1f" % (
gamma_local, weight_local)
while cycle < num_den_cycles:
#if self.model.restraints_manager.geometry.\
# generic_restraints_manager.den_manager.current_cycle == \
# self.model.restraints_manager.geometry.\
# generic_restraints_manager.den_manager.torsion_mid_point+1:
# self.params.tardy.\
# prolsq_repulsion_function_changes.k_rep = 1.0
print >> local_log, "DEN cycle %d" % (cycle + 1)
#print >> local_log, "Random seed: %d" % flex.get_random_seed()
r_free = self.fmodels.fmodel_xray().r_free()
print >> local_log, "rfree at start of SA cycle: %.4f" % r_free
print >> local_log, "k_rep = %.2f" % \
self.params.tardy.\
prolsq_repulsion_function_changes.k_rep
tardy.run(fmodels=self.fmodels,
model=self.model,
target_weights=self.target_weights,
params=self.params.tardy,
log=local_log,
format_for_phenix_refine=True,
call_back_after_step=False)
if self.params.den.bulk_solvent_and_scale:
self.bulk_solvent_and_scale(log=local_log)
self.fmodels.fmodel_xray(
).xray_structure = self.model.get_xray_structure()
if self.params.den.refine_adp:
self.adp_refinement(log=local_log)
self.model.torsion_ncs_restraints_update(log=local_log)
cycle += 1
self.model.restraints_manager.geometry.\
den_manager.current_cycle += 1
r_free = self.fmodels.fmodel_xray().r_free()
print >> local_log, "rfree at end of SA cycle: %f" % r_free
r_free = self.fmodels.fmodel_xray().r_free()
step_xray_structure = self.fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
step_eq_distances = self.model.restraints_manager.geometry.\
den_manager.get_current_eq_distances()
return (gamma_local, weight_local, r_free, step_xray_structure,
step_eq_distances)
def __init__(self,
fmodels,
model,
params,
target_weights,
macro_cycle,
ncs_manager=None,
log=None):
if log is None:
log = sys.stdout
# self.ncs_manager = ncs_manager
self.nproc = params.main.nproc
if self.nproc is Auto:
self.nproc = 1
self.verbose = params.den.verbose
self.log = log
self.fmodels = fmodels
self.model = model
self.params = params
self.target_weights = target_weights
self.adp_refinement_manager = None
self.macro_cycle = macro_cycle
self.tan_b_iso_max = 0
self.random_seed = params.main.random_seed
den_manager = model.restraints_manager. \
geometry.den_manager
print_statistics.make_header("DEN refinement", out=self.log)
pdb_hierarchy = self.model.get_hierarchy(sync_with_xray_structure=True)
if den_manager.get_n_proxies() == 0:
print_statistics.make_sub_header("DEN restraint nework",
out=self.log)
den_manager.build_den_proxies(pdb_hierarchy=pdb_hierarchy)
den_manager.build_den_restraints()
den_manager.show_den_summary(
sites_cart=self.model.get_sites_cart())
if den_manager.params.output_kinemage:
den_manager.output_kinemage(self.model.get_sites_cart())
print_statistics.make_sub_header(
"coordinate minimization before annealing", out=self.log)
self.minimize(ca_only=self.params.den.minimize_c_alpha_only)
self.save_scatterers_local = fmodels.fmodel_xray().\
xray_structure.deep_copy_scatterers().scatterers()
#DEN refinement start, turn on
if params.den.optimize:
grid = den_manager.get_optimization_grid()
print >> log, \
"Running DEN torsion optimization on %d processors..." % \
params.main.nproc
else:
grid = [(params.den.gamma, params.den.weight)]
grid_results = []
grid_so = []
if "torsion" in params.den.annealing_type:
print >> self.log, "Running torsion simulated annealing"
if ((params.den.optimize)
and ((self.nproc is Auto) or (self.nproc > 1))):
stdout_and_results = easy_mp.pool_map(
processes=params.main.nproc,
fixed_func=self.try_den_weight_torsion,
args=grid,
func_wrapper="buffer_stdout_stderr")
for so, r in stdout_and_results:
if (r is None):
raise RuntimeError((
"DEN weight optimization failed:" +
"\n%s\nThis is a " +
"serious error; please contact [email protected]."
) % so)
grid_so.append(so)
grid_results.append(r)
else:
for grid_pair in grid:
result = self.try_den_weight_torsion(grid_pair=grid_pair)
grid_results.append(result)
self.show_den_opt_summary_torsion(grid_results)
elif "cartesian" in params.den.annealing_type:
print >> self.log, "Running Cartesian simulated annealing"
if ((params.den.optimize)
and ((self.nproc is Auto) or (self.nproc > 1))):
stdout_and_results = easy_mp.pool_map(
processes=params.main.nproc,
fixed_func=self.try_den_weight_cartesian,
args=grid,
func_wrapper="buffer_stdout_stderr")
for so, r in stdout_and_results:
if (r is None):
raise RuntimeError((
"DEN weight optimization failed:" +
"\n%s\nThis is a " +
"serious error; please contact [email protected]."
) % so)
grid_so.append(so)
grid_results.append(r)
else:
for grid_pair in grid:
result = self.try_den_weight_cartesian(grid_pair=grid_pair)
grid_results.append(result)
self.show_den_opt_summary_cartesian(grid_results)
else:
raise "error in DEN annealing type"
low_r_free = 1.0
best_xray_structure = None
best_eq_distances = None
best_gamma = None
best_weight = None
best_so_i = None
for i, result in enumerate(grid_results):
cur_r_free = result[2]
if cur_r_free < low_r_free:
low_r_free = cur_r_free
best_gamma = result[0]
best_weight = result[1]
best_xray_structure = result[3]
best_eq_distances = result[4]
best_so_i = i
assert best_xray_structure is not None
if params.den.optimize:
print >> self.log, "\nbest gamma: %.1f" % best_gamma
print >> self.log, "best weight: %.1f\n" % best_weight
if params.den.verbose:
if len(grid_so) >= (best_so_i + 1):
print >> self.log, "\nBest annealing results:\n"
print >> self.log, grid_so[best_so_i]
fmodels.fmodel_xray().xray_structure.replace_scatterers(
best_xray_structure.deep_copy())
fmodels.update_xray_structure(
xray_structure=fmodels.fmodel_xray().xray_structure,
update_f_calc=True)
utils.assert_xray_structures_equal(
x1=fmodels.fmodel_xray().xray_structure,
x2=model.get_xray_structure())
model.restraints_manager.geometry.\
den_manager.import_eq_distances(eq_distances=best_eq_distances)
self.model.torsion_ncs_restraints_update(log=self.log)
