def __init__(
self,
restraints_manager,
pdb_hierarchy,
correct_special_position_tolerance,
riding_h_manager=None,
ncs_restraints_group_list=[], # These are actually for NCS CONSTRAINTS!
max_number_of_iterations=500,
number_of_macro_cycles=5,
selection=None,
bond=False,
nonbonded=False,
angle=False,
dihedral=False,
chirality=False,
planarity=False,
parallelity=False,
rmsd_bonds_termination_cutoff=0,
rmsd_angles_termination_cutoff=0,
alternate_nonbonded_off_on=False,
cdl=False,
rdl=False,
correct_hydrogens=False,
fix_rotamer_outliers=True,
allow_allowed_rotamers=True,
states_collector=None,
log=None,
mon_lib_srv=None,
ias_selection=None,
):
self.log = log
if self.log is None:
self.log = sys.stdout
self.pdb_hierarchy = pdb_hierarchy
self.ias_selection = ias_selection
self.minimized = None
self.mon_lib_srv = mon_lib_srv
if self.mon_lib_srv is None:
self.mon_lib_srv = monomer_library.server.server()
self.restraints_manager = restraints_manager
assert max_number_of_iterations + number_of_macro_cycles > 0
assert [
bond, nonbonded, angle, dihedral, chirality, planarity, parallelity
].count(False) < 7
self.cdl_proxies = None
self.rdl_proxies = None
self.rotamer_manager = None
if fix_rotamer_outliers:
from mmtbx.rotamer.rotamer_eval import RotamerEval
self.rotamer_manager = RotamerEval(mon_lib_srv=self.mon_lib_srv)
if (cdl):
from mmtbx.conformation_dependent_library.cdl_setup import setup_restraints
self.cdl_proxies = setup_restraints(
self.restraints_manager.geometry)
self.correct_hydrogens = correct_hydrogens
if (alternate_nonbonded_off_on and number_of_macro_cycles % 2 != 0):
number_of_macro_cycles += 1
import scitbx.lbfgs
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=max_number_of_iterations)
exception_handling_params = scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound=True)
geometry_restraints_flags = geometry_restraints.flags.flags(
bond=bond,
nonbonded=nonbonded,
angle=angle,
dihedral=dihedral,
chirality=chirality,
planarity=planarity,
parallelity=parallelity,
reference_coordinate=True,
reference_dihedral=True,
bond_similarity=True,
ramachandran_restraints=True)
self.update_cdl_restraints()
self.show()
for i_macro_cycle in xrange(number_of_macro_cycles):
print >> self.log, " macro-cycle:", i_macro_cycle
self.restraints_manager.geometry.update_ramachandran_restraints_phi_psi_targets(
sites_cart=self.pdb_hierarchy.atoms().extract_xyz())
if (alternate_nonbonded_off_on
and i_macro_cycle <= number_of_macro_cycles / 2):
geometry_restraints_flags.nonbonded = bool(i_macro_cycle % 2)
self.update_cdl_restraints(macro_cycle=i_macro_cycle)
if (fix_rotamer_outliers):
self.pdb_hierarchy, self.restraints_manager = add_rotamer_restraints(
pdb_hierarchy=self.pdb_hierarchy,
restraints_manager=self.restraints_manager,
selection=selection,
sigma=10,
mode="fix_outliers",
accept_allowed=allow_allowed_rotamers,
mon_lib_srv=self.mon_lib_srv,
rotamer_manager=self.rotamer_manager)
sites_cart = self.pdb_hierarchy.atoms().extract_xyz()
if rdl:
self.updaterdl(prefix="Update RDL restraints")
if (ncs_restraints_group_list is not None
and len(ncs_restraints_group_list)) > 0:
# do ncs minimization
print >> self.log, "Using NCS constraints."
xrs = self.pdb_hierarchy.extract_xray_structure(
).deep_copy_scatterers()
refine_selection = flex.size_t(xrange(xrs.scatterers().size()))
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_geometry_minimization(
xray_structure=xrs,
ncs_restraints_group_list=ncs_restraints_group_list, # CONSTRAINTS
refine_selection=refine_selection,
restraints_manager=self.restraints_manager.geometry,
refine_sites=True,
refine_transformations=False,
)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object=tfg_obj,
xray_structure=xrs,
ncs_restraints_group_list=
ncs_restraints_group_list, # CONSTRAINTS
refine_selection=refine_selection,
finite_grad_differences_test=False,
max_iterations=max_number_of_iterations,
refine_sites=True,
refine_transformations=False)
self.pdb_hierarchy.adopt_xray_structure(xrs)
else:
sites_cart_orig = sites_cart.deep_copy()
if ias_selection is not None and ias_selection.count(True) > 0:
sites_cart = sites_cart.select(~ias_selection)
self.minimized = lbfgs(
sites_cart=sites_cart,
riding_h_manager=riding_h_manager,
correct_special_position_tolerance=
correct_special_position_tolerance,
geometry_restraints_manager=restraints_manager.geometry,
geometry_restraints_flags=geometry_restraints_flags,
lbfgs_termination_params=lbfgs_termination_params,
lbfgs_exception_handling_params=exception_handling_params,
sites_cart_selection=selection,
rmsd_bonds_termination_cutoff=rmsd_bonds_termination_cutoff,
rmsd_angles_termination_cutoff=
rmsd_angles_termination_cutoff,
states_collector=states_collector,
site_labels=None)
if (ias_selection is not None):
for i_seq, ias_s in enumerate(
ias_selection
): # assumes that IAS appended to the back
if (not ias_s):
sites_cart_orig[i_seq] = sites_cart[i_seq]
else:
sites_cart_orig = sites_cart
self.pdb_hierarchy.atoms().set_xyz(sites_cart_orig)
self.show()
self.log.flush()
geometry_restraints_flags.nonbonded = nonbonded
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=max_number_of_iterations)
def run(processed_pdb_file, params=master_params().extract(), log=sys.stdout):
co = params
geometry_restraints_flags = geometry_restraints.flags.flags(default=True)
all_chain_proxies = processed_pdb_file.all_chain_proxies
reference_manager = None
if (co.restrain_c_alpha_positions):
assert 0, "Broken! - rewrite this part first."
from mmtbx.geometry_restraints import reference
ca_selection = all_chain_proxies.pdb_hierarchy.get_peptide_c_alpha_selection(
)
ca_sites_cart = \
all_chain_proxies.sites_cart.deep_copy().select(ca_selection)
reference_manager = reference.manager()
reference_manager.add_coordinate_restraints(sites_cart=ca_sites_cart,
selection=ca_selection)
geometry_restraints_manager = processed_pdb_file.\
geometry_restraints_manager(show_energies = False,
reference_manager=\
reference_manager)
special_position_settings = all_chain_proxies.special_position_settings
sites_cart = all_chain_proxies.sites_cart_exact().deep_copy()
atom_labels = [atom.id_str() for atom in all_chain_proxies.pdb_atoms]
geometry_restraints_manager.site_symmetry_table \
.show_special_position_shifts(
special_position_settings=special_position_settings,
site_labels=atom_labels,
sites_cart_original=all_chain_proxies.sites_cart,
sites_cart_exact=sites_cart,
out=log,
prefix=" ")
if (co.show_geometry_restraints):
geometry_restraints_manager.show_sorted(
flags=geometry_restraints_flags,
sites_cart=sites_cart,
site_labels=atom_labels)
pair_proxies = geometry_restraints_manager.pair_proxies(
sites_cart=all_chain_proxies.sites_cart,
flags=geometry_restraints_flags)
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
site_labels=atom_labels,
f=log,
max_items=10)
if (pair_proxies.nonbonded_proxies is not None):
pair_proxies.nonbonded_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
site_labels=atom_labels,
f=log,
max_items=10)
del pair_proxies
print >> log
log.flush()
if (co.alternate_nonbonded_off_on and co.macro_cycles % 2 != 0):
co.macro_cycles += 1
print >> log, "INFO: Number of macro cycles increased by one to ensure use of"
print >> log, " nonbonded interactions in last macro cycle."
print >> log
for i_macro_cycle in xrange(co.macro_cycles):
if (co.alternate_nonbonded_off_on):
geometry_restraints_flags.nonbonded = bool(i_macro_cycle % 2)
print >> log, "Use nonbonded interactions this macro cycle:", \
geometry_restraints_flags.nonbonded
minimized = lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=geometry_restraints_manager,
geometry_restraints_flags=geometry_restraints_flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=co.max_iterations),
lbfgs_exception_handling_params=scitbx.lbfgs.
exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound=True))
print >> log, "Energies at start of minimization:"
minimized.first_target_result.show(f=log)
print >> log
print >> log, "Number of minimization iterations:", minimized.minimizer.iter(
)
print >> log, "Root-mean-square coordinate difference: %.3f" % (
all_chain_proxies.sites_cart.rms_difference(sites_cart))
print >> log
print >> log, "Energies at end of minimization:"
minimized.final_target_result.show(f=log)
print >> log
geometry_restraints_manager.pair_proxies(
sites_cart=sites_cart,
flags=geometry_restraints_flags) \
.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=atom_labels,
f=log,
max_items=10)
print >> log
assert geometry_restraints_flags.nonbonded
return sites_cart
def run(args):
assert args in [[], ["--verbose"]]
if (len(args) != 0):
cout = sys.stdout
else:
cout = null_out()
edge_list_bonds = [(0,1),(0,4),(1,2),(2,3),(3,4)]
bond_list = [
(("C1*", "C2*"), 1.529),
(("C1*", "O4*"), 1.412),
(("C2*", "C3*"), 1.526),
(("C3*", "C4*"), 1.520),
(("C4*", "O4*"), 1.449)]
angle_list = [
(("C1*", "C2*", "C3*"), 101.3),
(("C2*", "C3*", "C4*"), 102.3),
(("C3*", "C4*", "O4*"), 104.2),
(("C4*", "O4*", "C1*"), 110.0)]
sites_cart, geo_manager = cctbx.geometry_restraints.manager \
.construct_non_crystallographic_conserving_bonds_and_angles(
sites_cart=sites_cart_3p,
edge_list_bonds=edge_list_bonds,
edge_list_angles=[])
for bond_atom_names,distance_ideal in bond_list:
i,j = [atom_names.index(atom_name) for atom_name in bond_atom_names]
bond_params = geo_manager.bond_params_table[i][j]
assert approx_equal(bond_params.distance_ideal, distance_ideal, eps=1.e-2)
bond_params.distance_ideal = distance_ideal
bond_params.weight = 1/0.02**2
assert geo_manager.angle_proxies is None
geo_manager.angle_proxies = cctbx.geometry_restraints.shared_angle_proxy()
for angle_atom_names,angle_ideal in angle_list:
i_seqs = [atom_names.index(atom_name) for atom_name in angle_atom_names]
geo_manager.angle_proxies.append(cctbx.geometry_restraints.angle_proxy(
i_seqs=i_seqs,
angle_ideal=angle_ideal,
weight=1/3**2))
geo_manager.show_sorted(
site_labels=atom_names, sites_cart=sites_cart, f=cout)
def lbfgs(sites_cart):
for i_lbfgs_restart in xrange(3):
minimized = cctbx.geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=geo_manager)
assert is_below_limit(value=minimized.final_target_value, limit=1e-10)
return minimized
lbfgs(sites_cart=sites_cart_3p)
lbfgs(sites_cart=sites_cart_2p)
conformer_counts = [0] * 4
sites_cart = sites_cart.deep_copy()
mt = flex.mersenne_twister(seed=0)
for i_trial in xrange(20):
while True:
for i in xrange(sites_cart.size()):
sites_cart[i] = mt.random_double_point_on_sphere()
try:
lbfgs(sites_cart=sites_cart)
except RuntimeError, e:
if (not str(e).startswith(
"Bond distance > max_reasonable_bond_distance: ")):
raise
else:
break
rmsd_list = flex.double()
for reference_sites in [
sites_cart_3p,
sites_cart_2p,
sites_cart_a,
sites_cart_b]:
sup = scitbx.math.superpose.least_squares_fit(
reference_sites=reference_sites,
other_sites=sites_cart)
rmsd = reference_sites.rms_difference(sup.other_sites_best_fit())
rmsd_list.append(rmsd)
oline = " ".join(["%.3f" % rmsd for rmsd in rmsd_list])
print >> cout, oline
assert is_below_limit(min(rmsd_list), 1e-3)
conformer_counts[flex.min_index(rmsd_list)] += 1
def run(args):
assert args in [[], ["--verbose"]]
if (len(args) != 0):
cout = sys.stdout
else:
cout = null_out()
edge_list_bonds = [(0, 1), (0, 4), (1, 2), (2, 3), (3, 4)]
bond_list = [(("C1*", "C2*"), 1.529), (("C1*", "O4*"), 1.412),
(("C2*", "C3*"), 1.526), (("C3*", "C4*"), 1.520),
(("C4*", "O4*"), 1.449)]
angle_list = [
(("C1*", "C2*", "C3*"), 101.3), (("C2*", "C3*", "C4*"), 102.3),
(("C3*", "C4*", "O4*"), 104.2), (("C4*", "O4*", "C1*"), 110.0)
]
sites_cart, geo_manager = cctbx.geometry_restraints.manager \
.construct_non_crystallographic_conserving_bonds_and_angles(
sites_cart=sites_cart_3p,
edge_list_bonds=edge_list_bonds,
edge_list_angles=[])
for bond_atom_names, distance_ideal in bond_list:
i, j = [atom_names.index(atom_name) for atom_name in bond_atom_names]
bond_params = geo_manager.bond_params_table[i][j]
assert approx_equal(bond_params.distance_ideal,
distance_ideal,
eps=1.e-2)
bond_params.distance_ideal = distance_ideal
bond_params.weight = 1 / 0.02**2
assert geo_manager.angle_proxies is None
geo_manager.angle_proxies = cctbx.geometry_restraints.shared_angle_proxy()
for angle_atom_names, angle_ideal in angle_list:
i_seqs = [
atom_names.index(atom_name) for atom_name in angle_atom_names
]
geo_manager.angle_proxies.append(
cctbx.geometry_restraints.angle_proxy(i_seqs=i_seqs,
angle_ideal=angle_ideal,
weight=1 / 3**2))
geo_manager.show_sorted(site_labels=atom_names,
sites_cart=sites_cart,
f=cout)
def lbfgs(sites_cart):
for i_lbfgs_restart in range(3):
minimized = cctbx.geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart, geometry_restraints_manager=geo_manager)
assert is_below_limit(value=minimized.final_target_value,
limit=1e-10)
return minimized
lbfgs(sites_cart=sites_cart_3p)
lbfgs(sites_cart=sites_cart_2p)
conformer_counts = [0] * 4
sites_cart = sites_cart.deep_copy()
mt = flex.mersenne_twister(seed=0)
for i_trial in range(20):
while True:
for i in range(sites_cart.size()):
sites_cart[i] = mt.random_double_point_on_sphere()
try:
lbfgs(sites_cart=sites_cart)
except RuntimeError as e:
if (not str(e).startswith(
"Bond distance > max_reasonable_bond_distance: ")):
raise
else:
break
rmsd_list = flex.double()
for reference_sites in [
sites_cart_3p, sites_cart_2p, sites_cart_a, sites_cart_b
]:
sup = scitbx.math.superpose.least_squares_fit(
reference_sites=reference_sites, other_sites=sites_cart)
rmsd = reference_sites.rms_difference(sup.other_sites_best_fit())
rmsd_list.append(rmsd)
oline = " ".join(["%.3f" % rmsd for rmsd in rmsd_list])
print(oline, file=cout)
assert is_below_limit(min(rmsd_list), 1e-3)
conformer_counts[flex.min_index(rmsd_list)] += 1
print("conformer_counts:", conformer_counts)
#
if (libtbx.env.has_module("iotbx")):
import iotbx.pdb.hierarchy
hierarchy = iotbx.pdb.hierarchy.root()
model = iotbx.pdb.hierarchy.model(id="")
chain = iotbx.pdb.hierarchy.chain(id="A")
model.append_chain(chain)
hierarchy.append_model(model)
#
sites_cart_pentagon = pentagon_sites_cart()
for i_stack, sites_cart in enumerate(
[sites_cart_3p, sites_cart_2p, sites_cart_a, sites_cart_b]):
atom_group = iotbx.pdb.hierarchy.atom_group(resname=" U",
altloc="")
sup = scitbx.math.superpose.least_squares_fit(
reference_sites=sites_cart_pentagon, other_sites=sites_cart)
sites_cart_out = sup.other_sites_best_fit()
for site_label, site_cart in zip(atom_names, sites_cart_out):
atom = iotbx.pdb.hierarchy.atom()
atom.name = " %-3s" % site_label
atom.xyz = matrix.col(site_cart) + matrix.col(
(0, 0, i_stack * 1.5))
atom.occ = 1
atom.b = 20
atom.element = " " + site_label[0]
atom_group.append_atom(atom)
residue_group = iotbx.pdb.hierarchy.residue_group(resseq="%4d" %
(i_stack + 1),
icode=" ")
residue_group.append_atom_group(atom_group)
chain.append_residue_group(residue_group)
hierarchy.atoms().reset_serial()
pdb_str = hierarchy.as_pdb_string(append_end=True)
file_name = "puckers.pdb"
print("Writing file:", file_name)
open(file_name, "w").write("""\
REMARK random_puckers.py
REMARK 1 = 3'
REMARK 2 = 2'
REMARK 3 = A
REMARK 4 = B
""" + pdb_str)
#
print("OK")
def run(processed_pdb_file, params=master_params().extract(), log=sys.stdout):
co = params
geometry_restraints_flags = geometry_restraints.flags.flags(default=True)
all_chain_proxies = processed_pdb_file.all_chain_proxies
reference_manager = None
if (co.restrain_c_alpha_positions):
assert 0, "Broken! - rewrite this part first."
from mmtbx.geometry_restraints import reference
ca_selection=all_chain_proxies.pdb_hierarchy.get_peptide_c_alpha_selection()
ca_sites_cart = \
all_chain_proxies.sites_cart.deep_copy().select(ca_selection)
reference_manager = reference.manager()
reference_manager.add_coordinate_restraints(
sites_cart=ca_sites_cart,
selection=ca_selection)
geometry_restraints_manager = processed_pdb_file.\
geometry_restraints_manager(show_energies = False,
reference_manager=\
reference_manager)
special_position_settings = all_chain_proxies.special_position_settings
sites_cart = all_chain_proxies.sites_cart_exact().deep_copy()
atom_labels = [atom.id_str() for atom in all_chain_proxies.pdb_atoms]
geometry_restraints_manager.site_symmetry_table \
.show_special_position_shifts(
special_position_settings=special_position_settings,
site_labels=atom_labels,
sites_cart_original=all_chain_proxies.sites_cart,
sites_cart_exact=sites_cart,
out=log,
prefix=" ")
if (co.show_geometry_restraints):
geometry_restraints_manager.show_sorted(
flags=geometry_restraints_flags,
sites_cart=sites_cart,
site_labels=atom_labels)
pair_proxies = geometry_restraints_manager.pair_proxies(
sites_cart=all_chain_proxies.sites_cart,
flags=geometry_restraints_flags)
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=atom_labels,
f=log,
max_items=10)
if (pair_proxies.nonbonded_proxies is not None):
pair_proxies.nonbonded_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
site_labels=atom_labels,
f=log,
max_items=10)
del pair_proxies
print >> log
log.flush()
if (co.alternate_nonbonded_off_on and co.macro_cycles % 2 != 0):
co.macro_cycles += 1
print >> log, "INFO: Number of macro cycles increased by one to ensure use of"
print >> log, " nonbonded interactions in last macro cycle."
print >> log
for i_macro_cycle in xrange(co.macro_cycles):
if (co.alternate_nonbonded_off_on):
geometry_restraints_flags.nonbonded = bool(i_macro_cycle % 2)
print >> log, "Use nonbonded interactions this macro cycle:", \
geometry_restraints_flags.nonbonded
minimized = lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=geometry_restraints_manager,
geometry_restraints_flags=geometry_restraints_flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=co.max_iterations),
lbfgs_exception_handling_params=
scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound=True))
print >> log, "Energies at start of minimization:"
minimized.first_target_result.show(f=log)
print >> log
print >> log, "Number of minimization iterations:", minimized.minimizer.iter()
print >> log, "Root-mean-square coordinate difference: %.3f" % (
all_chain_proxies.sites_cart.rms_difference(sites_cart))
print >> log
print >> log, "Energies at end of minimization:"
minimized.final_target_result.show(f=log)
print >> log
geometry_restraints_manager.pair_proxies(
sites_cart=sites_cart,
flags=geometry_restraints_flags) \
.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=atom_labels,
f=log,
max_items=10)
print >> log
assert geometry_restraints_flags.nonbonded
return sites_cart
def __init__(self,
restraints_manager,
pdb_hierarchy,
correct_special_position_tolerance,
ncs_restraints_group_list = [],
max_number_of_iterations = 500,
number_of_macro_cycles = 5,
selection = None,
bond = False,
nonbonded = False,
angle = False,
dihedral = False,
chirality = False,
planarity = False,
parallelity = False,
rmsd_bonds_termination_cutoff = 0,
rmsd_angles_termination_cutoff = 0,
alternate_nonbonded_off_on = False,
cdl = False,
rdl = False,
correct_hydrogens = False,
fix_rotamer_outliers = True,
allow_allowed_rotamers = True,
states_collector = None,
log = None,
mon_lib_srv = None):
self.log = log
if self.log is None:
self.log = sys.stdout
self.pdb_hierarchy = pdb_hierarchy
self.minimized = None
self.mon_lib_srv = mon_lib_srv
if self.mon_lib_srv is None:
self.mon_lib_srv = monomer_library.server.server()
self.restraints_manager = restraints_manager
assert max_number_of_iterations+number_of_macro_cycles > 0
assert [bond,nonbonded,angle,dihedral,chirality,planarity,
parallelity].count(False) < 7
self.cdl_proxies = None
self.rdl_proxies = None
self.rotamer_manager = None
if fix_rotamer_outliers:
from mmtbx.rotamer.rotamer_eval import RotamerEval
self.rotamer_manager = RotamerEval(mon_lib_srv=self.mon_lib_srv)
if(cdl):
from mmtbx.conformation_dependent_library.cdl_setup import setup_restraints
self.cdl_proxies = setup_restraints(self.restraints_manager.geometry)
self.correct_hydrogens = correct_hydrogens
if(alternate_nonbonded_off_on and number_of_macro_cycles % 2 != 0):
number_of_macro_cycles += 1
import scitbx.lbfgs
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = max_number_of_iterations)
exception_handling_params = scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound = True)
geometry_restraints_flags = geometry_restraints.flags.flags(
bond = bond,
nonbonded = nonbonded,
angle = angle,
dihedral = dihedral,
chirality = chirality,
planarity = planarity,
parallelity = parallelity,
reference_coordinate = True,
reference_dihedral = True,
bond_similarity = True,
ramachandran_restraints = True)
self.update_cdl_restraints()
self.show()
for i_macro_cycle in xrange(number_of_macro_cycles):
print >> self.log, " macro-cycle:", i_macro_cycle
self.restraints_manager.geometry.update_ramachandran_restraints_phi_psi_targets(
sites_cart=self.pdb_hierarchy.atoms().extract_xyz())
if(alternate_nonbonded_off_on and i_macro_cycle<=number_of_macro_cycles/2):
geometry_restraints_flags.nonbonded = bool(i_macro_cycle % 2)
self.correct_hydrogen_geometries(self.log)
self.update_cdl_restraints(macro_cycle=i_macro_cycle)
if(fix_rotamer_outliers):
self.pdb_hierarchy, self.restraints_manager = add_rotamer_restraints(
pdb_hierarchy = self.pdb_hierarchy,
restraints_manager = self.restraints_manager,
selection = selection,
sigma = 10,
mode = "fix_outliers",
accept_allowed = allow_allowed_rotamers,
mon_lib_srv = self.mon_lib_srv,
rotamer_manager = self.rotamer_manager)
sites_cart = self.pdb_hierarchy.atoms().extract_xyz()
if rdl:
self.updaterdl(prefix="Update RDL restraints")
# self.pdb_hierarchy.write_pdb_file("after_fix_%d.pdb" % i_macro_cycle)
# self.restraints_manager.write_geo_file(
# sites_cart=self.pdb_hierarchy.atoms().extract_xyz(),
# site_labels= [atom.id_str() for atom in self.pdb_hierarchy.atoms()],
# file_name="after_fix_%d.geo" % i_macro_cycle)
if (ncs_restraints_group_list is not None
and len(ncs_restraints_group_list)) > 0:
# do ncs minimization
print >> self.log, "Using NCS constraints."
xrs = self.pdb_hierarchy.extract_xray_structure().deep_copy_scatterers()
refine_selection = flex.size_t(xrange(xrs.scatterers().size()))
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_geometry_minimization(
xray_structure=xrs,
ncs_restraints_group_list=ncs_restraints_group_list,
refine_selection=refine_selection,
restraints_manager=self.restraints_manager.geometry,
refine_sites=True,
refine_transformations=False,
)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object = tfg_obj,
xray_structure = xrs,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = refine_selection,
finite_grad_differences_test = False,
max_iterations = max_number_of_iterations,
refine_sites = True,
refine_transformations = False)
self.pdb_hierarchy.adopt_xray_structure(xrs)
else:
self.minimized = lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance=correct_special_position_tolerance,
geometry_restraints_manager = restraints_manager.geometry,
geometry_restraints_flags = geometry_restraints_flags,
lbfgs_termination_params = lbfgs_termination_params,
lbfgs_exception_handling_params = exception_handling_params,
sites_cart_selection = selection,
rmsd_bonds_termination_cutoff = rmsd_bonds_termination_cutoff,
rmsd_angles_termination_cutoff = rmsd_angles_termination_cutoff,
states_collector = states_collector,
site_labels = None)
self.pdb_hierarchy.atoms().set_xyz(sites_cart)
self.show()
self.log.flush()
geometry_restraints_flags.nonbonded = nonbonded
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = max_number_of_iterations)
def __init__(self,
restraints_manager,
pdb_hierarchy,
correct_special_position_tolerance,
max_number_of_iterations = 500,
number_of_macro_cycles = 5,
selection = None,
bond = False,
nonbonded = False,
angle = False,
dihedral = False,
chirality = False,
planarity = False,
parallelity = False,
rmsd_bonds_termination_cutoff = 0,
rmsd_angles_termination_cutoff = 0,
alternate_nonbonded_off_on = False,
cdl = False,
correct_hydrogens = False,
fix_rotamer_outliers = True,
states_collector = None,
log = None):
self.log = log
if self.log is None:
self.log = sys.stdout
self.pdb_hierarchy = pdb_hierarchy
self.minimized = None
self.restraints_manager = restraints_manager
assert max_number_of_iterations+number_of_macro_cycles > 0
assert [bond,nonbonded,angle,dihedral,chirality,planarity,
parallelity].count(False) < 7
self.cdl_proxies = None
if(cdl):
from mmtbx.conformation_dependent_library.cdl_setup import setup_restraints
self.cdl_proxies = setup_restraints(restraints_manager.geometry)
self.correct_hydrogens = correct_hydrogens
if(alternate_nonbonded_off_on and number_of_macro_cycles % 2 != 0):
number_of_macro_cycles += 1
import scitbx.lbfgs
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = max_number_of_iterations)
exception_handling_params = scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound = True)
geometry_restraints_flags = geometry_restraints.flags.flags(
bond = bond,
nonbonded = nonbonded,
angle = angle,
dihedral = dihedral,
chirality = chirality,
planarity = planarity,
parallelity = parallelity,
reference_coordinate = True,
reference_dihedral = True,
bond_similarity = True,
ramachandran_restraints = True)
self.update_cdl_restraints()
self.show()
for i_macro_cycle in xrange(number_of_macro_cycles):
print >> self.log, " macro-cycle:", i_macro_cycle
if(alternate_nonbonded_off_on and i_macro_cycle<=number_of_macro_cycles/2):
geometry_restraints_flags.nonbonded = bool(i_macro_cycle % 2)
self.correct_hydrogen_geometries(log)
self.update_cdl_restraints(macro_cycle=i_macro_cycle)
if(fix_rotamer_outliers):
self.pdb_hierarchy, self.restraints_manager = add_rotamer_restraints(
pdb_hierarchy = self.pdb_hierarchy,
restraints_manager = self.restraints_manager,
selection = selection,
sigma = 10,
mode = "fix_outliers")
sites_cart = self.pdb_hierarchy.atoms().extract_xyz()
self.minimized = lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance=correct_special_position_tolerance,
geometry_restraints_manager = restraints_manager.geometry,
geometry_restraints_flags = geometry_restraints_flags,
lbfgs_termination_params = lbfgs_termination_params,
lbfgs_exception_handling_params = exception_handling_params,
sites_cart_selection = selection,
rmsd_bonds_termination_cutoff = rmsd_bonds_termination_cutoff,
rmsd_angles_termination_cutoff = rmsd_angles_termination_cutoff,
states_collector = states_collector,
site_labels = None)
self.pdb_hierarchy.atoms().set_xyz(sites_cart)
self.show()
geometry_restraints_flags.nonbonded = nonbonded
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations = max_number_of_iterations)