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,
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 __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)