def _minimize(self):
m1 = self.model.deep_copy()
rama_params = rama_master_phil.fetch().extract(
).ramachandran_plot_restraints
rama_params.favored = 'oldfield'
rama_params.allowed = 'oldfield'
rama_params.outlier = 'oldfield'
m1.set_ramachandran_plot_restraints(rama_params=rama_params)
run2(
restraints_manager=m1.get_restraints_manager(),
pdb_hierarchy=m1.get_hierarchy(),
correct_special_position_tolerance=1.0,
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=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True,
parallelity=True,
log=null_out())
m1.set_sites_cart_from_hierarchy(multiply_ncs=True)
return m1
def minimize(self, ca_only=False):
sel = "all"
restraint_sites_cart = self.model.get_sites_cart().deep_copy()
if ca_only:
restraint_sites_cart = self.model.get_sites_cart().\
deep_copy().select(self.model.get_atom_selection_cache().selection("name CA"))
sel = "name CA"
self.model.set_reference_coordinate_restraints(ref_model=self.model,
selection=sel,
exclude_outliers=False)
##### sanity check #####
# How this check was supposed to hold up when ca_only=True???
# When ca_only=True, number of restraints will be less than number of atoms.
# Good that users never change defaults (minimize_c_alpha_only = False).
#
# XXX finally, removing this assertion. On top of c_alpha_only case,
# it also fails (rightfully) when there are water molecules in the model,
# they are excluded. The same goes to hydrogens, but it seems no one yet
# tried den_refine for model with hydrogens on.
# n_rcp = self.model.get_restraints_manager().geometry.get_n_reference_coordinate_proxies()
# n_sc = len(restraint_sites_cart)
# assert n_rcp >= n_sc, "%d >= %d fail" % (n_rcp, n_sc)
########################
# selection = self.model.selection_moving
geometry_minimization.run2(
restraints_manager=self.model.get_restraints_manager(),
pdb_hierarchy=self.model.get_hierarchy(),
max_number_of_iterations=500,
correct_special_position_tolerance=1.0,
number_of_macro_cycles=1,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True)
self.model.set_sites_cart_from_hierarchy()
utils.assert_xray_structures_equal(
x1=self.fmodels.fmodel_xray().xray_structure,
x2=self.model.get_xray_structure())
self.model.restraints_manager.geometry.\
remove_reference_coordinate_restraints_in_place()
def minimize(self, ca_only=False):
pdb_hierarchy = self.model.get_hierarchy(sync_with_xray_structure=True)
if ca_only:
ca_selection = pdb_hierarchy.get_peptide_c_alpha_selection()
restraint_sites_cart = self.model.get_sites_cart().\
deep_copy().select(ca_selection)
restraint_selection = ca_selection
else:
restraint_sites_cart = self.model.get_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,
n_atoms_in_target_model=self.model.get_number_of_atoms())
##### sanity check #####
assert(self.model.restraints_manager.geometry.
get_n_reference_coordinate_proxies() >= len(restraint_sites_cart))
########################
# selection = self.model.selection_moving
geometry_minimization.run2(
restraints_manager = self.model.get_restraints_manager(),
pdb_hierarchy = self.model.get_hierarchy(),
max_number_of_iterations = 500,
correct_special_position_tolerance=1.0,
number_of_macro_cycles = 1,
bond = True,
nonbonded = True,
angle = True,
dihedral = True,
chirality = True,
planarity = True)
self.model.set_sites_cart_from_hierarchy()
utils.assert_xray_structures_equal(
x1 = self.fmodels.fmodel_xray().xray_structure,
x2 = self.model.get_xray_structure())
self.model.restraints_manager.geometry.\
remove_reference_coordinate_restraints_in_place()
def minimize(self, ca_only=False):
sel = "all"
restraint_sites_cart = self.model.get_sites_cart().deep_copy()
if ca_only:
restraint_sites_cart = self.model.get_sites_cart().\
deep_copy().select(ca_selection)
sel = "name CA"
self.model.set_reference_coordinate_restraints(ref_model=self.model,
selection=sel,
exclude_outliers=False)
##### sanity check #####
# How this check was supposed to hold up when ca_only=True???
# When ca_only=True, number of restraints will be less than number of atoms.
# Good that users never change defaults (minimize_c_alpha_only = False).
n_rcp = self.model.get_restraints_manager(
).geometry.get_n_reference_coordinate_proxies()
n_sc = len(restraint_sites_cart)
assert n_rcp >= n_sc, "%d >= %d fail" % (n_rcp, n_sc)
########################
# selection = self.model.selection_moving
geometry_minimization.run2(
restraints_manager=self.model.get_restraints_manager(),
pdb_hierarchy=self.model.get_hierarchy(),
max_number_of_iterations=500,
correct_special_position_tolerance=1.0,
number_of_macro_cycles=1,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True)
self.model.set_sites_cart_from_hierarchy()
utils.assert_xray_structures_equal(
x1=self.fmodels.fmodel_xray().xray_structure,
x2=self.model.get_xray_structure())
self.model.restraints_manager.geometry.\
remove_reference_coordinate_restraints_in_place()
def minimize_hierarchy(hierarchy, xrs, original_pdb_h, excl_string_selection, log=None):
from mmtbx.monomer_library.pdb_interpretation import grand_master_phil_str
from mmtbx.refinement.geometry_minimization import run2
from mmtbx.geometry_restraints import reference
if log is None:
log = null_out()
params_line = grand_master_phil_str
params = iotbx.phil.parse(input_string=params_line, process_includes=True).extract()
params.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
params.pdb_interpretation.peptide_link.ramachandran_restraints = True
params.pdb_interpretation.peptide_link.oldfield.weight_scale = 3
params.pdb_interpretation.peptide_link.oldfield.plot_cutoff = 0.03
params.pdb_interpretation.c_beta_restraints = True
processed_pdb_files_srv = mmtbx.utils.process_pdb_file_srv(
crystal_symmetry=xrs.crystal_symmetry(),
pdb_interpretation_params=params.pdb_interpretation,
stop_for_unknowns=False,
log=log,
cif_objects=None,
)
processed_pdb_file, junk = processed_pdb_files_srv.process_pdb_files(
raw_records=flex.split_lines(hierarchy.as_pdb_string())
)
grm = get_geometry_restraints_manager(processed_pdb_file, xrs)
asc = original_pdb_h.atom_selection_cache()
sel = asc.selection(excl_string_selection)
grm.geometry.append_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart=original_pdb_h.atoms().extract_xyz().select(sel), selection=sel, sigma=0.5
)
)
obj = run2(
restraints_manager=grm,
pdb_hierarchy=hierarchy,
correct_special_position_tolerance=1.0,
max_number_of_iterations=300,
number_of_macro_cycles=5,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True,
fix_rotamer_outliers=True,
log=log,
)
def exercise(tolerance=0.01):
for use_neutron_distances in [True, False]:
mon_lib_srv = monomer_library.server.server()
ener_lib = monomer_library.server.ener_lib()
inp = iotbx.pdb.input(lines=pdb_str.splitlines(), source_info=None)
params = iotbx.phil.parse(input_string=grand_master_phil_str,
process_includes=True).extract()
params.pdb_interpretation.use_neutron_distances = use_neutron_distances
model = mmtbx.model.manager(model_input=inp)
model.process(pdb_interpretation_params=params, make_restraints=True)
ph = model.get_hierarchy()
ph.write_pdb_file(file_name="input.pdb")
m = geometry_minimization.run2(
restraints_manager=model.get_restraints_manager(),
pdb_hierarchy=ph,
correct_special_position_tolerance=1.0,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True)
model.set_sites_cart_from_hierarchy()
suffix = "X"
if (use_neutron_distances): suffix = "N"
ph.write_pdb_file(file_name="output_%s.pdb" % suffix)
# check X-H distances: x-ray
cntr = 0
awl = iotbx.pdb.input(file_name="output_X.pdb").atoms_with_labels()
for a1 in awl:
n1 = a1.name.strip()
for a2 in awl:
n2 = a2.name.strip()
if ([n1, n2] == ["CD1", "HD1"] or [n1, n2] == ["CD2", "HD2"]
or [n1, n2] == ["CE1", "HE1"]
or [n1, n2] == ["CE2", "HE2"]):
assert approx_equal(dist(a1.xyz, a2.xyz), 0.93, tolerance)
cntr += 1
if (n1 == "OH" and n2 in ["HH", "DH"]):
assert approx_equal(dist(a1.xyz, a2.xyz), 0.84, tolerance)
cntr += 1
if ([n1, n2] == ["CB", "HB2"] or [n1, n2] == ["CB", "HB3"]
or [n1, n2] == ["CA", "HA"]):
assert approx_equal(dist(a1.xyz, a2.xyz), 0.97, tolerance)
cntr += 1
if (n1 == "O" and n2 in ["D1", "D2"] and a1.resname == "HOH"):
assert approx_equal(dist(a1.xyz, a2.xyz), 0.85, tolerance)
cntr += 1
assert cntr == 11, cntr
# check X-H distances: neutron
cntr = 0
awl = iotbx.pdb.input(file_name="output_N.pdb").atoms_with_labels()
for a1 in awl:
n1 = a1.name.strip()
for a2 in awl:
n2 = a2.name.strip()
if ([n1, n2] == ["CD1", "HD1"] or [n1, n2] == ["CD2", "HD2"]
or [n1, n2] == ["CE1", "HE1"]
or [n1, n2] == ["CE2", "HE2"]):
assert approx_equal(dist(a1.xyz, a2.xyz), 1.08, tolerance), """
dist(a1.xyz, a2.xyz) : %f
tolerance : %f
""" % (
dist(a1.xyz, a2.xyz),
tolerance,
)
cntr += 1
if (n1 == "OH" and n2 in ["HH", "DH"]):
assert approx_equal(dist(a1.xyz, a2.xyz), 0.98, tolerance)
cntr += 1
if ([n1, n2] == ["CB", "HB2"] or [n1, n2] == ["CB", "HB3"]
or [n1, n2] == ["CA", "HA"]):
assert approx_equal(dist(a1.xyz, a2.xyz), 1.09, tolerance)
cntr += 1
if (n1 == "O" and n2 in ["D1", "D2"] and a1.resname == "HOH"):
assert approx_equal(dist(a1.xyz, a2.xyz), 0.98, tolerance)
cntr += 1
assert cntr == 11, cntr
def substitute_ss(real_h,
xray_structure,
ss_annotation,
params = None,
grm=None,
use_plane_peptide_bond_restr=True,
fix_rotamer_outliers=True,
cif_objects=None,
log=null_out(),
rotamer_manager=None,
reference_map=None,
verbose=False):
"""
Substitute secondary structure elements in real_h hierarchy with ideal
ones _in_place_.
Returns reference torsion proxies - the only thing that cannot be restored
with little effort outside the procedure.
real_h - hierarcy to substitute secondary structure elements.
xray_structure - xray_structure - needed to get crystal symmetry (to
construct processed_pdb_file and xray_structure is needed to call
get_geometry_restraints_manager for no obvious reason).
ss_annotation - iotbx.pdb.annotation object.
"""
t0 = time()
if rotamer_manager is None:
rotamer_manager = RotamerEval()
for model in real_h.models():
for chain in model.chains():
if len(chain.conformers()) > 1:
raise Sorry("Alternative conformations are not supported.")
processed_params = process_params(params)
if not processed_params.enabled:
return None
expected_n_hbonds = 0
ann = ss_annotation
for h in ann.helices:
expected_n_hbonds += h.get_n_maximum_hbonds()
edited_h = real_h.deep_copy()
n_atoms_in_real_h = real_h.atoms_size()
selection_cache = real_h.atom_selection_cache()
# check the annotation for correctness (atoms are actually in hierarchy)
error_msg = "The following secondary structure annotations result in \n"
error_msg +="empty atom selections. They don't match the structre: \n"
t1 = time()
# Checking for SS selections
deleted_annotations = ann.remove_empty_annotations(
hierarchy=real_h,
asc=selection_cache)
if not deleted_annotations.is_empty():
if processed_params.skip_empty_ss_elements:
if len(deleted_annotations.helices) > 0:
print >> log, "Removing the following helices because there are"
print >> log, "no corresponding atoms in the model:"
for h in deleted_annotations.helices:
print >> log, h.as_pdb_str()
error_msg += " %s\n" % h
if len(deleted_annotations.sheets) > 0:
print >> log, "Removing the following sheets because there are"
print >> log, "no corresponding atoms in the model:"
for sh in deleted_annotations.sheets:
print >> log, sh.as_pdb_str()
error_msg += " %s\n" % sh.as_pdb_str(strand_id=st.strand_id)
else:
raise Sorry(error_msg)
phil_str = ann.as_restraint_groups()
# gathering initial special position atoms
special_position_settings = crystal.special_position_settings(
crystal_symmetry = xray_structure.crystal_symmetry())
site_symmetry_table = \
special_position_settings.site_symmetry_table(
sites_cart = real_h.atoms().extract_xyz(),
unconditional_general_position_flags=(
real_h.atoms().extract_occ() != 1))
original_spi = site_symmetry_table.special_position_indices()
t2 = time()
# Actually idelizing SS elements
log.write("Replacing ss-elements with ideal ones:\n")
log.flush()
for h in ann.helices:
log.write(" %s\n" % h.as_pdb_str())
log.flush()
selstring = h.as_atom_selections()
isel = selection_cache.iselection(selstring[0])
all_bsel = flex.bool(n_atoms_in_real_h, False)
all_bsel.set_selected(isel, True)
sel_h = real_h.select(all_bsel, copy_atoms=True)
ideal_h = get_helix(helix_class=h.helix_class,
pdb_hierarchy_template=sel_h,
rotamer_manager=rotamer_manager)
# edited_h.select(all_bsel).atoms().set_xyz(ideal_h.atoms().extract_xyz())
set_xyz_carefully(dest_h=edited_h.select(all_bsel), source_h=ideal_h)
for sh in ann.sheets:
s = " %s\n" % sh.as_pdb_str()
ss = s.replace("\n", "\n ")
log.write(ss[:-2])
log.flush()
for st in sh.strands:
selstring = st.as_atom_selections()
isel = selection_cache.iselection(selstring)
all_bsel = flex.bool(n_atoms_in_real_h, False)
all_bsel.set_selected(isel, True)
sel_h = real_h.select(all_bsel, copy_atoms=True)
ideal_h = secondary_structure_from_sequence(
pdb_str=beta_pdb_str,
sequence=None,
pdb_hierarchy_template=sel_h,
rotamer_manager=rotamer_manager,
)
set_xyz_carefully(edited_h.select(all_bsel), ideal_h)
# edited_h.select(all_bsel).atoms().set_xyz(ideal_h.atoms().extract_xyz())
t3 = time()
pre_result_h = edited_h
pre_result_h.reset_i_seq_if_necessary()
n_atoms = real_h.atoms_size()
bsel = flex.bool(n_atoms, False)
helix_selection = flex.bool(n_atoms, False)
sheet_selection = flex.bool(n_atoms, False)
other_selection = flex.bool(n_atoms, False)
ss_for_tors_selection = flex.bool(n_atoms, False)
nonss_for_tors_selection = flex.bool(n_atoms, False)
selection_cache = real_h.atom_selection_cache()
# set all CA atoms to True for other_selection
#isel = selection_cache.iselection("name ca")
isel = selection_cache.iselection("name ca or name n or name o or name c")
other_selection.set_selected(isel, True)
n_main_chain_atoms = other_selection.count(True)
isel = selection_cache.iselection("name ca or name n or name o or name c")
nonss_for_tors_selection.set_selected(isel, True)
main_chain_selection_prefix = "(name ca or name n or name o or name c) %s"
t4 = time()
print >> log, "Preparing selections..."
log.flush()
# Here we are just preparing selections
for h in ann.helices:
ss_sels = h.as_atom_selections()[0]
selstring = main_chain_selection_prefix % ss_sels
isel = selection_cache.iselection(selstring)
helix_selection.set_selected(isel, True)
other_selection.set_selected(isel, False)
isel = selection_cache.iselection(selstring)
ss_for_tors_selection.set_selected(isel, True)
nonss_for_tors_selection.set_selected(isel, False)
for sheet in ann.sheets:
for ss_sels in sheet.as_atom_selections():
selstring = main_chain_selection_prefix % ss_sels
isel = selection_cache.iselection(selstring)
sheet_selection.set_selected(isel, True)
other_selection.set_selected(isel, False)
isel = selection_cache.iselection(selstring)
ss_for_tors_selection.set_selected(isel, True)
nonss_for_tors_selection.set_selected(isel, False)
t5 = time()
isel = selection_cache.iselection(
"not name ca and not name n and not name o and not name c")
other_selection.set_selected(isel, False)
helix_sheet_intersection = helix_selection & sheet_selection
if helix_sheet_intersection.count(True) > 0:
sheet_selection = sheet_selection & ~helix_sheet_intersection
assert ((helix_selection | sheet_selection) & other_selection).count(True)==0
from mmtbx.monomer_library.pdb_interpretation import grand_master_phil_str
params_line = grand_master_phil_str
params_line += "secondary_structure {%s}" % secondary_structure.sec_str_master_phil_str
# print "params_line"
# print params_line
params = iotbx.phil.parse(input_string=params_line, process_includes=True)#.extract()
# This does not the same way for a strange reason. Need to investigate.
# The number of resulting hbonds is different later.
# w_params = params.extract()
# w_params.pdb_interpretation.secondary_structure.protein.remove_outliers = False
# w_params.pdb_interpretation.peptide_link.ramachandran_restraints = True
# w_params.pdb_interpretation.c_beta_restraints = True
# w_params.pdb_interpretation.secondary_structure.enabled = True
# params.format(python_object=w_params)
# params.show()
# print "="*80
# print "="*80
# print "="*80
if grm is None:
custom_par_text = "\n".join([
"pdb_interpretation.secondary_structure {protein.remove_outliers = False\n%s}" \
% phil_str,
"pdb_interpretation.peptide_link.ramachandran_restraints = True",
"c_beta_restraints = True",
"pdb_interpretation.secondary_structure.enabled=True",
"pdb_interpretation.clash_guard.nonbonded_distance_threshold=None",
"pdb_interpretation.max_reasonable_bond_distance=None",
# "pdb_interpretation.nonbonded_weight=500",
"pdb_interpretation.peptide_link.oldfield.weight_scale=3",
"pdb_interpretation.peptide_link.oldfield.plot_cutoff=0.03",
"pdb_interpretation.peptide_link.omega_esd_override_value=3",
"pdb_interpretation.peptide_link.apply_all_trans=True",
])
if use_plane_peptide_bond_restr:
custom_par_text += "\npdb_interpretation.peptide_link.apply_peptide_plane=True"
custom_pars = params.fetch(
source=iotbx.phil.parse(custom_par_text)).extract()
# params.format(python_object=custom_pars)
# params.show()
# STOP()
params = custom_pars
# params = w_params
t6 = time()
import mmtbx.utils
processed_pdb_files_srv = mmtbx.utils.\
process_pdb_file_srv(
crystal_symmetry= xray_structure.crystal_symmetry(),
pdb_interpretation_params = params.pdb_interpretation,
log=null_out(),
cif_objects=cif_objects)
if verbose:
print >> log, "Processing file..."
log.flush()
processed_pdb_file, junk = processed_pdb_files_srv.\
process_pdb_files(raw_records=flex.split_lines(real_h.as_pdb_string()))
t7 = time()
grm = get_geometry_restraints_manager(
processed_pdb_file, xray_structure)
t8 = time()
else:
ss_params = secondary_structure.default_params
ss_params.secondary_structure.protein.remove_outliers=False
ss_manager = secondary_structure.manager(
pdb_hierarchy=real_h,
geometry_restraints_manager=grm.geometry,
sec_str_from_pdb_file=ss_annotation,
params=ss_params.secondary_structure,
mon_lib_srv=None,
verbose=-1,
log=log)
grm.geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=real_h,
log=log)
real_h.reset_i_seq_if_necessary()
from mmtbx.geometry_restraints import reference
if reference_map is None:
if verbose:
print >> log, "Adding reference coordinate restraints..."
grm.geometry.append_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = real_h.atoms().extract_xyz().select(helix_selection),
selection = helix_selection,
sigma = processed_params.sigma_on_reference_helix))
grm.geometry.append_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = real_h.atoms().extract_xyz().select(sheet_selection),
selection = sheet_selection,
sigma = processed_params.sigma_on_reference_sheet))
grm.geometry.append_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = real_h.atoms().extract_xyz().select(other_selection),
selection = other_selection,
sigma = processed_params.sigma_on_reference_non_ss))
if verbose:
print >> log, "Adding chi torsion restraints..."
grm.geometry.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pre_result_h,
sites_cart = pre_result_h.atoms().extract_xyz().\
select(ss_for_tors_selection),
selection = ss_for_tors_selection,
chi_angles_only = False,
sigma = processed_params.sigma_on_torsion_ss)
grm.geometry.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pre_result_h,
sites_cart = real_h.atoms().extract_xyz().\
select(nonss_for_tors_selection),
selection = nonss_for_tors_selection,
chi_angles_only = False,
sigma = processed_params.sigma_on_torsion_nonss)
real_h.atoms().set_xyz(pre_result_h.atoms().extract_xyz())
#
# Check and correct for special positions
#
special_position_settings = crystal.special_position_settings(
crystal_symmetry = xray_structure.crystal_symmetry())
site_symmetry_table = \
special_position_settings.site_symmetry_table(
sites_cart = real_h.atoms().extract_xyz(),
unconditional_general_position_flags=(
real_h.atoms().extract_occ() != 1))
spi = site_symmetry_table.special_position_indices()
if spi.size() > 0:
print >> log, "Moving atoms from special positions:"
for spi_i in spi:
if spi_i not in original_spi:
new_coords = (
real_h.atoms()[spi_i].xyz[0]+0.2,
real_h.atoms()[spi_i].xyz[1]+0.2,
real_h.atoms()[spi_i].xyz[2]+0.2)
print >> log, " ", real_h.atoms()[spi_i].id_str(),
print >> log, tuple(real_h.atoms()[spi_i].xyz), "-->", new_coords
real_h.atoms()[spi_i].set_xyz(new_coords)
t9 = time()
if processed_params.file_name_before_regularization is not None:
grm.geometry.pair_proxies(sites_cart=real_h.atoms().extract_xyz())
if grm.geometry.ramachandran_manager is not None:
grm.geometry.ramachandran_manager.update_phi_psi_targets(
sites_cart=real_h.atoms().extract_xyz())
print >> log, "Outputting model before regularization %s" % processed_params.file_name_before_regularization
real_h.write_pdb_file(
file_name=processed_params.file_name_before_regularization)
geo_fname = processed_params.file_name_before_regularization[:-4]+'.geo'
print >> log, "Outputting geo file for regularization %s" % geo_fname
grm.write_geo_file(
site_labels=[atom.id_str() for atom in real_h.atoms()],
file_name=geo_fname)
#testing number of restraints
assert grm.geometry.get_n_den_proxies() == 0
if reference_map is None:
assert grm.geometry.get_n_reference_coordinate_proxies() == n_main_chain_atoms
refinement_log = null_out()
log.write(
"Refining geometry of substituted secondary structure elements...")
log.flush()
if verbose:
refinement_log = log
from mmtbx.refinement.geometry_minimization import run2
t10 = time()
if reference_map is None:
obj = run2(
restraints_manager = grm,
pdb_hierarchy = real_h,
correct_special_position_tolerance = 1.0,
max_number_of_iterations = processed_params.n_iter,
number_of_macro_cycles = processed_params.n_macro,
bond = True,
nonbonded = True,
angle = True,
dihedral = True,
chirality = True,
planarity = True,
fix_rotamer_outliers = fix_rotamer_outliers,
log = refinement_log)
else:
ref_xrs = real_h.extract_xray_structure(
crystal_symmetry=xray_structure.crystal_symmetry())
minimize_wrapper_with_map(
pdb_h=real_h,
xrs=ref_xrs,
target_map=reference_map,
grm=grm,
ncs_restraints_group_list=[],
mon_lib_srv=None,
ss_annotation=ss_annotation,
refine_ncs_operators=False,
number_of_cycles=processed_params.n_macro,
log=log)
real_h.write_pdb_file("after_ss_map_min.pdb")
log.write(" Done\n")
log.flush()
t11 = time()
# print >> log, "Initial checking, init : %.4f" % (t1-t0)
# print >> log, "Checking SS : %.4f" % (t2-t1)
# print >> log, "Initializing selections : %.4f" % (t4-t3)
# print >> log, "Looping for selections : %.4f" % (t5-t4)
# print >> log, "Finalizing selections : %.4f" % (t6-t5)
# print >> log, "PDB interpretation : %.4f" % (t7-t6)
# print >> log, "Get GRM : %.4f" % (t8-t7)
# print >> log, "Adding restraints to GRM : %.4f" % (t9-t8)
# print >> log, "Running GM : %.4f" % (t11-t10)
# print_hbond_proxies(grm.geometry,real_h)
return grm.geometry.get_chi_torsion_proxies()
def substitute_ss(real_h,
xray_structure,
ss_annotation,
params = None,
grm=None,
use_plane_peptide_bond_restr=True,
fix_rotamer_outliers=True,
cif_objects=None,
log=null_out(),
rotamer_manager=None,
reference_map=None,
verbose=False):
"""
Substitute secondary structure elements in real_h hierarchy with ideal
ones _in_place_.
Returns reference torsion proxies - the only thing that cannot be restored
with little effort outside the procedure.
real_h - hierarcy to substitute secondary structure elements.
xray_structure - xray_structure - needed to get crystal symmetry (to
construct processed_pdb_file and xray_structure is needed to call
get_geometry_restraints_manager for no obvious reason).
ss_annotation - iotbx.pdb.annotation object.
"""
t0 = time()
if rotamer_manager is None:
rotamer_manager = RotamerEval()
for model in real_h.models():
for chain in model.chains():
if len(chain.conformers()) > 1:
raise Sorry("Alternative conformations are not supported.")
processed_params = process_params(params)
if not processed_params.enabled:
return None
expected_n_hbonds = 0
ann = ss_annotation
for h in ann.helices:
expected_n_hbonds += h.get_n_maximum_hbonds()
edited_h = real_h.deep_copy()
n_atoms_in_real_h = real_h.atoms_size()
selection_cache = real_h.atom_selection_cache()
# check the annotation for correctness (atoms are actually in hierarchy)
error_msg = "The following secondary structure annotations result in \n"
error_msg +="empty atom selections. They don't match the structre: \n"
t1 = time()
# Checking for SS selections
deleted_annotations = ann.remove_empty_annotations(
hierarchy=real_h,
asc=selection_cache)
if not deleted_annotations.is_empty():
if processed_params.skip_empty_ss_elements:
if len(deleted_annotations.helices) > 0:
print >> log, "Removing the following helices because there are"
print >> log, "no corresponding atoms in the model:"
for h in deleted_annotations.helices:
print >> log, h.as_pdb_str()
error_msg += " %s\n" % h
if len(deleted_annotations.sheets) > 0:
print >> log, "Removing the following sheets because there are"
print >> log, "no corresponding atoms in the model:"
for sh in deleted_annotations.sheets:
print >> log, sh.as_pdb_str()
error_msg += " %s\n" % sh.as_pdb_str(strand_id=st.strand_id)
else:
raise Sorry(error_msg)
phil_str = ann.as_restraint_groups()
t2 = time()
# Actually idelizing SS elements
log.write("Replacing ss-elements with ideal ones:\n")
log.flush()
for h in ann.helices:
log.write(" %s\n" % h.as_pdb_str())
log.flush()
selstring = h.as_atom_selections()
isel = selection_cache.iselection(selstring[0])
all_bsel = flex.bool(n_atoms_in_real_h, False)
all_bsel.set_selected(isel, True)
sel_h = real_h.select(all_bsel, copy_atoms=True)
ideal_h = get_helix(helix_class=h.helix_class,
pdb_hierarchy_template=sel_h,
rotamer_manager=rotamer_manager)
# edited_h.select(all_bsel).atoms().set_xyz(ideal_h.atoms().extract_xyz())
set_xyz_carefully(dest_h=edited_h.select(all_bsel), source_h=ideal_h)
for sh in ann.sheets:
s = " %s\n" % sh.as_pdb_str()
ss = s.replace("\n", "\n ")
log.write(ss[:-2])
log.flush()
for st in sh.strands:
selstring = st.as_atom_selections()
isel = selection_cache.iselection(selstring)
all_bsel = flex.bool(n_atoms_in_real_h, False)
all_bsel.set_selected(isel, True)
sel_h = real_h.select(all_bsel, copy_atoms=True)
ideal_h = secondary_structure_from_sequence(
pdb_str=beta_pdb_str,
sequence=None,
pdb_hierarchy_template=sel_h,
rotamer_manager=rotamer_manager,
)
set_xyz_carefully(edited_h.select(all_bsel), ideal_h)
# edited_h.select(all_bsel).atoms().set_xyz(ideal_h.atoms().extract_xyz())
t3 = time()
pre_result_h = edited_h
pre_result_h.reset_i_seq_if_necessary()
n_atoms = real_h.atoms_size()
bsel = flex.bool(n_atoms, False)
helix_selection = flex.bool(n_atoms, False)
sheet_selection = flex.bool(n_atoms, False)
other_selection = flex.bool(n_atoms, False)
ss_for_tors_selection = flex.bool(n_atoms, False)
nonss_for_tors_selection = flex.bool(n_atoms, False)
selection_cache = real_h.atom_selection_cache()
# set all CA atoms to True for other_selection
#isel = selection_cache.iselection("name ca")
isel = selection_cache.iselection("name ca or name n or name o or name c")
other_selection.set_selected(isel, True)
n_main_chain_atoms = other_selection.count(True)
isel = selection_cache.iselection("name ca or name n or name o or name c")
nonss_for_tors_selection.set_selected(isel, True)
main_chain_selection_prefix = "(name ca or name n or name o or name c) %s"
t4 = time()
print >> log, "Preparing selections..."
log.flush()
# Here we are just preparing selections
for h in ann.helices:
ss_sels = h.as_atom_selections()[0]
selstring = main_chain_selection_prefix % ss_sels
isel = selection_cache.iselection(selstring)
helix_selection.set_selected(isel, True)
other_selection.set_selected(isel, False)
isel = selection_cache.iselection(selstring)
ss_for_tors_selection.set_selected(isel, True)
nonss_for_tors_selection.set_selected(isel, False)
for sheet in ann.sheets:
for ss_sels in sheet.as_atom_selections():
selstring = main_chain_selection_prefix % ss_sels
isel = selection_cache.iselection(selstring)
sheet_selection.set_selected(isel, True)
other_selection.set_selected(isel, False)
isel = selection_cache.iselection(selstring)
ss_for_tors_selection.set_selected(isel, True)
nonss_for_tors_selection.set_selected(isel, False)
t5 = time()
isel = selection_cache.iselection(
"not name ca and not name n and not name o and not name c")
other_selection.set_selected(isel, False)
helix_sheet_intersection = helix_selection & sheet_selection
if helix_sheet_intersection.count(True) > 0:
sheet_selection = sheet_selection & ~helix_sheet_intersection
assert ((helix_selection | sheet_selection) & other_selection).count(True)==0
from mmtbx.monomer_library.pdb_interpretation import grand_master_phil_str
params_line = grand_master_phil_str
params_line += "secondary_structure {%s}" % secondary_structure.sec_str_master_phil_str
# print "params_line"
# print params_line
params = iotbx.phil.parse(input_string=params_line, process_includes=True)#.extract()
# This does not the same way for a strange reason. Need to investigate.
# The number of resulting hbonds is different later.
# w_params = params.extract()
# w_params.pdb_interpretation.secondary_structure.protein.remove_outliers = False
# w_params.pdb_interpretation.peptide_link.ramachandran_restraints = True
# w_params.pdb_interpretation.c_beta_restraints = True
# w_params.pdb_interpretation.secondary_structure.enabled = True
# params.format(python_object=w_params)
# params.show()
# print "="*80
# print "="*80
# print "="*80
if grm is None:
custom_par_text = "\n".join([
"pdb_interpretation.secondary_structure {protein.remove_outliers = False\n%s}" \
% phil_str,
"pdb_interpretation.peptide_link.ramachandran_restraints = True",
"c_beta_restraints = True",
"pdb_interpretation.secondary_structure.enabled=True",
"pdb_interpretation.clash_guard.nonbonded_distance_threshold=None",
"pdb_interpretation.max_reasonable_bond_distance=None",
# "pdb_interpretation.nonbonded_weight=500",
"pdb_interpretation.peptide_link.oldfield.weight_scale=3",
"pdb_interpretation.peptide_link.oldfield.plot_cutoff=0.03",
"pdb_interpretation.peptide_link.omega_esd_override_value=3",
"pdb_interpretation.peptide_link.apply_all_trans=True",
])
if use_plane_peptide_bond_restr:
custom_par_text += "\npdb_interpretation.peptide_link.apply_peptide_plane=True"
custom_pars = params.fetch(
source=iotbx.phil.parse(custom_par_text)).extract()
# params.format(python_object=custom_pars)
# params.show()
# STOP()
params = custom_pars
# params = w_params
t6 = time()
import mmtbx.utils
processed_pdb_files_srv = mmtbx.utils.\
process_pdb_file_srv(
crystal_symmetry= xray_structure.crystal_symmetry(),
pdb_interpretation_params = params.pdb_interpretation,
log=null_out(),
cif_objects=cif_objects)
if verbose:
print >> log, "Processing file..."
log.flush()
processed_pdb_file, junk = processed_pdb_files_srv.\
process_pdb_files(raw_records=flex.split_lines(real_h.as_pdb_string()))
t7 = time()
grm = get_geometry_restraints_manager(
processed_pdb_file, xray_structure)
t8 = time()
else:
ss_manager = secondary_structure.manager(
pdb_hierarchy=real_h,
geometry_restraints_manager=grm.geometry,
sec_str_from_pdb_file=ss_annotation,
params=None,
mon_lib_srv=None,
verbose=-1,
log=log)
grm.geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=real_h,
log=log)
real_h.reset_i_seq_if_necessary()
from mmtbx.geometry_restraints import reference
if reference_map is None:
if verbose:
print >> log, "Adding reference coordinate restraints..."
grm.geometry.append_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = real_h.atoms().extract_xyz().select(helix_selection),
selection = helix_selection,
sigma = processed_params.sigma_on_reference_helix))
grm.geometry.append_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = real_h.atoms().extract_xyz().select(sheet_selection),
selection = sheet_selection,
sigma = processed_params.sigma_on_reference_sheet))
grm.geometry.append_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = real_h.atoms().extract_xyz().select(other_selection),
selection = other_selection,
sigma = processed_params.sigma_on_reference_non_ss))
if verbose:
print >> log, "Adding chi torsion restraints..."
grm.geometry.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pre_result_h,
sites_cart = pre_result_h.atoms().extract_xyz().\
select(ss_for_tors_selection),
selection = ss_for_tors_selection,
chi_angles_only = False,
sigma = processed_params.sigma_on_torsion_ss)
grm.geometry.add_chi_torsion_restraints_in_place(
pdb_hierarchy = pre_result_h,
sites_cart = real_h.atoms().extract_xyz().\
select(nonss_for_tors_selection),
selection = nonss_for_tors_selection,
chi_angles_only = False,
sigma = processed_params.sigma_on_torsion_nonss)
real_h.atoms().set_xyz(pre_result_h.atoms().extract_xyz())
t9 = time()
if processed_params.file_name_before_regularization is not None:
grm.geometry.pair_proxies(sites_cart=real_h.atoms().extract_xyz())
if grm.geometry.ramachandran_manager is not None:
grm.geometry.ramachandran_manager.update_phi_psi_targets(
sites_cart=real_h.atoms().extract_xyz())
print >> log, "Outputting model before regularization %s" % processed_params.file_name_before_regularization
real_h.write_pdb_file(
file_name=processed_params.file_name_before_regularization)
geo_fname = processed_params.file_name_before_regularization[:-4]+'.geo'
print >> log, "Outputting geo file for regularization %s" % geo_fname
grm.write_geo_file(
site_labels=[atom.id_str() for atom in real_h.atoms()],
file_name=geo_fname)
#testing number of restraints
assert grm.geometry.get_n_den_proxies() == 0
if reference_map is None:
assert grm.geometry.get_n_reference_coordinate_proxies() == n_main_chain_atoms
refinement_log = null_out()
log.write(
"Refining geometry of substituted secondary structure elements...")
log.flush()
if verbose:
refinement_log = log
from mmtbx.refinement.geometry_minimization import run2
t10 = time()
if reference_map is None:
obj = run2(
restraints_manager = grm,
pdb_hierarchy = real_h,
correct_special_position_tolerance = 1.0,
max_number_of_iterations = processed_params.n_iter,
number_of_macro_cycles = processed_params.n_macro,
bond = True,
nonbonded = True,
angle = True,
dihedral = True,
chirality = True,
planarity = True,
fix_rotamer_outliers = fix_rotamer_outliers,
log = refinement_log)
else:
ref_xrs = real_h.extract_xray_structure(
crystal_symmetry=xray_structure.crystal_symmetry())
minimize_wrapper_with_map(
pdb_h=real_h,
xrs=ref_xrs,
target_map=reference_map,
grm=grm,
ncs_restraints_group_list=[],
mon_lib_srv=None,
ss_annotation=ss_annotation,
refine_ncs_operators=False,
number_of_cycles=processed_params.n_macro,
log=log)
real_h.write_pdb_file("after_ss_map_min.pdb")
log.write(" Done\n")
log.flush()
t11 = time()
# print >> log, "Initial checking, init : %.4f" % (t1-t0)
# print >> log, "Checking SS : %.4f" % (t2-t1)
# print >> log, "Initializing selections : %.4f" % (t4-t3)
# print >> log, "Looping for selections : %.4f" % (t5-t4)
# print >> log, "Finalizing selections : %.4f" % (t6-t5)
# print >> log, "PDB interpretation : %.4f" % (t7-t6)
# print >> log, "Get GRM : %.4f" % (t8-t7)
# print >> log, "Adding restraints to GRM : %.4f" % (t9-t8)
# print >> log, "Running GM : %.4f" % (t11-t10)
# print_hbond_proxies(grm.geometry,real_h)
return grm.geometry.get_chi_torsion_proxies()