def exercise_1(mon_lib_srv, ener_lib):
pdb_in = simple_pdb()
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
sites_cart = pdb_hierarchy.atoms().extract_xyz()
proxies = reference.add_coordinate_restraints(sites_cart=sites_cart)
assert proxies.size() == 29, "expected 29, got %d" % proxies.size()
import boost.python
ext = boost.python.import_ext("mmtbx_reference_coordinate_ext")
grads = flex.vec3_double(sites_cart.size(), (0.0,0.0,0.0))
residual = ext.reference_coordinate_residual_sum(
sites_cart=sites_cart,
proxies=proxies,
gradient_array=grads)
assert approx_equal(residual, 0.0)
#test selection
ca_selection = pdb_hierarchy.get_peptide_c_alpha_selection()
ca_sites_cart = sites_cart.select(ca_selection)
proxies = reference.add_coordinate_restraints(
sites_cart=ca_sites_cart,
selection=ca_selection)
assert proxies.size() == 3, "expected 3, got %d" % proxies.size()
tst_iselection = flex.size_t()
for atom in pdb_hierarchy.atoms():
if atom.name == " CA " or atom.name == " N ":
tst_iselection.append(atom.i_seq)
tst_sites_cart = sites_cart.select(tst_iselection)
proxies = reference.add_coordinate_restraints(
sites_cart=tst_sites_cart,
selection=tst_iselection)
assert proxies.size() == 6, "expected 6, got %d" % proxies.size()
#test remove
selection = flex.bool([False]*29)
proxies = proxies.proxy_remove(selection=selection)
assert proxies.size() == 6, "expected 6, got %d" % proxies.size()
proxies = proxies.proxy_remove(selection=ca_selection)
assert proxies.size() == 3, "expected 3, got %d" % proxies.size()
selection = flex.bool([True]*29)
proxies = proxies.proxy_remove(selection=selection)
assert proxies.size() == 0, "expected 0, got %d" % proxies.size()
def exercise_1(mon_lib_srv, ener_lib):
pdb_in = simple_pdb()
params = pdb_interpretation.master_params.extract()
processed_pdb_file = pdb_interpretation.process(mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
pdb_inp=pdb_in,
log=StringIO())
grm = processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
sites_cart = pdb_hierarchy.atoms().extract_xyz()
proxies = reference.add_coordinate_restraints(sites_cart=sites_cart)
assert proxies.size() == 29, "expected 29, got %d" % proxies.size()
import boost.python
ext = boost.python.import_ext("mmtbx_reference_coordinate_ext")
grads = flex.vec3_double(sites_cart.size(), (0.0, 0.0, 0.0))
residual = ext.reference_coordinate_residual_sum(sites_cart=sites_cart,
proxies=proxies,
gradient_array=grads)
assert approx_equal(residual, 0.0)
#test selection
ca_selection = pdb_hierarchy.get_peptide_c_alpha_selection()
ca_sites_cart = sites_cart.select(ca_selection)
proxies = reference.add_coordinate_restraints(sites_cart=ca_sites_cart,
selection=ca_selection)
assert proxies.size() == 3, "expected 3, got %d" % proxies.size()
tst_iselection = flex.size_t()
for atom in pdb_hierarchy.atoms():
if atom.name == " CA " or atom.name == " N ":
tst_iselection.append(atom.i_seq)
tst_sites_cart = sites_cart.select(tst_iselection)
proxies = reference.add_coordinate_restraints(sites_cart=tst_sites_cart,
selection=tst_iselection)
assert proxies.size() == 6, "expected 6, got %d" % proxies.size()
#test remove
selection = flex.bool([False] * 29)
proxies = proxies.proxy_remove(selection=selection)
assert proxies.size() == 6, "expected 6, got %d" % proxies.size()
proxies = proxies.proxy_remove(selection=ca_selection)
assert proxies.size() == 3, "expected 3, got %d" % proxies.size()
selection = flex.bool([True] * 29)
proxies = proxies.proxy_remove(selection=selection)
assert proxies.size() == 0, "expected 0, got %d" % proxies.size()
def exercise_1():
pdb_in = simple_pdb()
pdb_hierarchy = pdb_in.construct_hierarchy()
sites_cart = pdb_hierarchy.atoms().extract_xyz()
proxies = reference.add_coordinate_restraints(sites_cart=sites_cart)
assert proxies.size() == 29, "expected 29, got %d" % proxies.size()
import boost.python
ext = boost.python.import_ext("mmtbx_reference_coordinate_ext")
grads = flex.vec3_double(sites_cart.size(), (0.0,0.0,0.0))
residual = ext.reference_coordinate_residual_sum(
sites_cart=sites_cart,
proxies=proxies,
gradient_array=grads)
assert approx_equal(residual, 0.0)
#test selection
ca_selection = pdb_hierarchy.get_peptide_c_alpha_selection()
ca_sites_cart = sites_cart.select(ca_selection)
proxies = reference.add_coordinate_restraints(
sites_cart=ca_sites_cart,
selection=ca_selection)
assert proxies.size() == 3, "expected 3, got %d" % proxies.size()
tst_iselection = flex.size_t()
for atom in pdb_hierarchy.atoms():
if atom.name == " CA " or atom.name == " N ":
tst_iselection.append(atom.i_seq)
tst_sites_cart = sites_cart.select(tst_iselection)
proxies = reference.add_coordinate_restraints(
sites_cart=tst_sites_cart,
selection=tst_iselection)
assert proxies.size() == 6, "expected 6, got %d" % proxies.size()
#test remove
selection = flex.bool([False]*29)
proxies = proxies.proxy_remove(selection=selection)
assert proxies.size() == 6, "expected 6, got %d" % proxies.size()
proxies = proxies.proxy_remove(selection=ca_selection)
assert proxies.size() == 3, "expected 3, got %d" % proxies.size()
selection = flex.bool([True]*29)
proxies = proxies.proxy_remove(selection=selection)
assert proxies.size() == 0, "expected 0, got %d" % proxies.size()
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 test_reference_coordinate(mon_lib_srv, ener_lib, prefix="tst_grm_pickling_ref_coor"):
from mmtbx.geometry_restraints import reference
# for some strange reason without importing this the code doesn't work...
from cctbx import adp_restraints # import dependency
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records3)
params = monomer_library.pdb_interpretation.master_params.extract()
params.reference_coordinate_restraints.enabled=False
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
strict_conflict_handling=False,
pdb_inp=pdb_inp,
log=null_out())
geo = processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
sites_cart = pdb_hierarchy.atoms().extract_xyz()
rcp = reference.add_coordinate_restraints(sites_cart=sites_cart)
geo.adopt_reference_coordinate_restraints_in_place(rcp)
# print "number of rcr proxies:", geo.get_n_reference_coordinate_proxies()
make_geo_pickle_unpickle(geo, processed_pdb_file.xray_structure(), prefix)
def make_wat_restraints(self, sigma):
raw_records = self.std_wat_pdb.as_pdb_string()
processed_pdb = monomer_library.pdb_interpretation.process(
mon_lib_srv=monomer_library.server.server(),
ener_lib=monomer_library.server.ener_lib(),
file_name=None,
raw_records=raw_records,
crystal_symmetry=self.std_wat_pdb.crystal_symmetry(),
force_symmetry=True)
geometry = processed_pdb.geometry_restraints_manager(
show_energies=False, plain_pairs_radius=5.0)
chain_proxy = processed_pdb.all_chain_proxies
sites_start = self.std_wat_xrs.sites_cart()
selection = chain_proxy.selection("Element O")
isel = selection.iselection()
harm_proxy = add_coordinate_restraints(
sites_cart=sites_start.select(isel), selection=isel, sigma=sigma)
restraints_manager = mmtbx.restraints.manager(geometry=geometry,
normalization=False)
restraints_manager.geometry.reference_coordinate_proxies = harm_proxy
return restraints_manager
def test_reference_coordinate(mon_lib_srv,
ener_lib,
prefix="tst_grm_pickling_ref_coor"):
from mmtbx.geometry_restraints import reference
# for some strange reason without importing this the code doesn't work...
from cctbx import adp_restraints # import dependency
pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records3)
params = monomer_library.pdb_interpretation.master_params.extract()
params.reference_coordinate_restraints.enabled = False
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
params=params,
strict_conflict_handling=False,
pdb_inp=pdb_inp,
log=sys.stdout)
geo = processed_pdb_file.geometry_restraints_manager()
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
sites_cart = pdb_hierarchy.atoms().extract_xyz()
rcp = reference.add_coordinate_restraints(sites_cart=sites_cart)
geo.adopt_reference_coordinate_restraints_in_place(rcp)
# print "number of rcr proxies:", geo.get_n_reference_coordinate_proxies()
make_geo_pickle_unpickle(geo, processed_pdb_file.xray_structure(), prefix)
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 minimize_wrapper_for_ramachandran(
model,
original_pdb_h,
excl_string_selection,
processed_pdb_file=None,
log=None,
reference_rotamers=True,
number_of_cycles=1,
run_first_minimization_without_reference=False,
oldfield_weight_scale=3,
oldfield_plot_cutoff=0.03,
nonbonded_weight=500,
reference_sigma=0.7):
""" Wrapper around geometry minimization specifically tuned for eliminating
Ramachandran outliers.
probably not working anymore... no processed_pdb_file available.
WARNING: no setting sites_cart at the end...
"""
grm = model.get_restraints_manager()
assert grm is not None
from mmtbx.geometry_restraints import reference
from mmtbx.geometry_restraints.torsion_restraints.reference_model import \
reference_model, reference_model_params
from libtbx.utils import null_out
from scitbx.array_family import flex
if log is None:
log = null_out()
# assert hierarchy.atoms_size()==xrs.scatterers().size(), "%d %d" % (
# hierarchy.atoms_size(), xrs.scatterers().size())
ncs_restraints_group_list = model.get_ncs_groups()
if ncs_restraints_group_list is None:
ncs_restraints_group_list = []
grm.geometry.pair_proxies(sites_cart=model.get_sites_cart())
if grm.geometry.ramachandran_manager is not None:
grm.geometry.ramachandran_manager.update_phi_psi_targets(
sites_cart=model.get_sites_cart())
if reference_rotamers and original_pdb_h is not None:
# make selection excluding rotamer outliers
from mmtbx.rotamer.rotamer_eval import RotamerEval
# print "Excluding rotamer outliers"
rotamer_manager = model.get_rotamer_manager()
non_rot_outliers_selection = flex.bool(model.get_number_of_atoms(),
False)
for m in original_pdb_h.models():
for chain in m.chains():
for conf in chain.conformers():
for res in conf.residues():
ev = rotamer_manager.evaluate_residue_2(res)
if ev != "OUTLIER" or ev is None:
for a in res.atoms():
non_rot_outliers_selection[a.i_seq] = True
# else:
# print " ", res.id_str()
if processed_pdb_file is not None:
rm_params = reference_model_params.extract()
rm_params.reference_model.enabled = True
rm_params.reference_model.strict_rotamer_matching = False
rm_params.reference_model.main_chain = False
rm = reference_model(processed_pdb_file=processed_pdb_file,
reference_file_list=None,
reference_hierarchy_list=[original_pdb_h],
mon_lib_srv=model.get_mon_lib_srv(),
ener_lib=model.get_ener_lib(),
has_hd=None,
params=rm_params.reference_model,
selection=non_rot_outliers_selection,
log=log)
rm.show_reference_summary(log=log)
grm.geometry.adopt_reference_dihedral_manager(rm)
# dealing with SS
if model.get_ss_annotation() is not None:
from mmtbx.secondary_structure import manager
ss_manager = manager(pdb_hierarchy=model.get_hierarchy(),
geometry_restraints_manager=grm.geometry,
sec_str_from_pdb_file=model.get_ss_annotation(),
params=None,
mon_lib_srv=model.get_mon_lib_srv(),
verbose=-1,
log=log)
grm.geometry.set_secondary_structure_restraints(
ss_manager=ss_manager, hierarchy=model.get_hierarchy(), log=log)
if run_first_minimization_without_reference:
obj = run2(restraints_manager=grm,
pdb_hierarchy=model.get_hierarchy(),
correct_special_position_tolerance=1.0,
ncs_restraints_group_list=ncs_restraints_group_list,
max_number_of_iterations=300,
number_of_macro_cycles=number_of_cycles,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True,
fix_rotamer_outliers=True,
log=log)
if original_pdb_h is not None:
if not excl_string_selection or len(excl_string_selection) == 0:
excl_string_selection = "all"
asc = original_pdb_h.atom_selection_cache()
sel = asc.selection(
"(%s) and (name CA or name C or name N or name O)" %
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=reference_sigma,
top_out_potential=True))
obj = run2(restraints_manager=grm,
pdb_hierarchy=model.get_hierarchy(),
correct_special_position_tolerance=1.0,
ncs_restraints_group_list=ncs_restraints_group_list,
max_number_of_iterations=300,
number_of_macro_cycles=number_of_cycles,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True,
fix_rotamer_outliers=True,
log=log)
grm.geometry.reference_dihedral_manager = None
def substitute_ss(
model, # changed in place
params = None,
use_plane_peptide_bond_restr=True,
fix_rotamer_outliers=True,
log=null_out(),
check_rotamer_clashes=True,
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.
"""
import mmtbx.utils
ss_annotation = model.get_ss_annotation()
t0 = time()
if model.get_hierarchy().models_size() > 1:
raise Sorry("Multi model files are not supported")
for m in model.get_hierarchy().models():
for chain in m.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
if ss_annotation is None:
return None
ann = ss_annotation
if model.ncs_constraints_present():
print >> log, "Using master NCS to reduce amount of work"
expected_n_hbonds = 0
for h in ann.helices:
expected_n_hbonds += h.get_n_maximum_hbonds()
edited_h = model.get_hierarchy().deep_copy()
n_atoms_in_real_h = model.get_number_of_atoms()
selection_cache = model.get_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=model.get_hierarchy(),
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 = model.crystal_symmetry())
site_symmetry_table = \
special_position_settings.site_symmetry_table(
sites_cart = model.get_sites_cart(),
unconditional_general_position_flags=(
model.get_atoms().extract_occ() != 1))
original_spi = site_symmetry_table.special_position_indices()
t2 = time()
# Actually idelizing SS elements
fixed_ss_selection = flex.bool(n_atoms_in_real_h, False)
log.write("Replacing ss-elements with ideal ones:\n")
log.flush()
ss_stats = gather_ss_stats(pdb_h=model.get_hierarchy())
n_idealized_elements = 0
master_bool_sel = model.get_master_selection()
if master_bool_sel is None or master_bool_sel.size() == 0:
master_bool_sel = flex.bool(model.get_number_of_atoms(), True)
elif isinstance(master_bool_sel, flex.size_t):
master_bool_sel = flex.bool(model.get_number_of_atoms(), master_bool_sel)
assert master_bool_sel.size() == model.get_number_of_atoms()
for h in ann.helices:
log.write(" %s\n" % h.as_pdb_str())
log.flush()
if processed_params.skip_good_ss_elements and ss_element_is_good(ss_stats, ([h],[])):
log.write(" skipping, good element.\n")
else:
selstring = h.as_atom_selections()
sel = selection_cache.selection(selstring[0])
isel = sel.iselection()
if (master_bool_sel & sel).iselection().size() == 0:
log.write(" skipping, not in NCS master.\n")
continue
n_idealized_elements += 1
log.write(" substitute with idealized one.\n")
fixed_ss_selection.set_selected(isel, True)
all_bsel = flex.bool(n_atoms_in_real_h, False)
all_bsel.set_selected(isel, True)
sel_h = model.get_hierarchy().select(all_bsel, copy_atoms=True)
ideal_h = get_helix(helix_class=h.helix_class,
pdb_hierarchy_template=sel_h,
rotamer_manager=model.get_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)
# set_xyz_smart(dest_h=edited_h.select(all_bsel), source_h=ideal_h) # does not work here
for sh in ann.sheets:
s = " %s\n" % sh.as_pdb_str()
ss = s.replace("\n", "\n ")
log.write(ss[:-2])
log.flush()
if processed_params.skip_good_ss_elements and ss_element_is_good(ss_stats, ([],[sh])):
log.write(" skipping, good element.\n")
else:
full_sh_selection = flex.bool(n_atoms_in_real_h, False)
for st in sh.strands:
selstring = st.as_atom_selections()
isel = selection_cache.iselection(selstring)
full_sh_selection.set_selected(isel, True)
if (master_bool_sel & full_sh_selection).iselection().size() == 0:
log.write(" skipping, not in NCS master.\n")
continue
n_idealized_elements += 1
log.write(" substitute with idealized one.\n")
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)
fixed_ss_selection.set_selected(isel, True)
sel_h = model.get_hierarchy().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=model.get_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())
if n_idealized_elements == 0:
log.write("Nothing was idealized.\n")
# Don't do geometry minimization and stuff if nothing was changed.
return None
# XXX here we want to adopt new coordinates
model.set_sites_cart(sites_cart=edited_h.atoms().extract_xyz())
if model.ncs_constraints_present():
model.set_sites_cart_from_hierarchy(multiply_ncs=True)
t3 = time()
# pre_result_h = edited_h
# pre_result_h.reset_i_seq_if_necessary()
bsel = flex.bool(n_atoms_in_real_h, False)
helix_selection = flex.bool(n_atoms_in_real_h, False)
sheet_selection = flex.bool(n_atoms_in_real_h, False)
other_selection = flex.bool(n_atoms_in_real_h, False)
ss_for_tors_selection = flex.bool(n_atoms_in_real_h, False)
nonss_for_tors_selection = flex.bool(n_atoms_in_real_h, False)
# 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 work 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
grm = model.get_restraints_manager()
ssm_log = null_out()
if verbose:
ssm_log = log
ss_params = secondary_structure.sec_str_master_phil.fetch().extract()
ss_params.secondary_structure.protein.remove_outliers=False
ss_manager = secondary_structure.manager(
pdb_hierarchy=model.get_hierarchy(),
geometry_restraints_manager=grm.geometry,
sec_str_from_pdb_file=ss_annotation,
params=ss_params.secondary_structure,
mon_lib_srv=None,
verbose=-1,
log=ssm_log)
grm.geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=model.get_hierarchy(),
log=ssm_log)
model.get_hierarchy().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 = model.get_sites_cart().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 = model.get_sites_cart().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 = model.get_sites_cart().select(other_selection),
selection = other_selection,
sigma = processed_params.sigma_on_reference_non_ss))
# XXX Somewhere here we actually should check placed side-chains for
# clashes because we used ones that were in original model and just moved
# them to nearest allowed rotamer. The idealization may affect a lot
# the orientation of side chain thus justifying changing rotamer on it
# to avoid clashes.
if check_rotamer_clashes:
print >> log, "Fixing/checking rotamers..."
# pre_result_h.write_pdb_file(file_name="before_rotamers.pdb")
br_txt = model.model_as_pdb()
with open("before_rotamers.pdb", 'w') as f:
f.write(br_txt)
mmtbx.utils.fix_rotamer_outliers(
model = model,
map_data=reference_map,
radius=5,
backrub_range=None, # don't sample backrub at this point
non_outliers_to_check=fixed_ss_selection, # bool selection
verbose=True,
log=log)
if verbose:
print >> log, "Adding chi torsion restraints..."
# only backbone
grm.geometry.add_chi_torsion_restraints_in_place(
pdb_hierarchy = model.get_hierarchy(),
sites_cart = model.get_sites_cart().\
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 = model.get_hierarchy(),
sites_cart = model.get_sites_cart().\
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
#
real_h = model.get_hierarchy() # just a shortcut here...
special_position_settings = crystal.special_position_settings(
crystal_symmetry = model.crystal_symmetry())
site_symmetry_table = \
special_position_settings.site_symmetry_table(
sites_cart = model.get_sites_cart(),
unconditional_general_position_flags=(
model.get_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)
model.set_sites_cart_from_hierarchy()
t9 = time()
if processed_params.file_name_before_regularization is not None:
grm.geometry.pair_proxies(sites_cart=model.get_sites_cart())
if grm.geometry.ramachandran_manager is not None:
grm.geometry.ramachandran_manager.update_phi_psi_targets(
sites_cart=model.get_sites_cart())
print >> log, "Outputting model before regularization %s" % processed_params.file_name_before_regularization
m_txt = model.model_as_pdb()
g_txt = model.restraints_as_geo()
with open(processed_params.file_name_before_regularization, 'w') as f:
f.write(m_txt)
geo_fname = processed_params.file_name_before_regularization[:-4]+'.geo'
print >> log, "Outputting geo file for regularization %s" % geo_fname
with open(geo_fname, 'w') as f:
f.write(g_txt)
#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, "" +\
"%d %d" % (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
t10 = time()
if reference_map is None:
minimize_wrapper_for_ramachandran(
model = model,
original_pdb_h = None,
excl_string_selection = "",
log = refinement_log,
number_of_cycles = processed_params.n_iter)
else:
ref_xrs = model.crystal_symmetry()
minimize_wrapper_with_map(
model = model,
target_map=reference_map,
refine_ncs_operators=False,
number_of_cycles=processed_params.n_macro,
log=log)
model.set_sites_cart_from_hierarchy()
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)
grm.geometry.remove_reference_coordinate_restraints_in_place()
return grm.geometry.get_chi_torsion_proxies()
def exercise_2():
for use_reference in [True, False, None]:
pdb_inp = iotbx.pdb.input(
lines=flex.std_string(pdb_str_2.splitlines()), source_info=None)
model = manager(
model_input=pdb_inp,
log=null_out())
grm = model.get_restraints_manager().geometry
xrs2 = model.get_xray_structure()
awl2 = model.get_hierarchy().atoms_with_labels()
pdb_inp3 = iotbx.pdb.input(source_info=None, lines=pdb_str_3)
xrs3 = pdb_inp3.xray_structure_simple()
ph3 = pdb_inp3.construct_hierarchy()
ph3.atoms().reset_i_seq()
awl3 = ph3.atoms_with_labels()
sites_cart_reference = flex.vec3_double()
selection = flex.size_t()
reference_names = ["CG", "CD", "NE", "CZ", "NH1", "NH2"]
for a2,a3 in zip(tuple(awl2), tuple(awl3)):
assert a2.resname == a3.resname
assert a2.name == a3.name
assert a2.i_seq == a3.i_seq
if(a2.resname == "ARG" and a2.name.strip() in reference_names):
selection.append(a2.i_seq)
sites_cart_reference.append(a3.xyz)
assert selection.size() == len(reference_names)
selection_bool = flex.bool(xrs2.scatterers().size(), selection)
if(use_reference):
grm.adopt_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = sites_cart_reference,
selection = selection,
sigma = 0.01))
elif(use_reference is None):
grm.adopt_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = sites_cart_reference,
selection = selection,
sigma = 0.01))
grm.remove_reference_coordinate_restraints_in_place(
selection = selection)
d1 = flex.mean(flex.sqrt((xrs2.sites_cart().select(selection) -
xrs3.sites_cart().select(selection)).dot()))
print("distance start (use_reference: %s): %6.4f"%(str(use_reference), d1))
assert d1>4.0
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
from cctbx import geometry_restraints
import mmtbx.refinement.geometry_minimization
import scitbx.lbfgs
grf = geometry_restraints.flags.flags(default=True)
sites_cart = xrs2.sites_cart()
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager = grm,
sites_cart_selection = flex.bool(sites_cart.size(), selection),
geometry_restraints_flags = grf,
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=5000))
xrs2.set_sites_cart(sites_cart = sites_cart)
d2 = flex.mean(flex.sqrt((xrs2.sites_cart().select(selection) -
xrs3.sites_cart().select(selection)).dot()))
print("distance final (use_reference: %s): %6.4f"%(str(use_reference), d2))
if(use_reference): assert d2<0.005, "failed: %f<0.05" % d2
else: assert d2>4.0, d2
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
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()
def whole_minimization(self):
t3 = time()
# pre_result_h = edited_h
# pre_result_h.reset_i_seq_if_necessary()
bsel = flex.bool(self.model.get_number_of_atoms(), False)
helix_selection = flex.bool(self.model.get_number_of_atoms(), False)
sheet_selection = flex.bool(self.model.get_number_of_atoms(), False)
other_selection = flex.bool(self.model.get_number_of_atoms(), False)
ss_for_tors_selection = flex.bool(self.model.get_number_of_atoms(), False)
nonss_for_tors_selection = flex.bool(self.model.get_number_of_atoms(), False)
# set all CA atoms to True for other_selection
#isel = self.model.get_atom_selection_cache().iselection("name ca")
isel = self.model.get_atom_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 = self.model.get_atom_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("Preparing selections...", file=self.log)
self.log.flush()
# Here we are just preparing selections
for h in self.ss_annotation.helices:
ss_sels = h.as_atom_selections()[0]
selstring = main_chain_selection_prefix % ss_sels
isel = self.model.get_atom_selection_cache().iselection(selstring)
helix_selection.set_selected(isel, True)
other_selection.set_selected(isel, False)
isel = self.model.get_atom_selection_cache().iselection(selstring)
ss_for_tors_selection.set_selected(isel, True)
nonss_for_tors_selection.set_selected(isel, False)
for sheet in self.ss_annotation.sheets:
for ss_sels in sheet.as_atom_selections():
selstring = main_chain_selection_prefix % ss_sels
isel = self.model.get_atom_selection_cache().iselection(selstring)
sheet_selection.set_selected(isel, True)
other_selection.set_selected(isel, False)
isel = self.model.get_atom_selection_cache().iselection(selstring)
ss_for_tors_selection.set_selected(isel, True)
nonss_for_tors_selection.set_selected(isel, False)
t5 = time()
# print("N idealized elements: %d" % n_idealized_elements, file=self.log)
# print("Initial checking, init : %.4f" % (t1-t0), file=self.log)
# print("Checking SS : %.4f" % (t2-t1), file=self.log)
# print("Changing SS : %.4f" % (t3-t2), file=self.log)
# print("Initializing selections : %.4f" % (t4-t3), file=self.log)
# print("Looping for selections : %.4f" % (t5-t4), file=self.log)
# with open('idealized.pdb', 'w') as f:
# f.write(self.model.model_as_pdb())
# return
isel = self.model.get_atom_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 work 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
grm = self.model.get_restraints_manager()
ssm_log = null_out()
if self.processed_params.verbose:
ssm_log = self.log
ss_params = secondary_structure.sec_str_master_phil.fetch().extract()
ss_params.secondary_structure.protein.remove_outliers=False
ss_manager = secondary_structure.manager(
pdb_hierarchy=self.model.get_hierarchy(),
geometry_restraints_manager=grm.geometry,
sec_str_from_pdb_file=self.ss_annotation,
params=ss_params.secondary_structure,
mon_lib_srv=None,
verbose=-1,
log=ssm_log)
grm.geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=self.model.get_hierarchy(),
log=ssm_log)
self.model.get_hierarchy().reset_i_seq_if_necessary()
from mmtbx.geometry_restraints import reference
if self.reference_map is None:
if self.processed_params.verbose:
print("Adding reference coordinate restraints...", file=self.log)
grm.geometry.append_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = self.model.get_sites_cart().select(helix_selection),
selection = helix_selection,
sigma = self.processed_params.sigma_on_reference_helix))
grm.geometry.append_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = self.model.get_sites_cart().select(sheet_selection),
selection = sheet_selection,
sigma = self.processed_params.sigma_on_reference_sheet))
grm.geometry.append_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = self.model.get_sites_cart().select(other_selection),
selection = other_selection,
sigma = self.processed_params.sigma_on_reference_non_ss))
# XXX Somewhere here we actually should check placed side-chains for
# clashes because we used ones that were in original model and just moved
# them to nearest allowed rotamer. The idealization may affect a lot
# the orientation of side chain thus justifying changing rotamer on it
# to avoid clashes.
if self.processed_params.fix_rotamer_outliers:
print("Fixing/checking rotamers...", file=self.log)
# pre_result_h.write_pdb_file(file_name="before_rotamers.pdb")
br_txt = self.model.model_as_pdb()
with open("before_rotamers.pdb", 'w') as f:
f.write(br_txt)
if(self.reference_map is None):
backbone_sample=False
else:
backbone_sample=True
result = mmtbx.refinement.real_space.fit_residues.run(
pdb_hierarchy = self.model.get_hierarchy(),
crystal_symmetry = self.model.crystal_symmetry(),
map_data = self.reference_map,
rotamer_manager = mmtbx.idealized_aa_residues.rotamer_manager.load(
rotamers="favored"),
sin_cos_table = scitbx.math.sin_cos_table(n=10000),
backbone_sample = backbone_sample,
mon_lib_srv = self.model.get_mon_lib_srv(),
log = self.log)
self.model.set_sites_cart(
sites_cart = result.pdb_hierarchy.atoms().extract_xyz())
if self.processed_params.verbose:
print("Adding chi torsion restraints...", file=self.log)
# only backbone
grm.geometry.add_chi_torsion_restraints_in_place(
pdb_hierarchy = self.model.get_hierarchy(),
sites_cart = self.model.get_sites_cart().\
select(ss_for_tors_selection),
selection = ss_for_tors_selection,
chi_angles_only = False,
sigma = self.processed_params.sigma_on_torsion_ss)
grm.geometry.add_chi_torsion_restraints_in_place(
pdb_hierarchy = self.model.get_hierarchy(),
sites_cart = self.model.get_sites_cart().\
select(nonss_for_tors_selection),
selection = nonss_for_tors_selection,
chi_angles_only = False,
sigma = self.processed_params.sigma_on_torsion_nonss)
# real_h.atoms().set_xyz(pre_result_h.atoms().extract_xyz())
#
# Check and correct for special positions
#
real_h = self.model.get_hierarchy() # just a shortcut here...
special_position_settings = crystal.special_position_settings(
crystal_symmetry = self.model.crystal_symmetry())
site_symmetry_table = \
special_position_settings.site_symmetry_table(
sites_cart = self.model.get_sites_cart(),
unconditional_general_position_flags=(
self.model.get_atoms().extract_occ() != 1))
spi = site_symmetry_table.special_position_indices()
if spi.size() > 0:
print("Moving atoms from special positions:", file=self.log)
for spi_i in spi:
if spi_i not in self.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(" ", real_h.atoms()[spi_i].id_str(), end=' ', file=self.log)
print(tuple(real_h.atoms()[spi_i].xyz), "-->", new_coords, file=self.log)
real_h.atoms()[spi_i].set_xyz(new_coords)
self.model.set_sites_cart_from_hierarchy()
self.model_before_regularization = self.model.deep_copy()
t9 = time()
if self.processed_params.file_name_before_regularization is not None:
grm.geometry.pair_proxies(sites_cart=self.model.get_sites_cart())
grm.geometry.update_ramachandran_restraints_phi_psi_targets(
hierarchy=self.model.get_hierarchy())
print("Outputting model before regularization %s" % self.processed_params.file_name_before_regularization, file=self.log)
m_txt = self.model.model_as_pdb()
g_txt = self.model.restraints_as_geo()
with open(self.processed_params.file_name_before_regularization, 'w') as f:
f.write(m_txt)
geo_fname = self.processed_params.file_name_before_regularization[:-4]+'.geo'
print("Outputting geo file for regularization %s" % geo_fname, file=self.log)
with open(geo_fname, 'w') as f:
f.write(g_txt)
#testing number of restraints
assert grm.geometry.get_n_den_proxies() == 0
if self.reference_map is None:
assert grm.geometry.get_n_reference_coordinate_proxies() == n_main_chain_atoms, "" +\
"%d %d" % (grm.geometry.get_n_reference_coordinate_proxies(), n_main_chain_atoms)
refinement_log = null_out()
self.log.write(
"Refining geometry of substituted secondary structure elements\n")
self.log.write(
" for %s macro_cycle(s).\n" % self.processed_params.n_macro)
self.log.flush()
if self.processed_params.verbose:
refinement_log = self.log
t10 = time()
if self.reference_map is None:
n_cycles = self.processed_params.n_macro
if self.processed_params.n_macro == Auto:
n_cycles=5
minimize_wrapper_for_ramachandran(
model = self.model,
original_pdb_h = None,
excl_string_selection = "",
log = refinement_log,
number_of_cycles = n_cycles)
else:
ref_xrs = self.model.crystal_symmetry()
minimize_wrapper_with_map(
model = self.model,
target_map=self.reference_map,
refine_ncs_operators=False,
number_of_cycles=self.processed_params.n_macro,
min_mode='simple_cycles',
log=self.log)
self.model.set_sites_cart_from_hierarchy()
self.log.write(" Done\n")
self.log.flush()
t11 = time()
# print("Initial checking, init : %.4f" % (t1-t0), file=self.log)
# print("Checking SS : %.4f" % (t2-t1), file=self.log)
# print("Initializing selections : %.4f" % (t4-t3), file=self.log)
# print("Looping for selections : %.4f" % (t5-t4), file=self.log)
# print("Finalizing selections : %.4f" % (t6-t5), file=self.log)
# print("PDB interpretation : %.4f" % (t7-t6), file=self.log)
# print("Get GRM : %.4f" % (t8-t7), file=self.log)
# print("Adding restraints to GRM : %.4f" % (t9-t8), file=self.log)
# print("Running GM : %.4f" % (t11-t10), file=self.log)
# print_hbond_proxies(grm.geometry,real_h)
grm.geometry.remove_reference_coordinate_restraints_in_place()
grm.geometry.remove_chi_torsion_restraints_in_place(nonss_for_tors_selection)
return grm.geometry.get_chi_torsion_proxies()
def minimize_wrapper_for_ramachandran(
hierarchy,
xrs,
original_pdb_h,
excl_string_selection,
grm=None,
log=None,
ncs_restraints_group_list=[],
ss_annotation=None,
mon_lib_srv=None,
ener_lib=None,
rotamer_manager=None,
reference_rotamers=True,
number_of_cycles=1,
run_first_minimization_without_reference=False,
oldfield_weight_scale=3,
oldfield_plot_cutoff=0.03,
nonbonded_weight=500,
reference_sigma=0.7):
""" Wrapper around geometry minimization specifically tuned for eliminating
Ramachandran outliers.
"""
try:
import cPickle as pickle
except ImportError:
import pickle
from time import time
from mmtbx.monomer_library.pdb_interpretation import grand_master_phil_str
from mmtbx.geometry_restraints import reference
from mmtbx.command_line.geometry_minimization import \
get_geometry_restraints_manager
from mmtbx.geometry_restraints.torsion_restraints.reference_model import \
reference_model, reference_model_params
from libtbx.utils import null_out
from scitbx.array_family import flex
if log is None:
log = null_out()
# assert hierarchy.atoms_size()==xrs.scatterers().size(), "%d %d" % (
# hierarchy.atoms_size(), xrs.scatterers().size())
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 = oldfield_weight_scale
params.pdb_interpretation.peptide_link.oldfield.plot_cutoff = oldfield_plot_cutoff
params.pdb_interpretation.nonbonded_weight = nonbonded_weight
params.pdb_interpretation.c_beta_restraints = True
params.pdb_interpretation.max_reasonable_bond_distance = None
params.pdb_interpretation.peptide_link.apply_peptide_plane = True
params.pdb_interpretation.ncs_search.enabled = True
params.pdb_interpretation.restraints_library.rdl = 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()))
mon_lib_srv = processed_pdb_files_srv.mon_lib_srv
ener_lib = processed_pdb_files_srv.ener_lib
ncs_restraints_group_list = []
if processed_pdb_file.ncs_obj is not None:
ncs_restraints_group_list = processed_pdb_file.ncs_obj.get_ncs_restraints_group_list(
)
if grm is None:
grm = get_geometry_restraints_manager(processed_pdb_file,
xrs,
params=params)
else:
grm.geometry.pair_proxies(sites_cart=hierarchy.atoms().extract_xyz())
if grm.geometry.ramachandran_manager is not None:
grm.geometry.ramachandran_manager.update_phi_psi_targets(
sites_cart=hierarchy.atoms().extract_xyz())
if reference_rotamers and original_pdb_h is not None:
# make selection excluding rotamer outliers
from mmtbx.rotamer.rotamer_eval import RotamerEval
# print "Excluding rotamer outliers"
if rotamer_manager is None:
rotamer_manager = RotamerEval(mon_lib_srv=mon_lib_srv)
non_rot_outliers_selection = flex.bool(hierarchy.atoms_size(), False)
for model in original_pdb_h.models():
for chain in model.chains():
for conf in chain.conformers():
for res in conf.residues():
ev = rotamer_manager.evaluate_residue_2(res)
if ev != "OUTLIER" or ev is None:
for a in res.atoms():
non_rot_outliers_selection[a.i_seq] = True
# else:
# print " ", res.id_str()
rm_params = reference_model_params.extract()
rm_params.reference_model.enabled = True
rm_params.reference_model.strict_rotamer_matching = False
rm_params.reference_model.main_chain = False
rm = reference_model(processed_pdb_file=processed_pdb_file,
reference_file_list=None,
reference_hierarchy_list=[original_pdb_h],
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
has_hd=None,
params=rm_params.reference_model,
selection=non_rot_outliers_selection,
log=log)
rm.show_reference_summary(log=log)
grm.geometry.adopt_reference_dihedral_manager(rm)
# dealing with SS
if ss_annotation is not None:
from mmtbx.secondary_structure import manager
ss_manager = manager(pdb_hierarchy=hierarchy,
geometry_restraints_manager=grm.geometry,
sec_str_from_pdb_file=ss_annotation,
params=None,
mon_lib_srv=mon_lib_srv,
verbose=-1,
log=log)
grm.geometry.set_secondary_structure_restraints(ss_manager=ss_manager,
hierarchy=hierarchy,
log=log)
# grm pickle-unpickle
# t0 = time()
# prefix="grm"
# pklfile = open("%s.pkl" % prefix, 'wb')
# pickle.dump(grm.geometry, pklfile)
# pklfile.close()
# t1 = time()
# pklfile = open("%s.pkl" % prefix, 'rb')
# grm_from_file = pickle.load(pklfile)
# pklfile.close()
# t2 = time()
# print "Time pickling/unpickling: %.4f, %.4f" % (t1-t0, t2-t1)
# grm.geometry=grm_from_file
if run_first_minimization_without_reference:
obj = run2(restraints_manager=grm,
pdb_hierarchy=hierarchy,
correct_special_position_tolerance=1.0,
ncs_restraints_group_list=ncs_restraints_group_list,
max_number_of_iterations=300,
number_of_macro_cycles=number_of_cycles,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True,
fix_rotamer_outliers=True,
log=log)
if original_pdb_h is not None:
if len(excl_string_selection) == 0:
excl_string_selection = "all"
asc = original_pdb_h.atom_selection_cache()
sel = asc.selection(
"(%s) and (name CA or name C or name N or name O)" %
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=reference_sigma,
top_out_potential=True))
# grm.geometry.write_geo_file(
# sites_cart=hierarchy.atoms().extract_xyz(),
# site_labels=[atom.id_str() for atom in hierarchy.atoms()],
# file_name="last_gm.geo")
obj = run2(restraints_manager=grm,
pdb_hierarchy=hierarchy,
correct_special_position_tolerance=1.0,
ncs_restraints_group_list=ncs_restraints_group_list,
max_number_of_iterations=300,
number_of_macro_cycles=number_of_cycles,
bond=True,
nonbonded=True,
angle=True,
dihedral=True,
chirality=True,
planarity=True,
fix_rotamer_outliers=True,
log=log)
grm.geometry.reference_dihedral_manager = None
def exercise_2(mon_lib_srv, ener_lib):
for use_reference in [True, False, None]:
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
raw_records = flex.std_string(pdb_str_2.splitlines()),
strict_conflict_handling = True,
force_symmetry = True,
log = None)
grm = processed_pdb_file.geometry_restraints_manager()
xrs2 = processed_pdb_file.xray_structure(show_summary = False)
awl2 = processed_pdb_file.all_chain_proxies.pdb_hierarchy.atoms_with_labels()
pdb_inp3 = iotbx.pdb.input(source_info=None, lines=pdb_str_3)
xrs3 = pdb_inp3.xray_structure_simple()
ph3 = pdb_inp3.construct_hierarchy()
ph3.atoms().reset_i_seq()
awl3 = ph3.atoms_with_labels()
sites_cart_reference = flex.vec3_double()
selection = flex.size_t()
reference_names = ["CG", "CD", "NE", "CZ", "NH1", "NH2"]
for a2,a3 in zip(tuple(awl2), tuple(awl3)):
assert a2.resname == a3.resname
assert a2.name == a3.name
assert a2.i_seq == a3.i_seq
if(a2.resname == "ARG" and a2.name.strip() in reference_names):
selection.append(a2.i_seq)
sites_cart_reference.append(a3.xyz)
assert selection.size() == len(reference_names)
selection_bool = flex.bool(xrs2.scatterers().size(), selection)
if(use_reference):
grm.adopt_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = sites_cart_reference,
selection = selection,
sigma = 0.01))
elif(use_reference is None):
grm.adopt_reference_coordinate_restraints_in_place(
reference.add_coordinate_restraints(
sites_cart = sites_cart_reference,
selection = selection,
sigma = 0.01))
grm.remove_reference_coordinate_restraints_in_place(
selection = selection)
d1 = flex.mean(flex.sqrt((xrs2.sites_cart().select(selection) -
xrs3.sites_cart().select(selection)).dot()))
print "distance start (use_reference: %s): %6.4f"%(str(use_reference), d1)
assert d1>4.0
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
from cctbx import geometry_restraints
import mmtbx.refinement.geometry_minimization
import scitbx.lbfgs
grf = geometry_restraints.flags.flags(default=True)
sites_cart = xrs2.sites_cart()
minimized = mmtbx.refinement.geometry_minimization.lbfgs(
sites_cart = sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager = grm,
sites_cart_selection = flex.bool(sites_cart.size(), selection),
geometry_restraints_flags = grf,
lbfgs_termination_params = scitbx.lbfgs.termination_parameters(
max_iterations=5000))
xrs2.set_sites_cart(sites_cart = sites_cart)
d2 = flex.mean(flex.sqrt((xrs2.sites_cart().select(selection) -
xrs3.sites_cart().select(selection)).dot()))
print "distance final (use_reference: %s): %6.4f"%(str(use_reference), d2)
if(use_reference): assert d2<0.005, "failed: %f<0.05" % d2
else: assert d2>4.0, d2
assert approx_equal(
flex.max(flex.sqrt((xrs2.sites_cart().select(~selection_bool) -
xrs3.sites_cart().select(~selection_bool)).dot())), 0)
def minimize_wrapper_for_ramachandran(
hierarchy,
xrs,
original_pdb_h,
excl_string_selection,
log=None,
ss_annotation = None,
reference_rotamers = True,
run_first_minimization_without_reference=False,
oldfield_weight_scale=3,
oldfield_plot_cutoff=0.03,
nonbonded_weight=500,
reference_sigma=0.7):
""" Wrapper around geometry minimization specifically tuned for eliminating
Ramachandran outliers.
"""
import pickle
from time import time
from mmtbx.monomer_library.pdb_interpretation import grand_master_phil_str
from mmtbx.geometry_restraints import reference
from mmtbx.command_line.geometry_minimization import \
get_geometry_restraints_manager
from mmtbx.geometry_restraints.torsion_restraints.reference_model import \
reference_model, reference_model_params
from libtbx.utils import null_out
from scitbx.array_family import flex
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=oldfield_weight_scale
params.pdb_interpretation.peptide_link.oldfield.plot_cutoff=oldfield_plot_cutoff
params.pdb_interpretation.nonbonded_weight = nonbonded_weight
params.pdb_interpretation.c_beta_restraints=True
params.pdb_interpretation.max_reasonable_bond_distance = None
params.pdb_interpretation.peptide_link.apply_peptide_plane = True
params.pdb_interpretation.ncs_search.enabled = True
params.pdb_interpretation.restraints_library.rdl = 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()))
mon_lib_srv = processed_pdb_files_srv.mon_lib_srv
ener_lib = processed_pdb_files_srv.ener_lib
ncs_restraints_group_list = []
if processed_pdb_file.ncs_obj is not None:
ncs_restraints_group_list = processed_pdb_file.ncs_obj.get_ncs_restraints_group_list()
grm = get_geometry_restraints_manager(
processed_pdb_file, xrs, params=params)
if reference_rotamers and original_pdb_h is not None:
# make selection excluding rotamer outliers
from mmtbx.rotamer.rotamer_eval import RotamerEval
rotamer_manager = RotamerEval(mon_lib_srv=mon_lib_srv)
non_rot_outliers_selection = flex.bool([False]*hierarchy.atoms().size())
for model in original_pdb_h.models():
for chain in model.chains():
for conf in chain.conformers():
for res in conf.residues():
ev = rotamer_manager.evaluate_residue_2(res)
if ev != "OUTLIER" or ev is None:
for a in res.atoms():
non_rot_outliers_selection[a.i_seq] = True
rm_params = reference_model_params.extract()
rm_params.reference_model.enabled=True
rm_params.reference_model.strict_rotamer_matching=False
rm_params.reference_model.main_chain=False
rm = reference_model(
processed_pdb_file=processed_pdb_file,
reference_file_list=None,
reference_hierarchy_list=[original_pdb_h],
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
has_hd=None,
params=rm_params.reference_model,
selection=non_rot_outliers_selection,
log=log)
rm.show_reference_summary(log=log)
grm.geometry.adopt_reference_dihedral_manager(rm)
# dealing with SS
if ss_annotation is not None:
from mmtbx.secondary_structure import manager
ss_manager = manager(
pdb_hierarchy=hierarchy,
geometry_restraints_manager=grm.geometry,
sec_str_from_pdb_file=ss_annotation,
params=None,
mon_lib_srv=mon_lib_srv,
verbose=-1,
log=log)
grm.geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=hierarchy,
log=log)
# grm pickle-unpickle
# t0 = time()
# prefix="grm"
# pklfile = open("%s.pkl" % prefix, 'wb')
# pickle.dump(grm.geometry, pklfile)
# pklfile.close()
# t1 = time()
# pklfile = open("%s.pkl" % prefix, 'rb')
# grm_from_file = pickle.load(pklfile)
# pklfile.close()
# t2 = time()
# print "Time pickling/unpickling: %.4f, %.4f" % (t1-t0, t2-t1)
# grm.geometry=grm_from_file
if run_first_minimization_without_reference:
obj = run2(
restraints_manager=grm,
pdb_hierarchy=hierarchy,
correct_special_position_tolerance=1.0,
ncs_restraints_group_list=ncs_restraints_group_list,
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)
if original_pdb_h is not None:
if len(excl_string_selection) == 0:
excl_string_selection = "all"
asc = original_pdb_h.atom_selection_cache()
sel = asc.selection("(%s) and (name CA or name C or name N or name O)" % 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 = reference_sigma,
top_out_potential=True))
obj = run2(
restraints_manager = grm,
pdb_hierarchy = hierarchy,
correct_special_position_tolerance = 1.0,
ncs_restraints_group_list=ncs_restraints_group_list,
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)