def test_reference_model(mon_lib_srv, ener_lib, prefix="tst_reference_model"):
from mmtbx.geometry_restraints.torsion_restraints.tst_reference_model import \
model_raw_records, reference_raw_records
from mmtbx.geometry_restraints.torsion_restraints.reference_model import \
reference_model
import mmtbx.model
# mstream = StringIO()
from libtbx.utils import multi_out
mstream = multi_out()
mstream.register("stdout", sys.stdout)
mstream_file_name = "polder.log"
mstreamfile = open(mstream_file_name, "w")
mstream.register("logfile", mstreamfile)
work_params = mmtbx.model.manager.get_default_pdb_interpretation_params()
work_params.reference_model.enabled = True
work_params.reference_model.fix_outliers = False
pdb_inp = iotbx.pdb.input(lines=model_raw_records.split('\n'),
source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp,
process_input=True,
pdb_interpretation_params=work_params)
reference_hierarchy_list = []
tmp_hierarchy = iotbx.pdb.input(
source_info=None,
lines=reference_raw_records.split('\n')).construct_hierarchy()
reference_hierarchy_list.append(tmp_hierarchy)
rm = reference_model(model=model,
reference_hierarchy_list=reference_hierarchy_list,
params=work_params.reference_model,
log=mstream)
assert rm.get_n_proxies() == 5, "Got %d, expected 5" % rm.get_n_proxies()
geometry, xrs = make_initial_grm(mon_lib_srv, ener_lib, model_raw_records)
geometry.adopt_reference_dihedral_manager(rm)
make_geo_pickle_unpickle(geometry, xrs, prefix)
def test_reference_model(mon_lib_srv, ener_lib, prefix="tst_reference_model"):
from mmtbx.geometry_restraints.torsion_restraints.tst_reference_model import \
model_raw_records, reference_raw_records
from mmtbx.geometry_restraints.torsion_restraints.reference_model import \
reference_model, reference_model_params
work_params = reference_model_params.extract()
work_params.reference_model.enabled = True
work_params.reference_model.fix_outliers = False
processed_pdb_file = monomer_library.pdb_interpretation.process(
mon_lib_srv=mon_lib_srv,
ener_lib=ener_lib,
raw_records=model_raw_records.split('\n'))
pdb_h = processed_pdb_file.all_chain_proxies.pdb_hierarchy
reference_hierarchy_list = []
tmp_hierarchy = iotbx.pdb.input(
source_info=None,
lines=reference_raw_records.split('\n')).construct_hierarchy()
reference_hierarchy_list.append(tmp_hierarchy)
rm = reference_model(
processed_pdb_file=processed_pdb_file,
reference_hierarchy_list=reference_hierarchy_list,
params=work_params.reference_model,
log=None)
assert rm.get_n_proxies() == 5, "Got %d, expected 5" % rm.get_n_proxies()
geometry, xrs = make_initial_grm(mon_lib_srv, ener_lib, model_raw_records)
geometry.adopt_reference_dihedral_manager(rm)
make_geo_pickle_unpickle(geometry, xrs, prefix)
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 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 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)
