def set_pdb_data(self, pdb_hierarchy, ignore_unk=False):
from mmtbx import secondary_structure
sec_str = secondary_structure.manager(pdb_hierarchy)
sec_str.show_summary()
self.set_data(pdb_hierarchy=pdb_hierarchy,
sec_str=sec_str,
auto_select=True,
ignore_unk=ignore_unk)
def set_pdb_data (self, pdb_hierarchy, ignore_unk=False) :
from mmtbx import secondary_structure
sec_str = secondary_structure.manager(pdb_hierarchy)
sec_str.show_summary()
self.set_data(
pdb_hierarchy=pdb_hierarchy,
sec_str=sec_str,
auto_select=True,
ignore_unk=ignore_unk)
def initialize_cartoon(self, sec_str=None):
if (sec_str is None):
from mmtbx import secondary_structure
manager = secondary_structure.manager(
pdb_hierarchy=self.pdb_hierarchy, xray_structure=None)
sec_str = manager.selections_as_ints()
from crys3d import ribbon
self.ribbon = ribbon.cartoon(pdb_hierarchy=self.pdb_hierarchy,
sec_str=sec_str)
self.ribbon.construct_geometry()
def get_grm(self):
# first make whole grm using self.whole_pdb_h
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.nonbonded_weight = 500
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= self.whole_xrs.crystal_symmetry(),
pdb_interpretation_params = params.pdb_interpretation,
stop_for_unknowns = False,
log=self.log,
cif_objects=None)
processed_pdb_file, junk = processed_pdb_files_srv.\
process_pdb_files(raw_records=flex.split_lines(self.whole_pdb_h.as_pdb_string()))
self.mon_lib_srv = processed_pdb_files_srv.mon_lib_srv
self.ener_lib = processed_pdb_files_srv.ener_lib
self.rotamer_manager = RotamerEval(mon_lib_srv=self.mon_lib_srv)
self.whole_grm = get_geometry_restraints_manager(
processed_pdb_file, self.whole_xrs, params=params)
# set SS restratins
if self.params.use_ss_restraints:
ss_manager = manager(
pdb_hierarchy=self.whole_pdb_h,
geometry_restraints_manager=self.whole_grm.geometry,
sec_str_from_pdb_file=self.filtered_whole_ann,
params=None,
mon_lib_srv=self.mon_lib_srv,
verbose=-1,
log=self.log)
# self.whole_pdb_h.write_pdb_file(file_name="for_ss.pdb")
self.whole_pdb_h.reset_atom_i_seqs()
self.whole_grm.geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=self.whole_pdb_h,
log=self.log)
# now select part of it for working with master hierarchy
if self.using_ncs:
self.master_grm = self.whole_grm.select(self.master_sel)
self.working_grm = self.master_grm
else:
self.working_grm = self.whole_grm
def initialize_cartoon (self, sec_str=None) :
if (sec_str is None) :
from mmtbx import secondary_structure
manager = secondary_structure.manager(
pdb_hierarchy=self.pdb_hierarchy,
xray_structure=None)
sec_str = manager.selections_as_ints()
from crys3d import ribbon
self.ribbon = ribbon.cartoon(pdb_hierarchy=self.pdb_hierarchy,
sec_str=sec_str)
self.ribbon.construct_geometry()
def set_ss_restraints(self, ss_annotation, params=None):
log = self.log
if not self.verbose:
log = null_out()
if self.params.use_ss_restraints and ss_annotation is not None:
ss_manager = manager(
pdb_hierarchy=self.model.get_hierarchy(),
geometry_restraints_manager=self.model.get_restraints_manager().geometry,
sec_str_from_pdb_file=ss_annotation,
params=None,
mon_lib_srv=self.model.get_mon_lib_srv(),
verbose=-1,
log=log)
self.model.get_restraints_manager().geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=self.model.get_hierarchy(),
log=log)
def run (args, viewer_class=selection_editor_mixin) :
import cStringIO
pdb_files = []
cif_files = []
show_ss_restraints = False
fast_connectivity = True
for arg in args :
if os.path.isfile(arg) :
import iotbx.pdb
if iotbx.pdb.is_pdb_file(arg) :
pdb_files.append(os.path.abspath(arg))
elif arg.endswith(".cif") :
cif_files.append(os.path.abspath(arg))
elif arg == "--ss" :
show_ss_restraints = True
elif arg in ["--thorough", "--slow", "--use_monomer_library"] :
fast_connectivity = False
if len(pdb_files) == 0 :
print "Please specify a PDB file (and optional CIFs) on the command line."
return
a = App(viewer_class=viewer_class)
a.frame.Show()
out = sys.stdout
if not "--debug" in args :
out = cStringIO.StringIO()
for file_name in pdb_files :
print "Reading PDB file %s" % file_name
from iotbx import file_reader
from mmtbx.monomer_library import pdb_interpretation
from mmtbx import secondary_structure
t1 = time.time()
if fast_connectivity :
pdb_in = file_reader.any_file(file_name, force_type="pdb")
pdb_hierarchy = pdb_in.file_object.hierarchy
atomic_bonds = pdb_hierarchy.distance_based_simple_two_way_bond_sets()
acp_selection = None
else :
processed_pdb_file = pdb_interpretation.run(args=[file_name]+cif_files,
log=out)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_hierarchy.atoms().reset_i_seq()
grm = processed_pdb_file.geometry_restraints_manager()
acp_selection = processed_pdb_file.all_chain_proxies.selection
if grm is None or grm.shell_sym_tables is None :
raise Sorry("Atomic bonds could not be calculated for this model. "+
"This is probably due to a missing CRYST1 record in the PDB file.")
atomic_bonds = grm.shell_sym_tables[0].full_simple_connectivity()
t2 = time.time()
print "%.2fs" % (t2-t1)
a.view_objects.add_model(file_name, pdb_hierarchy, atomic_bonds,
mmtbx_selection_function=acp_selection)
sec_str = secondary_structure.manager(
pdb_hierarchy=pdb_hierarchy,
xray_structure=None)
a.view_objects.set_sec_str(file_name, sec_str.selections_as_ints())
if show_ss_restraints and acp_selection is not None :
bonds_table = secondary_structure.process_structure(params=None,
processed_pdb_file=processed_pdb_file,
tmp_dir=os.getcwd(),
log=sys.stderr)
a.view_objects.set_noncovalent_bonds(file_name, bonds_table.bonds)
a.view_objects.flag_show_noncovalent_bonds = True
a.view_objects.set_model_base_color([1.0,1.0,1.0], file_name)
a.view_objects.set_color_mode("element")
a.view_objects.force_update(recenter=True)
a.MainLoop()
def exercise_helix_bonding_pattern_with_insertions():
alpha_h1_ends = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1 N ALA 1 1.643 -2.366 -1.408 1.00 0.00 N
ATOM 2 CA ALA 1 1.280 -3.608 -2.069 1.00 0.00 C
ATOM 3 C ALA 1 -0.114 -3.466 -2.684 1.00 0.00 C
ATOM 4 O ALA 1 -0.327 -3.827 -3.840 1.00 0.00 O
ATOM 5 CB ALA 1 1.361 -4.762 -1.068 1.00 0.00 C
ATOM 6 N ALA 1A -1.028 -2.938 -1.882 1.00 0.00 N
ATOM 7 CA ALA 1A -2.395 -2.743 -2.332 1.00 0.00 C
ATOM 8 C ALA 1A -2.396 -1.855 -3.579 1.00 0.00 C
ATOM 9 O ALA 1A -3.059 -2.167 -4.567 1.00 0.00 O
ATOM 10 CB ALA 1A -3.228 -2.150 -1.194 1.00 0.00 C
ATOM 11 N ALA 3 -1.646 -0.767 -3.491 1.00 0.00 N
ATOM 12 CA ALA 3 -1.551 0.168 -4.599 1.00 0.00 C
ATOM 13 C ALA 3 -1.044 -0.568 -5.841 1.00 0.00 C
ATOM 14 O ALA 3 -1.601 -0.419 -6.927 1.00 0.00 O
ATOM 15 CB ALA 3 -0.646 1.337 -4.205 1.00 0.00 C
ATOM 16 N ALA 4 0.008 -1.348 -5.639 1.00 0.00 N
ATOM 17 CA ALA 4 0.597 -2.109 -6.728 1.00 0.00 C
ATOM 18 C ALA 4 -0.466 -3.023 -7.340 1.00 0.00 C
ATOM 19 O ALA 4 -0.611 -3.085 -8.559 1.00 0.00 O
ATOM 20 CB ALA 4 1.808 -2.887 -6.211 1.00 0.00 C
ATOM 21 N ALA 5 -1.184 -3.711 -6.463 1.00 0.00 N
ATOM 22 CA ALA 5 -2.231 -4.619 -6.901 1.00 0.00 C
ATOM 23 C ALA 5 -3.253 -3.847 -7.737 1.00 0.00 C
ATOM 24 O ALA 5 -3.647 -4.296 -8.813 1.00 0.00 O
ATOM 25 CB ALA 5 -2.864 -5.294 -5.683 1.00 0.00 C
ATOM 26 N ALA 6 -3.654 -2.699 -7.211 1.00 0.00 N
ATOM 27 CA ALA 6 -4.623 -1.860 -7.896 1.00 0.00 C
ATOM 28 C ALA 6 -4.090 -1.499 -9.284 1.00 0.00 C
ATOM 29 O ALA 6 -4.809 -1.602 -10.276 1.00 0.00 O
ATOM 30 CB ALA 6 -4.919 -0.623 -7.045 1.00 0.00 C
ATOM 31 N ALA 7 -2.831 -1.084 -9.309 1.00 0.00 N
ATOM 32 CA ALA 7 -2.192 -0.708 -10.559 1.00 0.00 C
ATOM 33 C ALA 7 -2.243 -1.890 -11.529 1.00 0.00 C
ATOM 34 O ALA 7 -2.600 -1.727 -12.695 1.00 0.00 O
ATOM 35 CB ALA 7 -0.761 -0.243 -10.281 1.00 0.00 C
ATOM 36 N ALA 8 -1.881 -3.055 -11.012 1.00 0.00 N
ATOM 37 CA ALA 8 -1.882 -4.264 -11.817 1.00 0.00 C
ATOM 38 C ALA 8 -3.285 -4.496 -12.382 1.00 0.00 C
ATOM 39 O ALA 8 -3.442 -4.772 -13.570 1.00 0.00 O
ATOM 40 CB ALA 8 -1.391 -5.441 -10.972 1.00 0.00 C
ATOM 41 N ALA 9 -4.269 -4.376 -11.503 1.00 0.00 N
ATOM 42 CA ALA 9 -5.653 -4.568 -11.898 1.00 0.00 C
ATOM 43 C ALA 9 -6.000 -3.590 -13.022 1.00 0.00 C
ATOM 44 O ALA 9 -6.590 -3.978 -14.029 1.00 0.00 O
ATOM 45 CB ALA 9 -6.561 -4.400 -10.678 1.00 0.00 C
ATOM 46 N ALA 9A -5.617 -2.338 -12.812 1.00 0.00 N
ATOM 47 CA ALA 9A -5.879 -1.301 -13.795 1.00 0.00 C
ATOM 48 C ALA 9A -5.242 -1.695 -15.130 1.00 0.00 C
ATOM 49 O ALA 9A -5.880 -1.605 -16.177 1.00 0.00 O
ATOM 50 CB ALA 9A -5.358 0.040 -13.274 1.00 0.00 C
TER
""")
alpha_h1_ac = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1 N AALA 1 1.643 -2.366 -1.408 0.50 0.00 N
ATOM 2 CA AALA 1 1.280 -3.608 -2.069 0.50 0.00 C
ATOM 3 C AALA 1 -0.114 -3.466 -2.684 0.50 0.00 C
ATOM 4 O AALA 1 -0.327 -3.827 -3.840 0.50 0.00 O
ATOM 5 CB AALA 1 1.361 -4.762 -1.068 0.50 0.00 C
ATOM 6 N BALA 1 1.743 -2.366 -1.408 0.50 0.00 N
ATOM 7 CA BALA 1 1.380 -3.608 -2.069 0.50 0.00 C
ATOM 8 C BALA 1 -0.014 -3.466 -2.684 0.50 0.00 C
ATOM 9 O BALA 1 -0.227 -3.827 -3.840 0.50 0.00 O
ATOM 10 CB BALA 1 1.461 -4.762 -1.068 0.50 0.00 C
ATOM 11 N ALA 1A -1.028 -2.938 -1.882 1.00 0.00 N
ATOM 12 CA ALA 1A -2.395 -2.743 -2.332 1.00 0.00 C
ATOM 13 C ALA 1A -2.396 -1.855 -3.579 1.00 0.00 C
ATOM 14 O ALA 1A -3.059 -2.167 -4.567 1.00 0.00 O
ATOM 15 CB ALA 1A -3.228 -2.150 -1.194 1.00 0.00 C
ATOM 16 N ALA 3 -1.646 -0.767 -3.491 1.00 0.00 N
ATOM 17 CA ALA 3 -1.551 0.168 -4.599 1.00 0.00 C
ATOM 18 C ALA 3 -1.044 -0.568 -5.841 1.00 0.00 C
ATOM 19 O ALA 3 -1.601 -0.419 -6.927 1.00 0.00 O
ATOM 20 CB ALA 3 -0.646 1.337 -4.205 1.00 0.00 C
ATOM 21 N ALA 4 0.008 -1.348 -5.639 1.00 0.00 N
ATOM 22 CA ALA 4 0.597 -2.109 -6.728 1.00 0.00 C
ATOM 23 C ALA 4 -0.466 -3.023 -7.340 1.00 0.00 C
ATOM 24 O ALA 4 -0.611 -3.085 -8.559 1.00 0.00 O
ATOM 25 CB ALA 4 1.808 -2.887 -6.211 1.00 0.00 C
ATOM 26 N AALA 5 -1.184 -3.711 -6.463 0.50 0.00 N
ATOM 27 CA AALA 5 -2.231 -4.619 -6.901 0.50 0.00 C
ATOM 28 C AALA 5 -3.253 -3.847 -7.737 0.50 0.00 C
ATOM 29 O AALA 5 -3.647 -4.296 -8.813 0.50 0.00 O
ATOM 30 CB AALA 5 -2.864 -5.294 -5.683 0.50 0.00 C
ATOM 31 N BALA 5 -1.084 -3.711 -6.463 0.50 0.00 N
ATOM 32 CA BALA 5 -2.131 -4.619 -6.901 0.50 0.00 C
ATOM 33 C BALA 5 -3.153 -3.847 -7.737 0.50 0.00 C
ATOM 34 O BALA 5 -3.547 -4.296 -8.813 0.50 0.00 O
ATOM 35 CB BALA 5 -2.764 -5.294 -5.683 0.50 0.00 C
ATOM 36 N ALA 6 -3.654 -2.699 -7.211 1.00 0.00 N
ATOM 37 CA ALA 6 -4.623 -1.860 -7.896 1.00 0.00 C
ATOM 38 C ALA 6 -4.090 -1.499 -9.284 1.00 0.00 C
ATOM 39 O ALA 6 -4.809 -1.602 -10.276 1.00 0.00 O
ATOM 40 CB ALA 6 -4.919 -0.623 -7.045 1.00 0.00 C
ATOM 41 N ALA 7 -2.831 -1.084 -9.309 1.00 0.00 N
ATOM 42 CA ALA 7 -2.192 -0.708 -10.559 1.00 0.00 C
ATOM 43 C ALA 7 -2.243 -1.890 -11.529 1.00 0.00 C
ATOM 44 O ALA 7 -2.600 -1.727 -12.695 1.00 0.00 O
ATOM 45 CB ALA 7 -0.761 -0.243 -10.281 1.00 0.00 C
ATOM 46 N ALA 8 -1.881 -3.055 -11.012 1.00 0.00 N
ATOM 47 CA ALA 8 -1.882 -4.264 -11.817 1.00 0.00 C
ATOM 48 C ALA 8 -3.285 -4.496 -12.382 1.00 0.00 C
ATOM 49 O ALA 8 -3.442 -4.772 -13.570 1.00 0.00 O
ATOM 50 CB ALA 8 -1.391 -5.441 -10.972 1.00 0.00 C
ATOM 51 N ALA 9 -4.269 -4.376 -11.503 1.00 0.00 N
ATOM 52 CA ALA 9 -5.653 -4.568 -11.898 1.00 0.00 C
ATOM 53 C ALA 9 -6.000 -3.590 -13.022 1.00 0.00 C
ATOM 54 O ALA 9 -6.590 -3.978 -14.029 1.00 0.00 O
ATOM 55 CB ALA 9 -6.561 -4.400 -10.678 1.00 0.00 C
ATOM 56 N AALA 9A -5.617 -2.338 -12.812 0.50 0.00 N
ATOM 57 CA AALA 9A -5.879 -1.301 -13.795 0.50 0.00 C
ATOM 58 C AALA 9A -5.242 -1.695 -15.130 0.50 0.00 C
ATOM 59 O AALA 9A -5.880 -1.605 -16.177 0.50 0.00 O
ATOM 60 CB AALA 9A -5.358 0.040 -13.274 0.50 0.00 C
ATOM 62 N BALA 9A -5.517 -2.338 -12.812 0.50 0.00 N
ATOM 63 CA BALA 9A -5.779 -1.301 -13.795 0.50 0.00 C
ATOM 64 C BALA 9A -5.142 -1.695 -15.130 0.50 0.00 C
ATOM 65 O BALA 9A -5.780 -1.605 -16.177 0.50 0.00 O
ATOM 66 CB BALA 9A -5.258 0.040 -13.274 0.50 0.00 C
END
""")
alpha_annot_1_1 = """\
HELIX 1 1 ALA 1 ALA 9A 1 10
"""
alpha_annot_1_2 = """\
HELIX 1 1 ALA 1A ALA 9 1 10
"""
alpha_annot_1_3 = """\
HELIX 1 1 ALA 1A ALA 9A 1 10
"""
alpha_annot_1_4 = """\
HELIX 1 1 ALA 1 ALA 9 1 10
"""
alpha_annot_2 = """\
HELIX 1 1 ALA 2 ALA 5 1 10
"""
log = null_out()
n_hbonds = []
for pdb_inp, recs in [
(alpha_h1_ends, alpha_annot_1_1), #6
(alpha_h1_ends, alpha_annot_1_2), #4
(alpha_h1_ends, alpha_annot_1_3), #5
(alpha_h1_ends, alpha_annot_1_4), #5
(alpha_h1_ac, alpha_annot_1_1), #9
(alpha_h1_ac, alpha_annot_1_2), #5
(alpha_h1_ac, alpha_annot_1_3), #7
(alpha_h1_ac, alpha_annot_1_4), #7
]:
ioss_annotation = ioss.annotation.from_records(records = recs.split('\n'))
ann = ioss_annotation.as_restraint_groups(prefix_scope="secondary_structure")
defpars = iotbx.phil.parse(sec_str_master_phil_str)
custom_pars = defpars.fetch(iotbx.phil.parse(ann))
custom_pars_ex = custom_pars.extract()
ss_manager = manager(
pdb_inp.hierarchy,
sec_str_from_pdb_file=None,
params=custom_pars_ex.secondary_structure,
verbose=-1)
proxies_for_grm = ss_manager.create_protein_hbond_proxies(
annotation= None,
log = log)
n_hbonds.append(proxies_for_grm.size())
print n_hbonds
assert n_hbonds == [6, 4, 5, 5, 9, 5, 7, 7]
def run(args, params=None, out=sys.stdout, log=sys.stderr):
# params keyword is for running program from GUI dialog
if (((len(args) == 0) and (params is None)) or
((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help")))):
show_usage()
return
# parse command-line arguments
if (params is None):
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="file_name")
work_params = pcl.work.extract()
# or use parameters defined by GUI
else:
work_params = params
pdb_files = work_params.file_name
work_params.secondary_structure.enabled = True
assert work_params.format in [
"phenix", "phenix_refine", "phenix_bonds", "pymol", "refmac",
"kinemage", "pdb"
]
if work_params.quiet:
out = cStringIO.StringIO()
pdb_combined = iotbx.pdb.combine_unique_pdb_files(file_names=pdb_files)
pdb_structure = iotbx.pdb.input(source_info=None,
lines=flex.std_string(
pdb_combined.raw_records))
cs = pdb_structure.crystal_symmetry()
corrupted_cs = False
if cs is not None:
if [cs.unit_cell(), cs.space_group()].count(None) > 0:
corrupted_cs = True
cs = None
elif cs.unit_cell().volume() < 10:
corrupted_cs = True
cs = None
if cs is None:
if corrupted_cs:
print >> out, "Symmetry information is corrupted, "
else:
print >> out, "Symmetry information was not found, "
print >> out, "putting molecule in P1 box."
from cctbx import uctbx
atoms = pdb_structure.atoms()
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=atoms.extract_xyz(), buffer_layer=3)
atoms.set_xyz(new_xyz=box.sites_cart)
cs = box.crystal_symmetry()
defpars = mmtbx.model.manager.get_default_pdb_interpretation_params()
defpars.pdb_interpretation.automatic_linking.link_carbohydrates = False
defpars.pdb_interpretation.c_beta_restraints = False
defpars.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None
model = mmtbx.model.manager(model_input=pdb_structure,
crystal_symmetry=cs,
pdb_interpretation_params=defpars,
stop_for_unknowns=False)
pdb_hierarchy = model.get_hierarchy()
geometry = model.get_restraints_manager().geometry
if len(pdb_hierarchy.models()) != 1:
raise Sorry("Multiple models not supported.")
ss_from_file = None
if (hasattr(pdb_structure, "extract_secondary_structure")
and not work_params.ignore_annotation_in_file):
ss_from_file = pdb_structure.extract_secondary_structure()
m = manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry,
sec_str_from_pdb_file=ss_from_file,
params=work_params.secondary_structure,
verbose=work_params.verbose)
# bp_p = nucleic_acids.get_basepair_plane_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair,
# geometry)
# st_p = nucleic_acids.get_stacking_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.stacking_pair,
# geometry)
# hb_b, hb_a = nucleic_acids.get_basepair_hbond_proxies(pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair)
result_out = cStringIO.StringIO()
# prefix_scope="refinement.pdb_interpretation"
# prefix_scope=""
prefix_scope = ""
if work_params.format == "phenix_refine":
prefix_scope = "refinement.pdb_interpretation"
elif work_params.format == "phenix":
prefix_scope = "pdb_interpretation"
ss_phil = None
working_phil = m.as_phil_str(master_phil=sec_str_master_phil)
phil_diff = sec_str_master_phil.fetch_diff(source=working_phil)
if work_params.format in ["phenix", "phenix_refine"]:
comment = "\n".join([
"# These parameters are suitable for use in e.g. phenix.real_space_refine",
"# or geometry_minimization. To use them in phenix.refine add ",
"# 'refinement.' if front of pdb_interpretation."
])
if work_params.format == "phenix_refine":
comment = "\n".join([
"# These parameters are suitable for use in phenix.refine only.",
"# To use them in other Phenix tools remove ",
"# 'refinement.' if front of pdb_interpretation."
])
print >> result_out, comment
if (prefix_scope != ""):
print >> result_out, "%s {" % prefix_scope
if work_params.show_all_params:
working_phil.show(prefix=" ", out=result_out)
else:
phil_diff.show(prefix=" ", out=result_out)
if (prefix_scope != ""):
print >> result_out, "}"
elif work_params.format == "pdb":
print >> result_out, m.actual_sec_str.as_pdb_str()
elif work_params.format == "phenix_bonds":
raise Sorry("Not yet implemented.")
elif work_params.format in ["pymol", "refmac", "kinemage"]:
m.show_summary(log=out)
(hb_proxies, hb_angle_proxies, planarity_proxies,
parallelity_proxies) = m.create_all_new_restraints(
pdb_hierarchy=pdb_hierarchy, grm=geometry, log=out)
if hb_proxies.size() > 0:
if work_params.format == "pymol":
file_load_add = "load %s" % work_params.file_name[0]
# surprisingly, pymol handles filenames with whitespaces without quotes...
print >> result_out, file_load_add
bonds_in_format = hb_proxies.as_pymol_dashes(
pdb_hierarchy=pdb_hierarchy)
elif work_params.format == "kinemage":
bonds_in_format = hb_proxies.as_kinemage(
pdb_hierarchy=pdb_hierarchy)
else:
bonds_in_format = hb_proxies.as_refmac_restraints(
pdb_hierarchy=pdb_hierarchy)
print >> result_out, bonds_in_format
if hb_angle_proxies.size() > 0:
if work_params.format == "pymol":
angles_in_format = hb_angle_proxies.as_pymol_dashes(
pdb_hierarchy=pdb_hierarchy)
print >> result_out, angles_in_format
result = result_out.getvalue()
out_prefix = os.path.basename(work_params.file_name[0])
if work_params.output_prefix is not None:
out_prefix = work_params.output_prefix
filename = "%s_ss.eff" % out_prefix
if work_params.format == "pymol":
filename = "%s_ss.pml" % out_prefix
outf = open(filename, "w")
outf.write(result)
outf.close()
print >> out, result
return os.path.abspath(filename)
def get_reference_dihedral_proxies(self, processed_pdb_file):
complete_dihedral_proxies = utils.get_dihedrals_and_phi_psi(
processed_pdb_file=processed_pdb_file)
generated_reference_dihedral_proxies = \
cctbx.geometry_restraints.shared_dihedral_proxy()
sigma = self.params.sigma
limit = self.params.limit
ref_ss_m = None
ss_selection = None
if self.params.secondary_structure_only:
if (not libtbx.env.has_module(name="ksdssp")):
raise RuntimeError(
"ksdssp module is not configured, "+\
"cannot generate secondary structure reference")
ref_ss_m = {}
ss_selection = {}
for file in self.reference_file_list:
ref_ss_m[file] = secondary_structure.manager(
pdb_hierarchy=self.pdb_hierarchy_ref[file],
sec_str_from_pdb_file=None)
sec_str_from_pdb_file = ref_ss_m[file].actual_sec_str
if sec_str_from_pdb_file != None:
overall_selection = sec_str_from_pdb_file.overall_selection(
)
sel_cache_ref = self.pdb_hierarchy_ref[
file].atom_selection_cache()
bsel = sel_cache_ref.selection(string=overall_selection)
if bsel.all_eq(False):
raise Sorry("No atom selected")
ss_selection[file] = bsel
t_sum = 0
for dp in complete_dihedral_proxies:
key_work = ""
complete = True
for i_seq in dp.i_seqs:
if not self.selection[i_seq]:
complete = False
if not complete:
continue
for i_seq in dp.i_seqs:
key_work = key_work + self.i_seq_name_hash[i_seq]
#find matching key
key = None
file_match = None
for file in self.reference_file_list:
if key is not None or file not in self.match_map:
continue
else:
key = ""
ref_match = True
for i_seq in dp.i_seqs:
if ref_match:
map_part = self.match_map[file].get(i_seq)
if map_part is not None:
key_part = self.i_seq_name_hash_ref[file].get(
map_part)
if key_part is None:
ref_match = False
key = None
file_match = None
else:
key = key + key_part
else:
ref_match = False
key = None
file_match = None
if key is not None:
file_match = file
try:
reference_angle = self.reference_dihedral_hash[file_match][key]
except Exception:
continue
w_limit = limit
w_weight = 1 / sigma**2
if (self.params.secondary_structure_only
and ss_selection is not None
and ss_selection[file_match] is not None):
limit2 = 15.0
w_weight = 0.04
if (ss_selection[file_match][self.match_map[file_match][
dp.i_seqs[0]]] and ss_selection[file_match][
self.match_map[file_match][dp.i_seqs[1]]]
and ss_selection[file_match][self.match_map[file_match]
[dp.i_seqs[2]]]
and ss_selection[file_match][self.match_map[file_match]
[dp.i_seqs[3]]]):
limit2 = 30.0
w_weight = 1
dp_add = cctbx.geometry_restraints.dihedral_proxy(
i_seqs=dp.i_seqs,
angle_ideal=reference_angle,
weight=w_weight,
limit=w_limit,
top_out=TOP_OUT_FLAG)
generated_reference_dihedral_proxies.append(dp_add)
else:
dp_add = cctbx.geometry_restraints.dihedral_proxy(
i_seqs=dp.i_seqs,
angle_ideal=reference_angle,
weight=1 / sigma**2,
limit=limit,
top_out=TOP_OUT_FLAG)
# print "Already_there:", self._is_proxy_already_present(generated_reference_dihedral_proxies,dp_add)
# if not self._is_proxy_already_present(generated_reference_dihedral_proxies,dp_add):
generated_reference_dihedral_proxies.append(dp_add)
self.reference_dihedral_proxies = generated_reference_dihedral_proxies
def run(args, viewer_class=selection_editor_mixin):
import cStringIO
pdb_files = []
cif_files = []
show_ss_restraints = False
fast_connectivity = True
for arg in args:
if os.path.isfile(arg):
import iotbx.pdb
if iotbx.pdb.is_pdb_file(arg):
pdb_files.append(os.path.abspath(arg))
elif arg.endswith(".cif"):
cif_files.append(os.path.abspath(arg))
elif arg == "--ss":
show_ss_restraints = True
elif arg in ["--thorough", "--slow", "--use_monomer_library"]:
fast_connectivity = False
if len(pdb_files) == 0:
print(
"Please specify a PDB file (and optional CIFs) on the command line."
)
return
a = App(viewer_class=viewer_class)
a.frame.Show()
out = sys.stdout
if not "--debug" in args:
out = cStringIO.StringIO()
for file_name in pdb_files:
print("Reading PDB file %s" % file_name)
from iotbx import file_reader
from mmtbx.monomer_library import pdb_interpretation
from mmtbx import secondary_structure
t1 = time.time()
if fast_connectivity:
pdb_in = file_reader.any_file(file_name, force_type="pdb")
pdb_hierarchy = pdb_in.file_object.hierarchy
atomic_bonds = pdb_hierarchy.distance_based_simple_two_way_bond_sets(
)
acp_selection = None
else:
processed_pdb_file = pdb_interpretation.run(args=[file_name] +
cif_files,
log=out)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
pdb_hierarchy.atoms().reset_i_seq()
grm = processed_pdb_file.geometry_restraints_manager()
acp_selection = processed_pdb_file.all_chain_proxies.selection
if grm is None or grm.shell_sym_tables is None:
raise Sorry(
"Atomic bonds could not be calculated for this model. " +
"This is probably due to a missing CRYST1 record in the PDB file."
)
atomic_bonds = grm.shell_sym_tables[0].full_simple_connectivity()
t2 = time.time()
print("%.2fs" % (t2 - t1))
a.view_objects.add_model(file_name,
pdb_hierarchy,
atomic_bonds,
mmtbx_selection_function=acp_selection)
sec_str = secondary_structure.manager(pdb_hierarchy=pdb_hierarchy,
xray_structure=None)
a.view_objects.set_sec_str(file_name, sec_str.selections_as_ints())
if show_ss_restraints and acp_selection is not None:
bonds_table = secondary_structure.process_structure(
params=None,
processed_pdb_file=processed_pdb_file,
tmp_dir=os.getcwd(),
log=sys.stderr)
a.view_objects.set_noncovalent_bonds(file_name, bonds_table.bonds)
a.view_objects.flag_show_noncovalent_bonds = True
a.view_objects.set_model_base_color([1.0, 1.0, 1.0], file_name)
a.view_objects.set_color_mode("element")
a.view_objects.force_update(recenter=True)
a.MainLoop()
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)
def exercise_helix_bonding_pattern_with_insertions():
alpha_h1_ends = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1 N ALA 1 1.643 -2.366 -1.408 1.00 0.00 N
ATOM 2 CA ALA 1 1.280 -3.608 -2.069 1.00 0.00 C
ATOM 3 C ALA 1 -0.114 -3.466 -2.684 1.00 0.00 C
ATOM 4 O ALA 1 -0.327 -3.827 -3.840 1.00 0.00 O
ATOM 5 CB ALA 1 1.361 -4.762 -1.068 1.00 0.00 C
ATOM 6 N ALA 1A -1.028 -2.938 -1.882 1.00 0.00 N
ATOM 7 CA ALA 1A -2.395 -2.743 -2.332 1.00 0.00 C
ATOM 8 C ALA 1A -2.396 -1.855 -3.579 1.00 0.00 C
ATOM 9 O ALA 1A -3.059 -2.167 -4.567 1.00 0.00 O
ATOM 10 CB ALA 1A -3.228 -2.150 -1.194 1.00 0.00 C
ATOM 11 N ALA 3 -1.646 -0.767 -3.491 1.00 0.00 N
ATOM 12 CA ALA 3 -1.551 0.168 -4.599 1.00 0.00 C
ATOM 13 C ALA 3 -1.044 -0.568 -5.841 1.00 0.00 C
ATOM 14 O ALA 3 -1.601 -0.419 -6.927 1.00 0.00 O
ATOM 15 CB ALA 3 -0.646 1.337 -4.205 1.00 0.00 C
ATOM 16 N ALA 4 0.008 -1.348 -5.639 1.00 0.00 N
ATOM 17 CA ALA 4 0.597 -2.109 -6.728 1.00 0.00 C
ATOM 18 C ALA 4 -0.466 -3.023 -7.340 1.00 0.00 C
ATOM 19 O ALA 4 -0.611 -3.085 -8.559 1.00 0.00 O
ATOM 20 CB ALA 4 1.808 -2.887 -6.211 1.00 0.00 C
ATOM 21 N ALA 5 -1.184 -3.711 -6.463 1.00 0.00 N
ATOM 22 CA ALA 5 -2.231 -4.619 -6.901 1.00 0.00 C
ATOM 23 C ALA 5 -3.253 -3.847 -7.737 1.00 0.00 C
ATOM 24 O ALA 5 -3.647 -4.296 -8.813 1.00 0.00 O
ATOM 25 CB ALA 5 -2.864 -5.294 -5.683 1.00 0.00 C
ATOM 26 N ALA 6 -3.654 -2.699 -7.211 1.00 0.00 N
ATOM 27 CA ALA 6 -4.623 -1.860 -7.896 1.00 0.00 C
ATOM 28 C ALA 6 -4.090 -1.499 -9.284 1.00 0.00 C
ATOM 29 O ALA 6 -4.809 -1.602 -10.276 1.00 0.00 O
ATOM 30 CB ALA 6 -4.919 -0.623 -7.045 1.00 0.00 C
ATOM 31 N ALA 7 -2.831 -1.084 -9.309 1.00 0.00 N
ATOM 32 CA ALA 7 -2.192 -0.708 -10.559 1.00 0.00 C
ATOM 33 C ALA 7 -2.243 -1.890 -11.529 1.00 0.00 C
ATOM 34 O ALA 7 -2.600 -1.727 -12.695 1.00 0.00 O
ATOM 35 CB ALA 7 -0.761 -0.243 -10.281 1.00 0.00 C
ATOM 36 N ALA 8 -1.881 -3.055 -11.012 1.00 0.00 N
ATOM 37 CA ALA 8 -1.882 -4.264 -11.817 1.00 0.00 C
ATOM 38 C ALA 8 -3.285 -4.496 -12.382 1.00 0.00 C
ATOM 39 O ALA 8 -3.442 -4.772 -13.570 1.00 0.00 O
ATOM 40 CB ALA 8 -1.391 -5.441 -10.972 1.00 0.00 C
ATOM 41 N ALA 9 -4.269 -4.376 -11.503 1.00 0.00 N
ATOM 42 CA ALA 9 -5.653 -4.568 -11.898 1.00 0.00 C
ATOM 43 C ALA 9 -6.000 -3.590 -13.022 1.00 0.00 C
ATOM 44 O ALA 9 -6.590 -3.978 -14.029 1.00 0.00 O
ATOM 45 CB ALA 9 -6.561 -4.400 -10.678 1.00 0.00 C
ATOM 46 N ALA 9A -5.617 -2.338 -12.812 1.00 0.00 N
ATOM 47 CA ALA 9A -5.879 -1.301 -13.795 1.00 0.00 C
ATOM 48 C ALA 9A -5.242 -1.695 -15.130 1.00 0.00 C
ATOM 49 O ALA 9A -5.880 -1.605 -16.177 1.00 0.00 O
ATOM 50 CB ALA 9A -5.358 0.040 -13.274 1.00 0.00 C
TER
""")
alpha_h1_ac = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1 N AALA 1 1.643 -2.366 -1.408 0.50 0.00 N
ATOM 2 CA AALA 1 1.280 -3.608 -2.069 0.50 0.00 C
ATOM 3 C AALA 1 -0.114 -3.466 -2.684 0.50 0.00 C
ATOM 4 O AALA 1 -0.327 -3.827 -3.840 0.50 0.00 O
ATOM 5 CB AALA 1 1.361 -4.762 -1.068 0.50 0.00 C
ATOM 6 N BALA 1 1.743 -2.366 -1.408 0.50 0.00 N
ATOM 7 CA BALA 1 1.380 -3.608 -2.069 0.50 0.00 C
ATOM 8 C BALA 1 -0.014 -3.466 -2.684 0.50 0.00 C
ATOM 9 O BALA 1 -0.227 -3.827 -3.840 0.50 0.00 O
ATOM 10 CB BALA 1 1.461 -4.762 -1.068 0.50 0.00 C
ATOM 11 N ALA 1A -1.028 -2.938 -1.882 1.00 0.00 N
ATOM 12 CA ALA 1A -2.395 -2.743 -2.332 1.00 0.00 C
ATOM 13 C ALA 1A -2.396 -1.855 -3.579 1.00 0.00 C
ATOM 14 O ALA 1A -3.059 -2.167 -4.567 1.00 0.00 O
ATOM 15 CB ALA 1A -3.228 -2.150 -1.194 1.00 0.00 C
ATOM 16 N ALA 3 -1.646 -0.767 -3.491 1.00 0.00 N
ATOM 17 CA ALA 3 -1.551 0.168 -4.599 1.00 0.00 C
ATOM 18 C ALA 3 -1.044 -0.568 -5.841 1.00 0.00 C
ATOM 19 O ALA 3 -1.601 -0.419 -6.927 1.00 0.00 O
ATOM 20 CB ALA 3 -0.646 1.337 -4.205 1.00 0.00 C
ATOM 21 N ALA 4 0.008 -1.348 -5.639 1.00 0.00 N
ATOM 22 CA ALA 4 0.597 -2.109 -6.728 1.00 0.00 C
ATOM 23 C ALA 4 -0.466 -3.023 -7.340 1.00 0.00 C
ATOM 24 O ALA 4 -0.611 -3.085 -8.559 1.00 0.00 O
ATOM 25 CB ALA 4 1.808 -2.887 -6.211 1.00 0.00 C
ATOM 26 N AALA 5 -1.184 -3.711 -6.463 0.50 0.00 N
ATOM 27 CA AALA 5 -2.231 -4.619 -6.901 0.50 0.00 C
ATOM 28 C AALA 5 -3.253 -3.847 -7.737 0.50 0.00 C
ATOM 29 O AALA 5 -3.647 -4.296 -8.813 0.50 0.00 O
ATOM 30 CB AALA 5 -2.864 -5.294 -5.683 0.50 0.00 C
ATOM 31 N BALA 5 -1.084 -3.711 -6.463 0.50 0.00 N
ATOM 32 CA BALA 5 -2.131 -4.619 -6.901 0.50 0.00 C
ATOM 33 C BALA 5 -3.153 -3.847 -7.737 0.50 0.00 C
ATOM 34 O BALA 5 -3.547 -4.296 -8.813 0.50 0.00 O
ATOM 35 CB BALA 5 -2.764 -5.294 -5.683 0.50 0.00 C
ATOM 36 N ALA 6 -3.654 -2.699 -7.211 1.00 0.00 N
ATOM 37 CA ALA 6 -4.623 -1.860 -7.896 1.00 0.00 C
ATOM 38 C ALA 6 -4.090 -1.499 -9.284 1.00 0.00 C
ATOM 39 O ALA 6 -4.809 -1.602 -10.276 1.00 0.00 O
ATOM 40 CB ALA 6 -4.919 -0.623 -7.045 1.00 0.00 C
ATOM 41 N ALA 7 -2.831 -1.084 -9.309 1.00 0.00 N
ATOM 42 CA ALA 7 -2.192 -0.708 -10.559 1.00 0.00 C
ATOM 43 C ALA 7 -2.243 -1.890 -11.529 1.00 0.00 C
ATOM 44 O ALA 7 -2.600 -1.727 -12.695 1.00 0.00 O
ATOM 45 CB ALA 7 -0.761 -0.243 -10.281 1.00 0.00 C
ATOM 46 N ALA 8 -1.881 -3.055 -11.012 1.00 0.00 N
ATOM 47 CA ALA 8 -1.882 -4.264 -11.817 1.00 0.00 C
ATOM 48 C ALA 8 -3.285 -4.496 -12.382 1.00 0.00 C
ATOM 49 O ALA 8 -3.442 -4.772 -13.570 1.00 0.00 O
ATOM 50 CB ALA 8 -1.391 -5.441 -10.972 1.00 0.00 C
ATOM 51 N ALA 9 -4.269 -4.376 -11.503 1.00 0.00 N
ATOM 52 CA ALA 9 -5.653 -4.568 -11.898 1.00 0.00 C
ATOM 53 C ALA 9 -6.000 -3.590 -13.022 1.00 0.00 C
ATOM 54 O ALA 9 -6.590 -3.978 -14.029 1.00 0.00 O
ATOM 55 CB ALA 9 -6.561 -4.400 -10.678 1.00 0.00 C
ATOM 56 N AALA 9A -5.617 -2.338 -12.812 0.50 0.00 N
ATOM 57 CA AALA 9A -5.879 -1.301 -13.795 0.50 0.00 C
ATOM 58 C AALA 9A -5.242 -1.695 -15.130 0.50 0.00 C
ATOM 59 O AALA 9A -5.880 -1.605 -16.177 0.50 0.00 O
ATOM 60 CB AALA 9A -5.358 0.040 -13.274 0.50 0.00 C
ATOM 62 N BALA 9A -5.517 -2.338 -12.812 0.50 0.00 N
ATOM 63 CA BALA 9A -5.779 -1.301 -13.795 0.50 0.00 C
ATOM 64 C BALA 9A -5.142 -1.695 -15.130 0.50 0.00 C
ATOM 65 O BALA 9A -5.780 -1.605 -16.177 0.50 0.00 O
ATOM 66 CB BALA 9A -5.258 0.040 -13.274 0.50 0.00 C
END
""")
alpha_annot_1_1 = """\
HELIX 1 1 ALA 1 ALA 9A 1 10
"""
alpha_annot_1_2 = """\
HELIX 1 1 ALA 1A ALA 9 1 10
"""
alpha_annot_1_3 = """\
HELIX 1 1 ALA 1A ALA 9A 1 10
"""
alpha_annot_1_4 = """\
HELIX 1 1 ALA 1 ALA 9 1 10
"""
alpha_annot_2 = """\
HELIX 1 1 ALA 2 ALA 5 1 10
"""
log = null_out()
n_hbonds = []
for pdb_inp, recs in [
(alpha_h1_ends, alpha_annot_1_1), #6
(alpha_h1_ends, alpha_annot_1_2), #4
(alpha_h1_ends, alpha_annot_1_3), #5
(alpha_h1_ends, alpha_annot_1_4), #5
(alpha_h1_ac, alpha_annot_1_1), #9
(alpha_h1_ac, alpha_annot_1_2), #5
(alpha_h1_ac, alpha_annot_1_3), #7
(alpha_h1_ac, alpha_annot_1_4), #7
]:
ioss_annotation = ioss.annotation.from_records(
records=recs.split('\n'))
ann = ioss_annotation.as_restraint_groups(
prefix_scope="secondary_structure")
defpars = iotbx.phil.parse(sec_str_master_phil_str)
custom_pars = defpars.fetch(iotbx.phil.parse(ann))
custom_pars_ex = custom_pars.extract()
ss_manager = manager(pdb_inp.hierarchy,
sec_str_from_pdb_file=None,
params=custom_pars_ex.secondary_structure,
verbose=-1)
proxies_for_grm = ss_manager.create_protein_hbond_proxies(
annotation=None, log=log)
n_hbonds.append(proxies_for_grm.size())
print n_hbonds
assert n_hbonds == [6, 4, 5, 5, 9, 5, 7, 7]
def exercise_sheets_bonding_pattern_with_insertions():
pdb_apar_input = iotbx.pdb.hierarchy.input(pdb_string="""\
SCRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1
SCALE1 0.021524 0.012427 0.000000 0.00000
SCALE2 0.000000 0.024854 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005176 0.00000
ATOM 5 N TYR A 2 27.208 -20.701 0.590 1.00 7.29 N
ATOM 6 CA TYR A 2 27.617 -19.424 0.052 1.00 7.96 C
ATOM 7 C TYR A 2 26.483 -18.436 0.263 1.00 6.87 C
ATOM 8 O TYR A 2 25.303 -18.771 0.249 1.00 6.97 O
ATOM 9 CB TYR A 2 27.861 -19.541 -1.451 1.00 7.90 C
ATOM 10 CG TYR A 2 28.902 -20.556 -1.857 1.00 9.09 C
ATOM 11 CD1 TYR A 2 30.255 -20.336 -1.592 1.00 11.43 C
ATOM 12 CD2 TYR A 2 28.566 -21.697 -2.545 1.00 10.59 C
ATOM 13 CE1 TYR A 2 31.227 -21.244 -1.987 1.00 13.93 C
ATOM 14 CE2 TYR A 2 29.518 -22.630 -2.915 1.00 11.76 C
ATOM 15 CZ TYR A 2 30.847 -22.395 -2.659 1.00 13.67 C
ATOM 16 OH TYR A 2 31.792 -23.309 -3.059 1.00 18.26 O
ATOM 17 N SER A 2A 26.854 -17.177 0.412 1.00 6.66 N
ATOM 18 CA SER A 2A 25.899 -16.083 0.383 0.53 6.83 C
ATOM 20 C SER A 2A 26.500 -14.946 -0.440 1.00 5.61 C
ATOM 21 O SER A 2A 27.729 -14.822 -0.565 1.00 8.14 O
ATOM 22 CB SER A 2A 25.569 -15.634 1.795 0.53 7.38 C
ATOM 24 OG SER A 2A 26.740 -15.136 2.390 0.53 9.79 O
ATOM 26 N CYS A 2B 25.627 -14.135 -0.995 1.00 5.11 N
ATOM 27 CA CYS A 2B 26.070 -13.062 -1.865 1.00 5.65 C
ATOM 28 C CYS A 2B 25.043 -11.934 -1.798 1.00 4.54 C
ATOM 29 O CYS A 2B 23.856 -12.180 -1.528 1.00 5.60 O
ATOM 30 CB CYS A 2B 26.253 -13.557 -3.295 1.00 7.00 C
ATOM 31 SG CYS A 2B 24.806 -14.269 -4.119 1.00 8.88 S
ATOM 32 N ARG A 5 25.486 -10.691 -2.002 1.00 4.69 N
ATOM 33 CA ARG A 5 24.558 -9.545 -2.064 1.00 4.87 C
ATOM 34 C ARG A 5 25.196 -8.395 -2.796 1.00 4.57 C
ATOM 35 O ARG A 5 26.416 -8.238 -2.793 1.00 5.50 O
ATOM 36 CB ARG A 5 24.061 -9.108 -0.700 1.00 6.43 C
ATOM 37 CG ARG A 5 25.121 -8.566 0.219 1.00 6.96 C
ATOM 38 CD ARG A 5 24.461 -8.032 1.494 1.00 7.25 C
ATOM 39 NE ARG A 5 25.452 -7.547 2.440 1.00 7.63 N
ATOM 40 CZ ARG A 5 26.107 -8.341 3.280 1.00 9.10 C
ATOM 41 NH1 ARG A 5 25.867 -9.642 3.297 1.00 9.68 N
ATOM 42 NH2 ARG A 5 26.974 -7.836 4.146 1.00 10.30 N
ATOM 43 N ALA A 6 24.325 -7.563 -3.358 1.00 4.39 N
ATOM 44 CA ALA A 6 24.723 -6.362 -4.067 1.00 4.73 C
ATOM 45 C ALA A 6 23.693 -5.275 -3.769 1.00 4.15 C
ATOM 46 O ALA A 6 22.482 -5.458 -3.987 1.00 4.96 O
ATOM 47 CB ALA A 6 24.831 -6.626 -5.558 1.00 5.96 C
ATOM 48 N VAL A 7 24.165 -4.139 -3.284 1.00 4.97 N
ATOM 49 CA VAL A 7 23.374 -2.917 -3.085 1.00 4.42 C
ATOM 50 C VAL A 7 23.482 -2.046 -4.325 1.00 4.45 C
ATOM 51 O VAL A 7 24.589 -1.663 -4.717 1.00 5.55 O
ATOM 52 CB VAL A 7 23.830 -2.159 -1.806 1.00 5.09 C
ATOM 53 CG1 VAL A 7 23.111 -0.842 -1.686 1.00 5.65 C
ATOM 54 CG2 VAL A 7 23.612 -2.998 -0.570 1.00 6.88 C
ATOM 204 N MET A 31 18.177 -3.966 -4.656 1.00 4.72 N
ATOM 205 CA MET A 31 18.833 -4.887 -3.744 1.00 5.29 C
ATOM 206 C MET A 31 18.765 -6.294 -4.322 1.00 4.60 C
ATOM 207 O MET A 31 17.661 -6.738 -4.657 1.00 4.98 O
ATOM 208 CB MET A 31 18.097 -4.868 -2.387 1.00 6.39 C
ATOM 209 CG MET A 31 18.723 -5.755 -1.334 1.00 8.61 C
ATOM 210 SD MET A 31 20.248 -5.074 -0.655 1.00 11.04 S
ATOM 211 CE MET A 31 21.358 -6.427 -0.777 1.00 8.94 C
ATOM 212 N ALA A 32 19.899 -6.986 -4.412 1.00 3.90 N
ATOM 213 CA ALA A 32 19.934 -8.380 -4.864 1.00 3.55 C
ATOM 214 C ALA A 32 20.720 -9.194 -3.858 1.00 3.90 C
ATOM 215 O ALA A 32 21.762 -8.763 -3.393 1.00 5.01 O
ATOM 216 CB ALA A 32 20.552 -8.500 -6.255 1.00 4.55 C
ATOM 217 N SER A 33 20.230 -10.407 -3.567 1.00 4.02 N
ATOM 218 CA SER A 33 20.980 -11.288 -2.645 1.00 3.79 C
ATOM 219 C SER A 33 20.591 -12.727 -2.850 1.00 4.33 C
ATOM 220 O SER A 33 19.532 -13.045 -3.412 1.00 4.84 O
ATOM 221 CB SER A 33 20.830 -10.880 -1.167 1.00 4.55 C
ATOM 222 OG SER A 33 19.498 -11.105 -0.710 1.00 5.25 O
ATOM 223 N GLY A 34 21.415 -13.600 -2.283 1.00 4.96 N
ATOM 224 CA GLY A 34 21.104 -14.997 -2.335 1.00 4.50 C
ATOM 225 C GLY A 34 21.914 -15.837 -1.397 1.00 4.64 C
ATOM 226 O GLY A 34 22.836 -15.343 -0.732 1.00 4.96 O
ATOM 227 N THR A 35 21.521 -17.105 -1.329 1.00 4.35 N
ATOM 228 CA THR A 35 22.277 -18.138 -0.654 1.00 4.02 C
ATOM 229 C THR A 35 22.226 -19.392 -1.495 1.00 4.55 C
ATOM 230 O THR A 35 21.221 -19.652 -2.170 1.00 4.35 O
ATOM 231 CB THR A 35 21.715 -18.436 0.762 1.00 5.12 C
ATOM 232 OG1 THR A 35 20.356 -18.929 0.668 1.00 5.51 O
ATOM 233 CG2 THR A 35 21.733 -17.222 1.670 1.00 5.97 C
ATOM 234 N SER A 35A 23.294 -20.178 -1.426 1.00 4.63 N
ATOM 235 CA SER A 35A 23.402 -21.406 -2.221 1.00 4.58 C
ATOM 236 C SER A 35A 24.387 -22.368 -1.553 1.00 5.05 C
ATOM 237 O SER A 35A 24.929 -22.095 -0.497 1.00 6.22 O
ATOM 238 CB SER A 35A 23.881 -21.071 -3.639 1.00 5.69 C
ATOM 239 OG SER A 35A 25.213 -20.561 -3.633 1.00 7.12 O
""")
pdb_par_input = iotbx.pdb.hierarchy.input(pdb_string="""\
CRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1
SCALE1 0.021524 0.012427 0.000000 0.00000
SCALE2 0.000000 0.024854 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005176 0.00000
ATOM 67 N ALA A 15 5.011 -5.031 -8.967 1.00 5.73 N
ATOM 68 CA ALA A 15 4.943 -6.455 -9.287 1.00 6.16 C
ATOM 69 C ALA A 15 5.610 -7.252 -8.166 1.00 6.39 C
ATOM 70 O ALA A 15 6.751 -7.007 -7.857 1.00 9.87 O
ATOM 71 CB ALA A 15 5.684 -6.739 -10.604 1.00 7.46 C
ATOM 72 N THR A 15A 4.929 -8.263 -7.636 1.00 5.49 N
ATOM 73 C THR A 15A 5.316 -10.600 -7.084 1.00 5.07 C
ATOM 74 O THR A 15A 4.214 -11.002 -7.422 1.00 6.51 O
ATOM 75 CA THR A 15A 5.513 -9.172 -6.657 1.00 5.70 C
ATOM 76 CB THR A 15A 4.864 -9.001 -5.276 1.00 8.31 C
ATOM 77 N GLY A 17 6.393 -11.375 -7.067 1.00 4.56 N
ATOM 78 CA GLY A 17 6.325 -12.770 -7.439 1.00 4.26 C
ATOM 79 C GLY A 17 7.219 -13.654 -6.621 1.00 4.41 C
ATOM 80 O GLY A 17 8.263 -13.233 -6.114 1.00 5.01 O
ATOM 81 N SER A 18 6.827 -14.921 -6.561 1.00 4.24 N
ATOM 82 CA SER A 18 7.657 -15.945 -5.959 1.00 4.02 C
ATOM 83 C SER A 18 7.539 -17.244 -6.724 1.00 3.64 C
ATOM 84 O SER A 18 6.482 -17.526 -7.331 1.00 4.07 O
ATOM 85 CB SER A 18 7.335 -16.157 -4.481 1.00 5.86 C
ATOM 86 N ALA A 19 8.573 -18.049 -6.627 1.00 3.19 N
ATOM 87 CA ALA A 19 8.578 -19.414 -7.195 1.00 3.31 C
ATOM 88 C ALA A 19 9.370 -20.307 -6.238 1.00 3.20 C
ATOM 89 O ALA A 19 10.484 -19.956 -5.817 1.00 4.21 O
ATOM 90 CB ALA A 19 9.235 -19.415 -8.574 1.00 3.85 C
ATOM 91 N THR A 20 8.825 -21.476 -5.940 1.00 3.77 N
ATOM 92 CA THR A 20 9.478 -22.432 -5.047 1.00 3.70 C
ATOM 93 C THR A 20 9.444 -23.827 -5.640 1.00 3.56 C
ATOM 94 O THR A 20 8.383 -24.281 -6.108 1.00 4.14 O
ATOM 95 CB THR A 20 8.787 -22.430 -3.673 1.00 4.76 C
ATOM 96 N THR A 20A 10.560 -24.542 -5.569 1.00 4.00 N
ATOM 97 CA THR A 20A 10.597 -25.962 -5.876 1.00 4.05 C
ATOM 98 C THR A 20A 10.984 -26.770 -4.636 1.00 4.53 C
ATOM 99 O THR A 20A 11.770 -26.361 -3.802 1.00 5.04 O
ATOM 100 CB THR A 20A 11.488 -26.293 -7.083 1.00 4.38 C
ATOM 189 N GLN A 40 0.280 -6.099 -9.049 1.00 6.35 N
ATOM 190 CA GLN A 40 0.087 -7.454 -9.580 1.00 6.35 C
ATOM 191 C GLN A 40 0.964 -8.417 -8.788 1.00 6.09 C
ATOM 192 O GLN A 40 2.080 -8.093 -8.393 1.00 6.87 O
ATOM 193 CB GLN A 40 0.461 -7.523 -11.060 1.00 7.52 C
ATOM 194 N THR A 41 0.419 -9.596 -8.544 1.00 6.66 N
ATOM 195 CA THR A 41 1.108 -10.640 -7.800 1.00 6.93 C
ATOM 196 C THR A 41 0.932 -12.005 -8.414 1.00 6.82 C
ATOM 197 O THR A 41 -0.069 -12.258 -9.104 1.00 8.79 O
ATOM 198 CB THR A 41 0.633 -10.636 -6.352 1.00 10.84 C
ATOM 199 N ALA A 42 1.951 -12.847 -8.263 1.00 6.44 N
ATOM 200 CA ALA A 42 1.923 -14.209 -8.797 1.00 6.59 C
ATOM 201 C ALA A 42 2.829 -15.117 -7.992 1.00 5.51 C
ATOM 202 O ALA A 42 3.835 -14.684 -7.420 1.00 5.94 O
ATOM 203 CB ALA A 42 2.327 -14.218 -10.264 1.00 9.02 C
ATOM 204 N LYS A 42A 2.479 -16.398 -7.978 1.00 6.26 N
ATOM 205 CA LYS A 42A 3.247 -17.395 -7.256 1.00 6.48 C
ATOM 206 C LYS A 42A 3.186 -18.741 -7.955 1.00 5.78 C
ATOM 207 O LYS A 42A 2.206 -19.041 -8.623 1.00 9.40 O
ATOM 208 CB LYS A 42A 2.727 -17.535 -5.836 1.00 8.81 C
ATOM 209 N SER A 44 4.243 -19.534 -7.818 1.00 4.43 N
ATOM 210 CA SER A 44 4.241 -20.890 -8.325 1.00 4.28 C
ATOM 211 C SER A 44 4.998 -21.811 -7.358 1.00 4.09 C
ATOM 212 O SER A 44 5.865 -21.377 -6.584 1.00 4.53 O
ATOM 213 CB SER A 44 4.831 -20.949 -9.731 1.00 5.33 C
ATOM 214 N PHE A 45 4.660 -23.091 -7.444 1.00 4.39 N
ATOM 215 CA PHE A 45 5.198 -24.135 -6.576 1.00 4.44 C
ATOM 216 C PHE A 45 5.222 -25.415 -7.389 1.00 4.16 C
ATOM 217 O PHE A 45 4.183 -25.754 -7.979 1.00 5.11 O
ATOM 218 CB PHE A 45 4.254 -24.281 -5.370 1.00 5.22 C
ATOM 219 N ALA A 45A 6.347 -26.119 -7.403 1.00 3.62 N
ATOM 220 CA ALA A 45A 6.443 -27.338 -8.202 1.00 3.99 C
ATOM 221 C ALA A 45A 7.579 -28.205 -7.717 1.00 4.57 C
ATOM 222 O ALA A 45A 8.479 -27.750 -7.000 1.00 4.79 O
ATOM 223 CB ALA A 45A 6.607 -27.026 -9.678 1.00 4.52 C
TER
END
""")
pdb_par_ac_input = iotbx.pdb.hierarchy.input(pdb_string="""\
CRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1
SCALE1 0.021524 0.012427 0.000000 0.00000
SCALE2 0.000000 0.024854 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005176 0.00000
ATOM 1 N AALA A 15 5.011 -5.031 -8.967 0.50 5.73 N
ATOM 2 CA AALA A 15 4.943 -6.455 -9.287 0.50 6.16 C
ATOM 3 C AALA A 15 5.610 -7.252 -8.166 0.50 6.39 C
ATOM 4 O AALA A 15 6.751 -7.007 -7.857 0.50 9.87 O
ATOM 5 CB AALA A 15 5.684 -6.739 -10.604 0.50 7.46 C
ATOM 6 N BALA A 15 5.111 -5.031 -8.967 0.50 5.73 N
ATOM 7 CA BALA A 15 5.043 -6.455 -9.287 0.50 6.16 C
ATOM 8 C BALA A 15 5.710 -7.252 -8.166 0.50 6.39 C
ATOM 9 O BALA A 15 6.851 -7.007 -7.857 0.50 9.87 O
ATOM 10 CB BALA A 15 5.784 -6.739 -10.604 0.50 7.46 C
ATOM 11 N ATHR A 15A 4.929 -8.263 -7.636 0.50 5.49 N
ATOM 12 C ATHR A 15A 5.316 -10.600 -7.084 0.50 5.07 C
ATOM 13 O ATHR A 15A 4.214 -11.002 -7.422 0.50 6.51 O
ATOM 14 CA ATHR A 15A 5.513 -9.172 -6.657 0.50 5.70 C
ATOM 15 CB ATHR A 15A 4.864 -9.001 -5.276 0.50 8.31 C
ATOM 16 N BTHR A 15A 5.029 -8.263 -7.636 0.50 5.49 N
ATOM 17 C BTHR A 15A 5.416 -10.600 -7.084 0.50 5.07 C
ATOM 18 O BTHR A 15A 4.314 -11.002 -7.422 0.50 6.51 O
ATOM 19 CA BTHR A 15A 5.613 -9.172 -6.657 0.50 5.70 C
ATOM 20 CB BTHR A 15A 4.964 -9.001 -5.276 0.50 8.31 C
ATOM 21 N GLY A 17 6.393 -11.375 -7.067 1.00 4.56 N
ATOM 22 CA GLY A 17 6.325 -12.770 -7.439 1.00 4.26 C
ATOM 23 C GLY A 17 7.219 -13.654 -6.621 1.00 4.41 C
ATOM 24 O GLY A 17 8.263 -13.233 -6.114 1.00 5.01 O
ATOM 25 N SER A 18 6.827 -14.921 -6.561 1.00 4.24 N
ATOM 26 CA SER A 18 7.657 -15.945 -5.959 1.00 4.02 C
ATOM 27 C SER A 18 7.539 -17.244 -6.724 1.00 3.64 C
ATOM 28 O SER A 18 6.482 -17.526 -7.331 1.00 4.07 O
ATOM 29 CB SER A 18 7.335 -16.157 -4.481 1.00 5.86 C
ATOM 30 N ALA A 19 8.573 -18.049 -6.627 1.00 3.19 N
ATOM 31 CA ALA A 19 8.578 -19.414 -7.195 1.00 3.31 C
ATOM 32 C ALA A 19 9.370 -20.307 -6.238 1.00 3.20 C
ATOM 33 O ALA A 19 10.484 -19.956 -5.817 1.00 4.21 O
ATOM 34 CB ALA A 19 9.235 -19.415 -8.574 1.00 3.85 C
ATOM 35 N THR A 20 8.825 -21.476 -5.940 1.00 3.77 N
ATOM 36 CA THR A 20 9.478 -22.432 -5.047 1.00 3.70 C
ATOM 37 C THR A 20 9.444 -23.827 -5.640 1.00 3.56 C
ATOM 38 O THR A 20 8.383 -24.281 -6.108 1.00 4.14 O
ATOM 39 CB THR A 20 8.787 -22.430 -3.673 1.00 4.76 C
ATOM 40 N THR A 21 10.560 -24.542 -5.569 1.00 4.00 N
ATOM 41 CA THR A 21 10.597 -25.962 -5.876 1.00 4.05 C
ATOM 42 C THR A 21 10.984 -26.770 -4.636 1.00 4.53 C
ATOM 43 O THR A 21 11.770 -26.361 -3.802 1.00 5.04 O
ATOM 44 CB THR A 21 11.488 -26.293 -7.083 1.00 4.38 C
ATOM 45 N GLN A 40 0.280 -6.099 -9.049 1.00 6.35 N
ATOM 46 CA GLN A 40 0.087 -7.454 -9.580 1.00 6.35 C
ATOM 47 C GLN A 40 0.964 -8.417 -8.788 1.00 6.09 C
ATOM 48 O GLN A 40 2.080 -8.093 -8.393 1.00 6.87 O
ATOM 49 CB GLN A 40 0.461 -7.523 -11.060 1.00 7.52 C
ATOM 50 N THR A 41 0.419 -9.596 -8.544 1.00 6.66 N
ATOM 51 CA THR A 41 1.108 -10.640 -7.800 1.00 6.93 C
ATOM 52 C THR A 41 0.932 -12.005 -8.414 1.00 6.82 C
ATOM 53 O THR A 41 -0.069 -12.258 -9.104 1.00 8.79 O
ATOM 54 CB THR A 41 0.633 -10.636 -6.352 1.00 10.84 C
ATOM 55 N ALA A 42 1.951 -12.847 -8.263 1.00 6.44 N
ATOM 56 CA ALA A 42 1.923 -14.209 -8.797 1.00 6.59 C
ATOM 57 C ALA A 42 2.829 -15.117 -7.992 1.00 5.51 C
ATOM 58 O ALA A 42 3.835 -14.684 -7.420 1.00 5.94 O
ATOM 59 CB ALA A 42 2.327 -14.218 -10.264 1.00 9.02 C
ATOM 60 N LYS A 42A 2.479 -16.398 -7.978 1.00 6.26 N
ATOM 61 CA LYS A 42A 3.247 -17.395 -7.256 1.00 6.48 C
ATOM 62 C LYS A 42A 3.186 -18.741 -7.955 1.00 5.78 C
ATOM 63 O LYS A 42A 2.206 -19.041 -8.623 1.00 9.40 O
ATOM 64 CB LYS A 42A 2.727 -17.535 -5.836 1.00 8.81 C
ATOM 65 N SER A 44 4.243 -19.534 -7.818 1.00 4.43 N
ATOM 66 CA SER A 44 4.241 -20.890 -8.325 1.00 4.28 C
ATOM 67 C SER A 44 4.998 -21.811 -7.358 1.00 4.09 C
ATOM 68 O SER A 44 5.865 -21.377 -6.584 1.00 4.53 O
ATOM 69 CB SER A 44 4.831 -20.949 -9.731 1.00 5.33 C
ATOM 70 N PHE A 45 4.660 -23.091 -7.444 1.00 4.39 N
ATOM 71 CA PHE A 45 5.198 -24.135 -6.576 1.00 4.44 C
ATOM 72 C PHE A 45 5.222 -25.415 -7.389 1.00 4.16 C
ATOM 73 O PHE A 45 4.183 -25.754 -7.979 1.00 5.11 O
ATOM 74 CB PHE A 45 4.254 -24.281 -5.370 1.00 5.22 C
ATOM 75 N ALA A 46 6.347 -26.119 -7.403 1.00 3.62 N
ATOM 76 CA ALA A 46 6.443 -27.338 -8.202 1.00 3.99 C
ATOM 77 C ALA A 46 7.579 -28.205 -7.717 1.00 4.57 C
ATOM 78 O ALA A 46 8.479 -27.750 -7.000 1.00 4.79 O
ATOM 79 CB ALA A 46 6.607 -27.026 -9.678 1.00 4.52 C
TER 80 ALA A 46
END
""")
s_apar_records1 = """\
SHEET 1 A 2 TYR A 2 VAL A 7 0
SHEET 2 A 2 MET A 31 SER A 35A-1 O ALA A 35A N ALA A 2
"""
s_apar_records2 = """\
SHEET 1 A 2 TYR A 2 VAL A 7 0
SHEET 2 A 2 MET A 31 SER A 35A-1 O ALA A 32 N ALA A 6
"""
s_apar_records3 = """\
SHEET 1 A 2 SER A 2A VAL A 7 0
SHEET 2 A 2 MET A 31 SER A 35A-1 O ALA A 32 N ALA A 6
"""
s_par_records1 = """\
SHEET 1 B 2 ALA A 15 THR A 20A 0
SHEET 2 B 2 GLN A 40 ALA A 45A 1 O GLN A 40 N THR A 15A
"""
s_par_records2 = """\
SHEET 1 B 2 ALA A 15 THR A 20A 0
SHEET 2 B 2 GLN A 40 ALA A 45A 1 O GLN A 44 N THR A 20
"""
s_par_records3 = """\
SHEET 1 B 2 ALA A 15A THR A 20A 0
SHEET 2 B 2 GLN A 40 ALA A 45 1 O GLN A 44 N THR A 20
"""
log = null_out()
# defpars = sec_str_master_phil
n_hbonds = []
for pdb_inp, recs in [
(pdb_apar_input, s_apar_records1), # 6
(pdb_apar_input, s_apar_records2), # 6
(pdb_apar_input, s_apar_records3), # 4
(pdb_par_input, s_par_records1), # 6
(pdb_par_input, s_par_records2), # 6
(pdb_par_input, s_par_records3), # 5
(pdb_par_ac_input, s_par_records1), # 8 hbonds
]:
ioss_annotation = ioss.annotation.from_records(
records=recs.split('\n'))
ann = ioss_annotation.as_restraint_groups(
prefix_scope="secondary_structure")
defpars = iotbx.phil.parse(sec_str_master_phil_str)
custom_pars = defpars.fetch(iotbx.phil.parse(ann))
custom_pars_ex = custom_pars.extract()
ss_manager = manager(pdb_inp.hierarchy,
sec_str_from_pdb_file=None,
params=custom_pars_ex.secondary_structure,
verbose=-1)
proxies_for_grm = ss_manager.create_protein_hbond_proxies(
annotation=None, log=log)
# print proxies_for_grm.size()
n_hbonds.append(proxies_for_grm.size())
assert n_hbonds == [6, 6, 4, 6, 6, 5, 8]
def get_reference_dihedral_proxies(self, processed_pdb_file):
complete_dihedral_proxies = utils.get_dihedrals_and_phi_psi(
processed_pdb_file=processed_pdb_file)
generated_reference_dihedral_proxies = \
cctbx.geometry_restraints.shared_dihedral_proxy()
sigma = self.params.sigma
limit = self.params.limit
ref_ss_m = None
ss_selection = None
if self.params.secondary_structure_only:
if (not libtbx.env.has_module(name="ksdssp")):
raise RuntimeError(
"ksdssp module is not configured, "+\
"cannot generate secondary structure reference")
ref_ss_m = {}
ss_selection = {}
for file in self.reference_file_list:
ref_ss_m[file] = secondary_structure.manager(
pdb_hierarchy=self.pdb_hierarchy_ref[file],
sec_str_from_pdb_file=None)
sec_str_from_pdb_file = ref_ss_m[file].actual_sec_str
if sec_str_from_pdb_file != None:
overall_selection = sec_str_from_pdb_file.overall_selection()
sel_cache_ref = self.pdb_hierarchy_ref[file].atom_selection_cache()
bsel = sel_cache_ref.selection(string=overall_selection)
if bsel.all_eq(False):
raise Sorry("No atom selected")
ss_selection[file] = bsel
t_sum = 0
for dp in complete_dihedral_proxies:
key_work = ""
complete = True
for i_seq in dp.i_seqs:
if not self.selection[i_seq]:
complete = False
if not complete:
continue
for i_seq in dp.i_seqs:
key_work = key_work + self.i_seq_name_hash[i_seq]
#find matching key
key = None
file_match = None
for file in self.reference_file_list:
if key is not None or file not in self.match_map:
continue
else:
key = ""
ref_match = True
for i_seq in dp.i_seqs:
if ref_match:
map_part = self.match_map[file].get(i_seq)
if map_part is not None:
key_part = self.i_seq_name_hash_ref[file].get(map_part)
if key_part is None:
ref_match = False
key = None
file_match = None
else:
key = key+key_part
else:
ref_match = False
key = None
file_match = None
if key is not None:
file_match = file
try:
reference_angle = self.reference_dihedral_hash[file_match][key]
except Exception:
continue
w_limit = limit
w_weight = 1/sigma**2
if (self.params.secondary_structure_only and ss_selection is not None
and ss_selection[file_match] is not None):
limit2 = 15.0
w_weight = 0.04
if (ss_selection[file_match][self.match_map[file_match][dp.i_seqs[0]]] and
ss_selection[file_match][self.match_map[file_match][dp.i_seqs[1]]] and
ss_selection[file_match][self.match_map[file_match][dp.i_seqs[2]]] and
ss_selection[file_match][self.match_map[file_match][dp.i_seqs[3]]]):
limit2 = 30.0
w_weight = 1
dp_add = cctbx.geometry_restraints.dihedral_proxy(
i_seqs=dp.i_seqs,
angle_ideal=reference_angle,
weight=w_weight,
limit=w_limit,
top_out=TOP_OUT_FLAG)
generated_reference_dihedral_proxies.append(dp_add)
else:
dp_add = cctbx.geometry_restraints.dihedral_proxy(
i_seqs=dp.i_seqs,
angle_ideal=reference_angle,
weight=1/sigma**2,
limit=limit,
top_out=TOP_OUT_FLAG)
# print "Already_there:", self._is_proxy_already_present(generated_reference_dihedral_proxies,dp_add)
# if not self._is_proxy_already_present(generated_reference_dihedral_proxies,dp_add):
generated_reference_dihedral_proxies.append(dp_add)
self.reference_dihedral_proxies = generated_reference_dihedral_proxies
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 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 run (args, params=None, out=sys.stdout, log=sys.stderr) :
# params keyword is for running program from GUI dialog
if ( ((len(args) == 0) and (params is None)) or
((len(args) > 0) and ((args[0] == "-h") or (args[0] == "--help"))) ):
show_usage()
return
# parse command-line arguments
if (params is None):
pcl = iotbx.phil.process_command_line_with_files(
args=args,
master_phil_string=master_phil_str,
pdb_file_def="file_name")
work_params = pcl.work.extract()
# or use parameters defined by GUI
else:
work_params = params
pdb_files = work_params.file_name
work_params.secondary_structure.enabled=True
assert work_params.format in ["phenix", "phenix_refine", "phenix_bonds",
"pymol", "refmac", "kinemage", "pdb"]
if work_params.quiet :
out = cStringIO.StringIO()
pdb_combined = iotbx.pdb.combine_unique_pdb_files(file_names=pdb_files)
pdb_structure = iotbx.pdb.input(source_info=None,
lines=flex.std_string(pdb_combined.raw_records))
cs = pdb_structure.crystal_symmetry()
corrupted_cs = False
if cs is not None:
if [cs.unit_cell(), cs.space_group()].count(None) > 0:
corrupted_cs = True
cs = None
elif cs.unit_cell().volume() < 10:
corrupted_cs = True
cs = None
if cs is None:
if corrupted_cs:
print >> out, "Symmetry information is corrupted, "
else:
print >> out, "Symmetry information was not found, "
print >> out, "putting molecule in P1 box."
from cctbx import uctbx
atoms = pdb_structure.atoms()
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=atoms.extract_xyz(),
buffer_layer=3)
atoms.set_xyz(new_xyz=box.sites_cart)
cs = box.crystal_symmetry()
from mmtbx.monomer_library import pdb_interpretation, server
import mmtbx
import mmtbx.command_line.geometry_minimization
mon_lib_srv = server.server()
ener_lib = server.ener_lib()
defpars = mmtbx.command_line.geometry_minimization.master_params().extract()
defpars.pdb_interpretation.automatic_linking.link_carbohydrates=False
defpars.pdb_interpretation.c_beta_restraints=False
defpars.pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
processed_pdb_file = pdb_interpretation.process(
mon_lib_srv = mon_lib_srv,
ener_lib = ener_lib,
pdb_inp = pdb_structure,
crystal_symmetry = cs,
params = defpars.pdb_interpretation,
force_symmetry = True)
pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy
geometry = processed_pdb_file.geometry_restraints_manager()
geometry.pair_proxies(processed_pdb_file.xray_structure().sites_cart())
pdb_hierarchy.atoms().reset_i_seq()
if len(pdb_hierarchy.models()) != 1 :
raise Sorry("Multiple models not supported.")
ss_from_file = None
if hasattr(pdb_structure, "extract_secondary_structure"):
ss_from_file = pdb_structure.extract_secondary_structure()
m = manager(pdb_hierarchy=pdb_hierarchy,
geometry_restraints_manager=geometry,
sec_str_from_pdb_file=ss_from_file,
params=work_params.secondary_structure,
verbose=work_params.verbose)
# bp_p = nucleic_acids.get_basepair_plane_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair,
# geometry)
# st_p = nucleic_acids.get_stacking_proxies(
# pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.stacking_pair,
# geometry)
# hb_b, hb_a = nucleic_acids.get_basepair_hbond_proxies(pdb_hierarchy,
# m.params.secondary_structure.nucleic_acid.base_pair)
result_out = cStringIO.StringIO()
# prefix_scope="refinement.pdb_interpretation"
# prefix_scope=""
prefix_scope=""
if work_params.format == "phenix_refine":
prefix_scope = "refinement.pdb_interpretation"
elif work_params.format == "phenix":
prefix_scope = "pdb_interpretation"
ss_phil = None
working_phil = m.as_phil_str(master_phil=sec_str_master_phil)
phil_diff = sec_str_master_phil.fetch_diff(source=working_phil)
if work_params.format in ["phenix", "phenix_refine"]:
comment = "\n".join([
"# These parameters are suitable for use in e.g. phenix.real_space_refine",
"# or geometry_minimization. To use them in phenix.refine add ",
"# 'refinement.' if front of pdb_interpretation."])
if work_params.format == "phenix_refine":
comment = "\n".join([
"# These parameters are suitable for use in phenix.refine only.",
"# To use them in other Phenix tools remove ",
"# 'refinement.' if front of pdb_interpretation."])
print >> result_out, comment
if (prefix_scope != "") :
print >> result_out, "%s {" % prefix_scope
if work_params.show_all_params :
working_phil.show(prefix=" ", out=result_out)
else :
phil_diff.show(prefix=" ", out=result_out)
if (prefix_scope != "") :
print >> result_out, "}"
elif work_params.format == "pdb":
print >> result_out, m.actual_sec_str.as_pdb_str()
elif work_params.format == "phenix_bonds" :
raise Sorry("Not yet implemented.")
elif work_params.format in ["pymol", "refmac", "kinemage"] :
m.show_summary(log=out)
(hb_proxies, hb_angle_proxies, planarity_proxies,
parallelity_proxies) = m.create_all_new_restraints(
pdb_hierarchy=pdb_hierarchy,
grm=geometry,
log=out)
if hb_proxies.size() > 0:
if work_params.format == "pymol" :
bonds_in_format = hb_proxies.as_pymol_dashes(
pdb_hierarchy=pdb_hierarchy)
elif work_params.format == "kinemage" :
bonds_in_format = hb_proxies.as_kinemage(
pdb_hierarchy=pdb_hierarchy)
else :
bonds_in_format = hb_proxies.as_refmac_restraints(
pdb_hierarchy=pdb_hierarchy)
print >> result_out, bonds_in_format
result = result_out.getvalue()
filename = "%s_ss.eff" %os.path.basename(work_params.file_name[0])
outf = open(filename, "w")
outf.write(result)
outf.close()
print >> out, result
return os.path.abspath(filename)
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(
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 run(self):
t_0 = time()
ncs_obj = iotbx.ncs.input(
hierarchy=self.whole_pdb_h,
chain_max_rmsd=4.0,
chain_similarity_threshold=0.99,
residue_match_radius=999.0)
print >> self.log, "Found NCS groups:"
ncs_obj.show(format='phil', log=self.log)
ncs_restr_group_list = ncs_obj.get_ncs_restraints_group_list(
raise_sorry=False)
self.using_ncs = False
total_ncs_selected_atoms = 0
master_sel = flex.size_t([])
filtered_ncs_restr_group_list = self.filter_ncs_restraints_group_list(
self.whole_pdb_h, ncs_restr_group_list)
if len(filtered_ncs_restr_group_list) > 0:
self.using_ncs = True
master_sel = flex.bool(self.whole_pdb_h.atoms_size(), True)
for ncs_gr in filtered_ncs_restr_group_list:
for copy in ncs_gr.copies:
master_sel.set_selected(copy.iselection, False)
self.master_pdb_h = self.whole_pdb_h.select(master_sel)
self.master_sel=master_sel
self.master_pdb_h.reset_atom_i_seqs()
if self.using_ncs:
self.master_pdb_h.write_pdb_file("%s_master_h.pdb" % self.params.output_prefix)
self.working_pdb_h = self.master_pdb_h
else:
self.working_pdb_h = self.whole_pdb_h
self.working_pdb_h.reset_atom_i_seqs()
self.ann = ioss.annotation.from_phil(
phil_helices=self.params.secondary_structure.protein.helix,
phil_sheets=self.params.secondary_structure.protein.sheet,
pdb_hierarchy=self.whole_pdb_h)
self.working_xrs = self.working_pdb_h.extract_xray_structure(crystal_symmetry=self.cs)
if self.using_ncs:
self.whole_xrs = self.whole_pdb_h.extract_xray_structure(crystal_symmetry=self.cs)
else:
self.whole_xrs = self.working_xrs
if self.params.use_map_for_reference:
# self.prepare_reference_map(xrs=self.whole_xrs, pdb_h=self.whole_pdb_h)
# self.prepare_reference_map_2(xrs=self.whole_xrs, pdb_h=self.whole_pdb_h)
self.prepare_reference_map_3(xrs=self.whole_xrs, pdb_h=self.whole_pdb_h)
# STOP()
if self.ann.get_n_helices() + self.ann.get_n_sheets() == 0:
self.ann = self.pdb_input.extract_secondary_structure()
self.original_ann = None
self.filtered_whole_ann = None
if self.ann is not None:
self.original_ann = self.ann.deep_copy()
print >> self.log, "Original SS annotation"
print >> self.log, self.original_ann.as_pdb_str()
self.ann.remove_short_annotations()
self.filtered_whole_ann = self.ann.deep_copy()
self.ann.remove_empty_annotations(
hierarchy=self.working_pdb_h)
self.filtered_whole_ann.remove_empty_annotations(
hierarchy=self.whole_pdb_h)
# self.ann.concatenate_consecutive_helices()
self.ann.split_helices_with_prolines(
hierarchy=self.working_pdb_h,
asc=None)
self.filtered_whole_ann.split_helices_with_prolines(
hierarchy=self.whole_pdb_h,
asc=None)
# print >> self.log, "Splitted SS annotation"
# print >> self.log, ann.as_pdb_str()
print >> self.log, "Filtered SS annotation"
print >> self.log, self.ann.as_pdb_str()
# getting grm with SS restraints
self.get_grm()
if (self.ann is None or
self.ann.get_n_helices() + self.ann.get_n_sheets() == 0 or
not self.params.ss_idealization.enabled):
print >> self.log, "No secondary structure annotations found or SS idealization is disabled."
print >> self.log, "Secondary structure substitution step will be skipped"
self.log.flush()
# here we want to do geometry minimization anyway!
negate_selection = None
if self.reference_map is None:
outlier_selection_txt = mmtbx.building.loop_closure.utils. \
rama_outliers_selection(self.working_pdb_h, self.rama_manager, 1)
print >> self.log, "outlier_selection_txt", outlier_selection_txt
negate_selection = "all"
if outlier_selection_txt != "" and outlier_selection_txt is not None:
negate_selection = "not (%s)" % outlier_selection_txt
self.minimize(
hierarchy=self.whole_pdb_h,
xrs=self.whole_xrs,
original_pdb_h=self.whole_pdb_h,
grm=self.whole_grm,
ncs_restraints_group_list=filtered_ncs_restr_group_list,
excl_string_selection=negate_selection,
ss_annotation=self.ann,
reference_map=self.reference_map)
# self.original_boxed_hierarchy.write_pdb_file(file_name="original_boxed_h_1.pdb")
else:
self.params.ss_idealization.file_name_before_regularization = \
"%s_ss_before_reg.pdb" % self.params.output_prefix
ssb.substitute_ss(
real_h=self.working_pdb_h,
xray_structure=self.working_xrs,
ss_annotation=self.ann,
params=self.params.ss_idealization,
grm=self.working_grm,
fix_rotamer_outliers=True,
cif_objects=self.cif_objects,
verbose=True,
reference_map=self.reference_map,
rotamer_manager=self.rotamer_manager,
log=self.log)
self.log.flush()
self.after_ss_idealization = geometry_no_grm(
pdb_hierarchy=iotbx.pdb.input(
source_info=None,
lines=self.working_pdb_h.as_pdb_string()).construct_hierarchy(),
molprobity_scores=True)
# Write resulting pdb file.
self.shift_and_write_result(
hierarchy=self.working_pdb_h,
fname_suffix="ss_ideal",
grm=self.working_grm)
# STOP()
self.params.loop_idealization.minimize_whole = not self.using_ncs
# self.params.loop_idealization.enabled = False
# self.params.loop_idealization.variant_search_level = 0
loop_ideal = loop_idealization(
pdb_hierarchy=self.working_pdb_h,
params=self.params.loop_idealization,
secondary_structure_annotation=self.ann,
reference_map=self.reference_map,
crystal_symmetry=self.working_xrs.crystal_symmetry(),
grm=self.working_grm,
rama_manager=self.rama_manager,
rotamer_manager=self.rotamer_manager,
log=self.log,
verbose=True)
self.log.flush()
# STOP()
self.shift_and_write_result(
hierarchy=loop_ideal.resulting_pdb_h,
fname_suffix="rama_ideal",
grm=self.working_grm)
self.after_loop_idealization = geometry_no_grm(
pdb_hierarchy=iotbx.pdb.input(
source_info=None,
lines=loop_ideal.resulting_pdb_h.as_pdb_string()).construct_hierarchy(),
molprobity_scores=True)
# fixing remaining rotamer outliers
fixed_rot_pdb_h = loop_ideal.resulting_pdb_h.deep_copy()
fixed_rot_pdb_h.reset_atom_i_seqs()
if (self.params.additionally_fix_rotamer_outliers and
self.after_loop_idealization.rotamer_outliers > 0.004):
print >> self.log, "Processing pdb file again for fixing rotamers..."
self.log.flush()
print >> self.log, "Fixing rotamers..."
self.log.flush()
self.shift_and_write_result(
hierarchy=fixed_rot_pdb_h,
fname_suffix="just_before_rota")
fixed_rot_pdb_h = fix_rotamer_outliers(
pdb_hierarchy=fixed_rot_pdb_h,
grm=self.working_grm.geometry,
xrs=self.working_xrs,
map_data=self.reference_map,
mon_lib_srv=self.mon_lib_srv,
rotamer_manager=self.rotamer_manager,
verbose=True)
self.shift_and_write_result(
hierarchy=fixed_rot_pdb_h,
fname_suffix="rota_ideal",
grm=self.working_grm)
cs_to_write = self.cs if self.shift_vector is None else None
self.after_rotamer_fixing = geometry_no_grm(
pdb_hierarchy=iotbx.pdb.input(
source_info=None,
lines=fixed_rot_pdb_h.as_pdb_string()).construct_hierarchy(),
molprobity_scores=True)
ref_hierarchy_for_final_gm = self.original_boxed_hierarchy
if not self.params.use_starting_model_for_final_gm:
ref_hierarchy_for_final_gm = self.whole_pdb_h
ref_hierarchy_for_final_gm.reset_atom_i_seqs()
if self.params.additionally_fix_rotamer_outliers:
ssb.set_xyz_smart(self.working_pdb_h, fixed_rot_pdb_h)
if self.using_ncs:
print >> self.log, "Using ncs"
# multiply back and do geometry_minimization for the whole molecule
for ncs_gr in ncs_restr_group_list:
master_h = self.whole_pdb_h.select(ncs_gr.master_iselection)
for c in ncs_gr.copies:
new_sites = master_h.atoms().extract_xyz()
new_c_sites = c.r.elems * new_sites + c.t
self.whole_pdb_h.select(c.iselection).atoms().set_xyz(new_c_sites)
self.log.flush()
else:
# still need to run gm if rotamers were fixed
print >> self.log, "Not using ncs"
# need to update SS manager for the whole model here.
if self.params.use_ss_restraints:
ss_manager = manager(
pdb_hierarchy=self.whole_pdb_h,
geometry_restraints_manager=self.whole_grm.geometry,
sec_str_from_pdb_file=self.filtered_whole_ann,
params=None,
mon_lib_srv=self.mon_lib_srv,
verbose=-1,
log=self.log)
self.whole_grm.geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=self.whole_pdb_h,
log=self.log)
print >> self.log, "loop_ideal.ref_exclusion_selection", loop_ideal.ref_exclusion_selection
print >> self.log, "Minimizing whole model"
self.minimize(
hierarchy=self.whole_pdb_h,
xrs=self.whole_xrs,
grm=self.whole_grm,
ncs_restraints_group_list=filtered_ncs_restr_group_list,
original_pdb_h=ref_hierarchy_for_final_gm,
excl_string_selection=loop_ideal.ref_exclusion_selection,
ss_annotation=self.ann,
reference_map = self.reference_map)
self.shift_and_write_result(
hierarchy=self.whole_pdb_h,
fname_suffix="all_idealized",
grm=self.whole_grm)
self.final_model_statistics = geometry_no_grm(
pdb_hierarchy=iotbx.pdb.input(
source_info=None,
lines=self.whole_pdb_h.as_pdb_string()).construct_hierarchy(),
molprobity_scores=True)
# self.original_boxed_hierarchy.write_pdb_file(file_name="original_boxed_end.pdb")
self.time_for_run = time() - t_0
def exercise_sheets_bonding_pattern_with_insertions():
pdb_apar_input = iotbx.pdb.hierarchy.input(pdb_string = """\
SCRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1
SCALE1 0.021524 0.012427 0.000000 0.00000
SCALE2 0.000000 0.024854 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005176 0.00000
ATOM 5 N TYR A 2 27.208 -20.701 0.590 1.00 7.29 N
ATOM 6 CA TYR A 2 27.617 -19.424 0.052 1.00 7.96 C
ATOM 7 C TYR A 2 26.483 -18.436 0.263 1.00 6.87 C
ATOM 8 O TYR A 2 25.303 -18.771 0.249 1.00 6.97 O
ATOM 9 CB TYR A 2 27.861 -19.541 -1.451 1.00 7.90 C
ATOM 10 CG TYR A 2 28.902 -20.556 -1.857 1.00 9.09 C
ATOM 11 CD1 TYR A 2 30.255 -20.336 -1.592 1.00 11.43 C
ATOM 12 CD2 TYR A 2 28.566 -21.697 -2.545 1.00 10.59 C
ATOM 13 CE1 TYR A 2 31.227 -21.244 -1.987 1.00 13.93 C
ATOM 14 CE2 TYR A 2 29.518 -22.630 -2.915 1.00 11.76 C
ATOM 15 CZ TYR A 2 30.847 -22.395 -2.659 1.00 13.67 C
ATOM 16 OH TYR A 2 31.792 -23.309 -3.059 1.00 18.26 O
ATOM 17 N SER A 2A 26.854 -17.177 0.412 1.00 6.66 N
ATOM 18 CA SER A 2A 25.899 -16.083 0.383 0.53 6.83 C
ATOM 20 C SER A 2A 26.500 -14.946 -0.440 1.00 5.61 C
ATOM 21 O SER A 2A 27.729 -14.822 -0.565 1.00 8.14 O
ATOM 22 CB SER A 2A 25.569 -15.634 1.795 0.53 7.38 C
ATOM 24 OG SER A 2A 26.740 -15.136 2.390 0.53 9.79 O
ATOM 26 N CYS A 2B 25.627 -14.135 -0.995 1.00 5.11 N
ATOM 27 CA CYS A 2B 26.070 -13.062 -1.865 1.00 5.65 C
ATOM 28 C CYS A 2B 25.043 -11.934 -1.798 1.00 4.54 C
ATOM 29 O CYS A 2B 23.856 -12.180 -1.528 1.00 5.60 O
ATOM 30 CB CYS A 2B 26.253 -13.557 -3.295 1.00 7.00 C
ATOM 31 SG CYS A 2B 24.806 -14.269 -4.119 1.00 8.88 S
ATOM 32 N ARG A 5 25.486 -10.691 -2.002 1.00 4.69 N
ATOM 33 CA ARG A 5 24.558 -9.545 -2.064 1.00 4.87 C
ATOM 34 C ARG A 5 25.196 -8.395 -2.796 1.00 4.57 C
ATOM 35 O ARG A 5 26.416 -8.238 -2.793 1.00 5.50 O
ATOM 36 CB ARG A 5 24.061 -9.108 -0.700 1.00 6.43 C
ATOM 37 CG ARG A 5 25.121 -8.566 0.219 1.00 6.96 C
ATOM 38 CD ARG A 5 24.461 -8.032 1.494 1.00 7.25 C
ATOM 39 NE ARG A 5 25.452 -7.547 2.440 1.00 7.63 N
ATOM 40 CZ ARG A 5 26.107 -8.341 3.280 1.00 9.10 C
ATOM 41 NH1 ARG A 5 25.867 -9.642 3.297 1.00 9.68 N
ATOM 42 NH2 ARG A 5 26.974 -7.836 4.146 1.00 10.30 N
ATOM 43 N ALA A 6 24.325 -7.563 -3.358 1.00 4.39 N
ATOM 44 CA ALA A 6 24.723 -6.362 -4.067 1.00 4.73 C
ATOM 45 C ALA A 6 23.693 -5.275 -3.769 1.00 4.15 C
ATOM 46 O ALA A 6 22.482 -5.458 -3.987 1.00 4.96 O
ATOM 47 CB ALA A 6 24.831 -6.626 -5.558 1.00 5.96 C
ATOM 48 N VAL A 7 24.165 -4.139 -3.284 1.00 4.97 N
ATOM 49 CA VAL A 7 23.374 -2.917 -3.085 1.00 4.42 C
ATOM 50 C VAL A 7 23.482 -2.046 -4.325 1.00 4.45 C
ATOM 51 O VAL A 7 24.589 -1.663 -4.717 1.00 5.55 O
ATOM 52 CB VAL A 7 23.830 -2.159 -1.806 1.00 5.09 C
ATOM 53 CG1 VAL A 7 23.111 -0.842 -1.686 1.00 5.65 C
ATOM 54 CG2 VAL A 7 23.612 -2.998 -0.570 1.00 6.88 C
ATOM 204 N MET A 31 18.177 -3.966 -4.656 1.00 4.72 N
ATOM 205 CA MET A 31 18.833 -4.887 -3.744 1.00 5.29 C
ATOM 206 C MET A 31 18.765 -6.294 -4.322 1.00 4.60 C
ATOM 207 O MET A 31 17.661 -6.738 -4.657 1.00 4.98 O
ATOM 208 CB MET A 31 18.097 -4.868 -2.387 1.00 6.39 C
ATOM 209 CG MET A 31 18.723 -5.755 -1.334 1.00 8.61 C
ATOM 210 SD MET A 31 20.248 -5.074 -0.655 1.00 11.04 S
ATOM 211 CE MET A 31 21.358 -6.427 -0.777 1.00 8.94 C
ATOM 212 N ALA A 32 19.899 -6.986 -4.412 1.00 3.90 N
ATOM 213 CA ALA A 32 19.934 -8.380 -4.864 1.00 3.55 C
ATOM 214 C ALA A 32 20.720 -9.194 -3.858 1.00 3.90 C
ATOM 215 O ALA A 32 21.762 -8.763 -3.393 1.00 5.01 O
ATOM 216 CB ALA A 32 20.552 -8.500 -6.255 1.00 4.55 C
ATOM 217 N SER A 33 20.230 -10.407 -3.567 1.00 4.02 N
ATOM 218 CA SER A 33 20.980 -11.288 -2.645 1.00 3.79 C
ATOM 219 C SER A 33 20.591 -12.727 -2.850 1.00 4.33 C
ATOM 220 O SER A 33 19.532 -13.045 -3.412 1.00 4.84 O
ATOM 221 CB SER A 33 20.830 -10.880 -1.167 1.00 4.55 C
ATOM 222 OG SER A 33 19.498 -11.105 -0.710 1.00 5.25 O
ATOM 223 N GLY A 34 21.415 -13.600 -2.283 1.00 4.96 N
ATOM 224 CA GLY A 34 21.104 -14.997 -2.335 1.00 4.50 C
ATOM 225 C GLY A 34 21.914 -15.837 -1.397 1.00 4.64 C
ATOM 226 O GLY A 34 22.836 -15.343 -0.732 1.00 4.96 O
ATOM 227 N THR A 35 21.521 -17.105 -1.329 1.00 4.35 N
ATOM 228 CA THR A 35 22.277 -18.138 -0.654 1.00 4.02 C
ATOM 229 C THR A 35 22.226 -19.392 -1.495 1.00 4.55 C
ATOM 230 O THR A 35 21.221 -19.652 -2.170 1.00 4.35 O
ATOM 231 CB THR A 35 21.715 -18.436 0.762 1.00 5.12 C
ATOM 232 OG1 THR A 35 20.356 -18.929 0.668 1.00 5.51 O
ATOM 233 CG2 THR A 35 21.733 -17.222 1.670 1.00 5.97 C
ATOM 234 N SER A 35A 23.294 -20.178 -1.426 1.00 4.63 N
ATOM 235 CA SER A 35A 23.402 -21.406 -2.221 1.00 4.58 C
ATOM 236 C SER A 35A 24.387 -22.368 -1.553 1.00 5.05 C
ATOM 237 O SER A 35A 24.929 -22.095 -0.497 1.00 6.22 O
ATOM 238 CB SER A 35A 23.881 -21.071 -3.639 1.00 5.69 C
ATOM 239 OG SER A 35A 25.213 -20.561 -3.633 1.00 7.12 O
""")
pdb_par_input = iotbx.pdb.hierarchy.input(pdb_string = """\
CRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1
SCALE1 0.021524 0.012427 0.000000 0.00000
SCALE2 0.000000 0.024854 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005176 0.00000
ATOM 67 N ALA A 15 5.011 -5.031 -8.967 1.00 5.73 N
ATOM 68 CA ALA A 15 4.943 -6.455 -9.287 1.00 6.16 C
ATOM 69 C ALA A 15 5.610 -7.252 -8.166 1.00 6.39 C
ATOM 70 O ALA A 15 6.751 -7.007 -7.857 1.00 9.87 O
ATOM 71 CB ALA A 15 5.684 -6.739 -10.604 1.00 7.46 C
ATOM 72 N THR A 15A 4.929 -8.263 -7.636 1.00 5.49 N
ATOM 73 C THR A 15A 5.316 -10.600 -7.084 1.00 5.07 C
ATOM 74 O THR A 15A 4.214 -11.002 -7.422 1.00 6.51 O
ATOM 75 CA THR A 15A 5.513 -9.172 -6.657 1.00 5.70 C
ATOM 76 CB THR A 15A 4.864 -9.001 -5.276 1.00 8.31 C
ATOM 77 N GLY A 17 6.393 -11.375 -7.067 1.00 4.56 N
ATOM 78 CA GLY A 17 6.325 -12.770 -7.439 1.00 4.26 C
ATOM 79 C GLY A 17 7.219 -13.654 -6.621 1.00 4.41 C
ATOM 80 O GLY A 17 8.263 -13.233 -6.114 1.00 5.01 O
ATOM 81 N SER A 18 6.827 -14.921 -6.561 1.00 4.24 N
ATOM 82 CA SER A 18 7.657 -15.945 -5.959 1.00 4.02 C
ATOM 83 C SER A 18 7.539 -17.244 -6.724 1.00 3.64 C
ATOM 84 O SER A 18 6.482 -17.526 -7.331 1.00 4.07 O
ATOM 85 CB SER A 18 7.335 -16.157 -4.481 1.00 5.86 C
ATOM 86 N ALA A 19 8.573 -18.049 -6.627 1.00 3.19 N
ATOM 87 CA ALA A 19 8.578 -19.414 -7.195 1.00 3.31 C
ATOM 88 C ALA A 19 9.370 -20.307 -6.238 1.00 3.20 C
ATOM 89 O ALA A 19 10.484 -19.956 -5.817 1.00 4.21 O
ATOM 90 CB ALA A 19 9.235 -19.415 -8.574 1.00 3.85 C
ATOM 91 N THR A 20 8.825 -21.476 -5.940 1.00 3.77 N
ATOM 92 CA THR A 20 9.478 -22.432 -5.047 1.00 3.70 C
ATOM 93 C THR A 20 9.444 -23.827 -5.640 1.00 3.56 C
ATOM 94 O THR A 20 8.383 -24.281 -6.108 1.00 4.14 O
ATOM 95 CB THR A 20 8.787 -22.430 -3.673 1.00 4.76 C
ATOM 96 N THR A 20A 10.560 -24.542 -5.569 1.00 4.00 N
ATOM 97 CA THR A 20A 10.597 -25.962 -5.876 1.00 4.05 C
ATOM 98 C THR A 20A 10.984 -26.770 -4.636 1.00 4.53 C
ATOM 99 O THR A 20A 11.770 -26.361 -3.802 1.00 5.04 O
ATOM 100 CB THR A 20A 11.488 -26.293 -7.083 1.00 4.38 C
ATOM 189 N GLN A 40 0.280 -6.099 -9.049 1.00 6.35 N
ATOM 190 CA GLN A 40 0.087 -7.454 -9.580 1.00 6.35 C
ATOM 191 C GLN A 40 0.964 -8.417 -8.788 1.00 6.09 C
ATOM 192 O GLN A 40 2.080 -8.093 -8.393 1.00 6.87 O
ATOM 193 CB GLN A 40 0.461 -7.523 -11.060 1.00 7.52 C
ATOM 194 N THR A 41 0.419 -9.596 -8.544 1.00 6.66 N
ATOM 195 CA THR A 41 1.108 -10.640 -7.800 1.00 6.93 C
ATOM 196 C THR A 41 0.932 -12.005 -8.414 1.00 6.82 C
ATOM 197 O THR A 41 -0.069 -12.258 -9.104 1.00 8.79 O
ATOM 198 CB THR A 41 0.633 -10.636 -6.352 1.00 10.84 C
ATOM 199 N ALA A 42 1.951 -12.847 -8.263 1.00 6.44 N
ATOM 200 CA ALA A 42 1.923 -14.209 -8.797 1.00 6.59 C
ATOM 201 C ALA A 42 2.829 -15.117 -7.992 1.00 5.51 C
ATOM 202 O ALA A 42 3.835 -14.684 -7.420 1.00 5.94 O
ATOM 203 CB ALA A 42 2.327 -14.218 -10.264 1.00 9.02 C
ATOM 204 N LYS A 42A 2.479 -16.398 -7.978 1.00 6.26 N
ATOM 205 CA LYS A 42A 3.247 -17.395 -7.256 1.00 6.48 C
ATOM 206 C LYS A 42A 3.186 -18.741 -7.955 1.00 5.78 C
ATOM 207 O LYS A 42A 2.206 -19.041 -8.623 1.00 9.40 O
ATOM 208 CB LYS A 42A 2.727 -17.535 -5.836 1.00 8.81 C
ATOM 209 N SER A 44 4.243 -19.534 -7.818 1.00 4.43 N
ATOM 210 CA SER A 44 4.241 -20.890 -8.325 1.00 4.28 C
ATOM 211 C SER A 44 4.998 -21.811 -7.358 1.00 4.09 C
ATOM 212 O SER A 44 5.865 -21.377 -6.584 1.00 4.53 O
ATOM 213 CB SER A 44 4.831 -20.949 -9.731 1.00 5.33 C
ATOM 214 N PHE A 45 4.660 -23.091 -7.444 1.00 4.39 N
ATOM 215 CA PHE A 45 5.198 -24.135 -6.576 1.00 4.44 C
ATOM 216 C PHE A 45 5.222 -25.415 -7.389 1.00 4.16 C
ATOM 217 O PHE A 45 4.183 -25.754 -7.979 1.00 5.11 O
ATOM 218 CB PHE A 45 4.254 -24.281 -5.370 1.00 5.22 C
ATOM 219 N ALA A 45A 6.347 -26.119 -7.403 1.00 3.62 N
ATOM 220 CA ALA A 45A 6.443 -27.338 -8.202 1.00 3.99 C
ATOM 221 C ALA A 45A 7.579 -28.205 -7.717 1.00 4.57 C
ATOM 222 O ALA A 45A 8.479 -27.750 -7.000 1.00 4.79 O
ATOM 223 CB ALA A 45A 6.607 -27.026 -9.678 1.00 4.52 C
TER
END
""")
pdb_par_ac_input = iotbx.pdb.hierarchy.input(pdb_string = """\
CRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1
SCALE1 0.021524 0.012427 0.000000 0.00000
SCALE2 0.000000 0.024854 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005176 0.00000
ATOM 1 N AALA A 15 5.011 -5.031 -8.967 0.50 5.73 N
ATOM 2 CA AALA A 15 4.943 -6.455 -9.287 0.50 6.16 C
ATOM 3 C AALA A 15 5.610 -7.252 -8.166 0.50 6.39 C
ATOM 4 O AALA A 15 6.751 -7.007 -7.857 0.50 9.87 O
ATOM 5 CB AALA A 15 5.684 -6.739 -10.604 0.50 7.46 C
ATOM 6 N BALA A 15 5.111 -5.031 -8.967 0.50 5.73 N
ATOM 7 CA BALA A 15 5.043 -6.455 -9.287 0.50 6.16 C
ATOM 8 C BALA A 15 5.710 -7.252 -8.166 0.50 6.39 C
ATOM 9 O BALA A 15 6.851 -7.007 -7.857 0.50 9.87 O
ATOM 10 CB BALA A 15 5.784 -6.739 -10.604 0.50 7.46 C
ATOM 11 N ATHR A 15A 4.929 -8.263 -7.636 0.50 5.49 N
ATOM 12 C ATHR A 15A 5.316 -10.600 -7.084 0.50 5.07 C
ATOM 13 O ATHR A 15A 4.214 -11.002 -7.422 0.50 6.51 O
ATOM 14 CA ATHR A 15A 5.513 -9.172 -6.657 0.50 5.70 C
ATOM 15 CB ATHR A 15A 4.864 -9.001 -5.276 0.50 8.31 C
ATOM 16 N BTHR A 15A 5.029 -8.263 -7.636 0.50 5.49 N
ATOM 17 C BTHR A 15A 5.416 -10.600 -7.084 0.50 5.07 C
ATOM 18 O BTHR A 15A 4.314 -11.002 -7.422 0.50 6.51 O
ATOM 19 CA BTHR A 15A 5.613 -9.172 -6.657 0.50 5.70 C
ATOM 20 CB BTHR A 15A 4.964 -9.001 -5.276 0.50 8.31 C
ATOM 21 N GLY A 17 6.393 -11.375 -7.067 1.00 4.56 N
ATOM 22 CA GLY A 17 6.325 -12.770 -7.439 1.00 4.26 C
ATOM 23 C GLY A 17 7.219 -13.654 -6.621 1.00 4.41 C
ATOM 24 O GLY A 17 8.263 -13.233 -6.114 1.00 5.01 O
ATOM 25 N SER A 18 6.827 -14.921 -6.561 1.00 4.24 N
ATOM 26 CA SER A 18 7.657 -15.945 -5.959 1.00 4.02 C
ATOM 27 C SER A 18 7.539 -17.244 -6.724 1.00 3.64 C
ATOM 28 O SER A 18 6.482 -17.526 -7.331 1.00 4.07 O
ATOM 29 CB SER A 18 7.335 -16.157 -4.481 1.00 5.86 C
ATOM 30 N ALA A 19 8.573 -18.049 -6.627 1.00 3.19 N
ATOM 31 CA ALA A 19 8.578 -19.414 -7.195 1.00 3.31 C
ATOM 32 C ALA A 19 9.370 -20.307 -6.238 1.00 3.20 C
ATOM 33 O ALA A 19 10.484 -19.956 -5.817 1.00 4.21 O
ATOM 34 CB ALA A 19 9.235 -19.415 -8.574 1.00 3.85 C
ATOM 35 N THR A 20 8.825 -21.476 -5.940 1.00 3.77 N
ATOM 36 CA THR A 20 9.478 -22.432 -5.047 1.00 3.70 C
ATOM 37 C THR A 20 9.444 -23.827 -5.640 1.00 3.56 C
ATOM 38 O THR A 20 8.383 -24.281 -6.108 1.00 4.14 O
ATOM 39 CB THR A 20 8.787 -22.430 -3.673 1.00 4.76 C
ATOM 40 N THR A 21 10.560 -24.542 -5.569 1.00 4.00 N
ATOM 41 CA THR A 21 10.597 -25.962 -5.876 1.00 4.05 C
ATOM 42 C THR A 21 10.984 -26.770 -4.636 1.00 4.53 C
ATOM 43 O THR A 21 11.770 -26.361 -3.802 1.00 5.04 O
ATOM 44 CB THR A 21 11.488 -26.293 -7.083 1.00 4.38 C
ATOM 45 N GLN A 40 0.280 -6.099 -9.049 1.00 6.35 N
ATOM 46 CA GLN A 40 0.087 -7.454 -9.580 1.00 6.35 C
ATOM 47 C GLN A 40 0.964 -8.417 -8.788 1.00 6.09 C
ATOM 48 O GLN A 40 2.080 -8.093 -8.393 1.00 6.87 O
ATOM 49 CB GLN A 40 0.461 -7.523 -11.060 1.00 7.52 C
ATOM 50 N THR A 41 0.419 -9.596 -8.544 1.00 6.66 N
ATOM 51 CA THR A 41 1.108 -10.640 -7.800 1.00 6.93 C
ATOM 52 C THR A 41 0.932 -12.005 -8.414 1.00 6.82 C
ATOM 53 O THR A 41 -0.069 -12.258 -9.104 1.00 8.79 O
ATOM 54 CB THR A 41 0.633 -10.636 -6.352 1.00 10.84 C
ATOM 55 N ALA A 42 1.951 -12.847 -8.263 1.00 6.44 N
ATOM 56 CA ALA A 42 1.923 -14.209 -8.797 1.00 6.59 C
ATOM 57 C ALA A 42 2.829 -15.117 -7.992 1.00 5.51 C
ATOM 58 O ALA A 42 3.835 -14.684 -7.420 1.00 5.94 O
ATOM 59 CB ALA A 42 2.327 -14.218 -10.264 1.00 9.02 C
ATOM 60 N LYS A 42A 2.479 -16.398 -7.978 1.00 6.26 N
ATOM 61 CA LYS A 42A 3.247 -17.395 -7.256 1.00 6.48 C
ATOM 62 C LYS A 42A 3.186 -18.741 -7.955 1.00 5.78 C
ATOM 63 O LYS A 42A 2.206 -19.041 -8.623 1.00 9.40 O
ATOM 64 CB LYS A 42A 2.727 -17.535 -5.836 1.00 8.81 C
ATOM 65 N SER A 44 4.243 -19.534 -7.818 1.00 4.43 N
ATOM 66 CA SER A 44 4.241 -20.890 -8.325 1.00 4.28 C
ATOM 67 C SER A 44 4.998 -21.811 -7.358 1.00 4.09 C
ATOM 68 O SER A 44 5.865 -21.377 -6.584 1.00 4.53 O
ATOM 69 CB SER A 44 4.831 -20.949 -9.731 1.00 5.33 C
ATOM 70 N PHE A 45 4.660 -23.091 -7.444 1.00 4.39 N
ATOM 71 CA PHE A 45 5.198 -24.135 -6.576 1.00 4.44 C
ATOM 72 C PHE A 45 5.222 -25.415 -7.389 1.00 4.16 C
ATOM 73 O PHE A 45 4.183 -25.754 -7.979 1.00 5.11 O
ATOM 74 CB PHE A 45 4.254 -24.281 -5.370 1.00 5.22 C
ATOM 75 N ALA A 46 6.347 -26.119 -7.403 1.00 3.62 N
ATOM 76 CA ALA A 46 6.443 -27.338 -8.202 1.00 3.99 C
ATOM 77 C ALA A 46 7.579 -28.205 -7.717 1.00 4.57 C
ATOM 78 O ALA A 46 8.479 -27.750 -7.000 1.00 4.79 O
ATOM 79 CB ALA A 46 6.607 -27.026 -9.678 1.00 4.52 C
TER 80 ALA A 46
END
""")
s_apar_records1 = """\
SHEET 1 A 2 TYR A 2 VAL A 7 0
SHEET 2 A 2 MET A 31 SER A 35A-1 O ALA A 35A N ALA A 2
"""
s_apar_records2 = """\
SHEET 1 A 2 TYR A 2 VAL A 7 0
SHEET 2 A 2 MET A 31 SER A 35A-1 O ALA A 32 N ALA A 6
"""
s_apar_records3 = """\
SHEET 1 A 2 SER A 2A VAL A 7 0
SHEET 2 A 2 MET A 31 SER A 35A-1 O ALA A 32 N ALA A 6
"""
s_par_records1 = """\
SHEET 1 B 2 ALA A 15 THR A 20A 0
SHEET 2 B 2 GLN A 40 ALA A 45A 1 O GLN A 40 N THR A 15A
"""
s_par_records2 = """\
SHEET 1 B 2 ALA A 15 THR A 20A 0
SHEET 2 B 2 GLN A 40 ALA A 45A 1 O GLN A 44 N THR A 20
"""
s_par_records3 = """\
SHEET 1 B 2 ALA A 15A THR A 20A 0
SHEET 2 B 2 GLN A 40 ALA A 45 1 O GLN A 44 N THR A 20
"""
log = null_out()
# defpars = sec_str_master_phil
n_hbonds = []
for pdb_inp, recs in [
(pdb_apar_input, s_apar_records1), # 6
(pdb_apar_input, s_apar_records2), # 6
(pdb_apar_input, s_apar_records3), # 4
(pdb_par_input, s_par_records1), # 6
(pdb_par_input, s_par_records2), # 6
(pdb_par_input, s_par_records3), # 5
(pdb_par_ac_input, s_par_records1), # 8 hbonds
]:
ioss_annotation = ioss.annotation.from_records(records = recs.split('\n'))
ann = ioss_annotation.as_restraint_groups(prefix_scope="secondary_structure")
defpars = iotbx.phil.parse(sec_str_master_phil_str)
custom_pars = defpars.fetch(iotbx.phil.parse(ann))
custom_pars_ex = custom_pars.extract()
ss_manager = manager(
pdb_inp.hierarchy,
sec_str_from_pdb_file=None,
params=custom_pars_ex.secondary_structure,
verbose=-1)
proxies_for_grm = ss_manager.create_protein_hbond_proxies(
annotation= None,
log = log)
# print proxies_for_grm.size()
n_hbonds.append(proxies_for_grm.size())
assert n_hbonds == [6, 6, 4, 6, 6, 5, 8]
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 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 __init__(self,
pdb_h,
xrs,
target_map,
grm=None,
ncs_restraints_group_list=[],
mon_lib_srv=None,
rotamer_manager=None,
ss_annotation=None,
refine_ncs_operators=False,
number_of_cycles=1,
log=None):
from mmtbx.refinement.geometry_minimization import add_rotamer_restraints
from mmtbx.model_statistics import geometry_no_grm
self.pdb_h = pdb_h
self.xrs = xrs
self.log = log
self.cs = self.xrs.crystal_symmetry()
print >> self.log, "Minimizing using reference map..."
self.log.flush()
self.grm = grm
# create a new one
# copy-paste from cctbx_project/mmtbx/refinement/geometry_minimization.py:
# minimize_wrapper_for_ramachandran
if self.grm is None:
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 libtbx.utils import null_out
from scitbx.array_family import flex
import mmtbx.utils
if self.log is None:
self.log = null_out()
params_line = grand_master_phil_str
import iotbx.phil
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.nonbonded_weight = 500
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= self.cs,
pdb_interpretation_params = params.pdb_interpretation,
stop_for_unknowns = False,
log=self.log,
cif_objects=None)
processed_pdb_file, junk = processed_pdb_files_srv.\
process_pdb_files(raw_records=flex.split_lines(self.pdb_h.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)
# dealing with SS
if ss_annotation is not None:
from mmtbx.secondary_structure import manager
ss_manager = manager(
pdb_hierarchy=self.pdb_h,
geometry_restraints_manager=grm.geometry,
sec_str_from_pdb_file=ss_annotation,
params=None,
mon_lib_srv=mon_lib_srv,
verbose=-1,
log=self.log)
grm.geometry.set_secondary_structure_restraints(
ss_manager=ss_manager,
hierarchy=self.pdb_h,
log=self.log)
else:
self.grm.geometry.pair_proxies(
sites_cart=self.pdb_h.atoms().extract_xyz())
if self.grm.geometry.ramachandran_manager is not None:
self.grm.geometry.ramachandran_manager.update_phi_psi_targets(
sites_cart=self.pdb_h.atoms().extract_xyz())
ncs_groups=None
if len(ncs_restraints_group_list) > 0:
ncs_groups=ncs_restraints_group_list
if rotamer_manager is None:
from mmtbx.rotamer.rotamer_eval import RotamerEval
rotamer_manager = RotamerEval(mon_lib_srv=mon_lib_srv)
self.pdb_h.write_pdb_file(file_name="rsr_before_rot_fix.pdb",
crystal_symmetry=self.xrs.crystal_symmetry())
# STOP()
selection_real_space = xrs.backbone_selection()
# selection_real_space = None
import mmtbx.refinement.real_space.weight
self.w = None
for x in xrange(number_of_cycles):
print >> self.log, " Updating rotamer restraints..."
self.pdb_h, grm = add_rotamer_restraints(
pdb_hierarchy = self.pdb_h,
restraints_manager = grm,
selection = None,
sigma = 5,
mode = "fix_outliers",
accept_allowed = False,
mon_lib_srv = mon_lib_srv,
rotamer_manager = rotamer_manager)
self.xrs = self.pdb_h.extract_xray_structure(crystal_symmetry=self.cs)
self.pdb_h.write_pdb_file(file_name="rsr_after_rot_fix.pdb",
crystal_symmetry=self.xrs.crystal_symmetry())
# if True:
if ncs_restraints_group_list is None or len(ncs_restraints_group_list)==0:
#No NCS
if self.w is None:
print >> self.log, " Determining weight..."
self.log.flush()
self.weight = mmtbx.refinement.real_space.weight.run(
map_data = target_map,
xray_structure = self.xrs,
pdb_hierarchy = self.pdb_h,
geometry_restraints_manager = grm,
rms_bonds_limit = 0.015,
rms_angles_limit = 1.0)
# division is to put more weight onto restraints. Checked. Works.
self.w = self.weight.weight/3.0
# self.w = self.weight.weight
# self.w =2
# print >> self.log, self.w
for s in self.weight.msg_strings:
print >> self.log, s
print >> self.log, " Minimizing..."
print >> self.log, " with weight %f" % self.w
self.log.flush()
refine_object = simple(
target_map = target_map,
selection = None,
max_iterations = 150,
geometry_restraints_manager = grm.geometry,
selection_real_space = selection_real_space,
states_accumulator = None,
ncs_groups = ncs_groups)
refine_object.refine(weight = self.w, xray_structure = self.xrs)
self.rmsd_bonds_final, self.rmsd_angles_final = refine_object.rmsds()
print >> log, "RMSDS:", self.rmsd_bonds_final, self.rmsd_angles_final
# print >> log, "sizes:", len(refine_object.sites_cart()), len(self.xrs.scatterers())
self.xrs=self.xrs.replace_sites_cart(
new_sites=refine_object.sites_cart(), selection=None)
# print >> log, "sizes", self.xrs.scatterers()
else:
# Yes NCS
# copy-paste from macro_cycle_real_space.py
import mmtbx.ncs.ncs_utils as nu
nu.get_list_of_best_ncs_copy_map_correlation(
ncs_groups = ncs_restraints_group_list,
xray_structure = self.xrs,
map_data = target_map,
d_min = 3)
if self.w is None:
print >> self.log, " Determining weight... (NCS)",
self.weight = mmtbx.refinement.real_space.weight.run(
map_data = target_map,
xray_structure = self.xrs,#.select(sel_master),
pdb_hierarchy = self.pdb_h,#.select(sel_master),
geometry_restraints_manager = grm,
rms_bonds_limit = 0.01,
rms_angles_limit = 1.0,
ncs_groups = ncs_restraints_group_list)
# division supposed to put more weight onto restraints. Need checking.
self.w = self.weight.weight/3.0
for s in self.weight.msg_strings:
print >> self.log, s
print >> self.log, " Minimizing... (NCS)"
actions = [[True, False], ]
if refine_ncs_operators:
actions = [[False, True], [True, False]]
for action in actions:
refine_sites, refine_transformations = action
tfg_obj = mmtbx.refinement.minimization_ncs_constraints.\
target_function_and_grads_real_space(
map_data = target_map,
xray_structure = self.xrs,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = None,
real_space_gradients_delta = 1,
restraints_manager = grm,
data_weight = self.w,
refine_sites = refine_sites,
refine_transformations = refine_transformations)
minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs(
target_and_grads_object = tfg_obj,
xray_structure = self.xrs,
ncs_restraints_group_list = ncs_restraints_group_list,
refine_selection = None,
finite_grad_differences_test = False,
max_iterations = 100,
refine_sites = refine_sites,
refine_transformations = refine_transformations)
self.xrs = tfg_obj.xray_structure
# self.structure_monitor.update(
# xray_structure = tfg_obj.xray_structure,
# accept_as_is = True)
self.pdb_h.adopt_xray_structure(self.xrs)
# ms = geometry_no_grm(
# pdb_hierarchy=self.pdb_h,
# molprobity_scores=True)
# print >> self.log, ms.format_molprobity_scores(prefix=" ")
# print >> log, "pdb_h", self.pdb_h.atoms_size()
self.pdb_h.write_pdb_file("after_map_min.pdb")