def create_protein_hbond_proxies(self, annotation=None, log=sys.stdout):
# assert as_regular_bond_proxies=True
if annotation is None:
annotation = self.actual_sec_str
remove_outliers = self.params.secondary_structure.protein.remove_outliers
from scitbx.array_family import flex
atoms = self.pdb_hierarchy.atoms()
hbond_counts = flex.int(atoms.size(), 0)
distance_ideal = self.params.secondary_structure.protein.distance_ideal_n_o
distance_cut = self.params.secondary_structure.protein.distance_cut_n_o
if (distance_cut is None):
distance_cut = -1
generated_proxies = geometry_restraints.shared_bond_simple_proxy()
hb_angle_proxies = []
if self.params.secondary_structure.protein.enabled:
for helix in self.params.secondary_structure.protein.helix:
if helix.selection is not None:
print >> log, " Processing helix ", helix.selection
proxies, angle_proxies = proteins.create_helix_hydrogen_bond_proxies(
params=helix,
pdb_hierarchy=self.pdb_hierarchy,
selection_cache=self.selection_cache,
weight=1.0,
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
restrain_hbond_angles=self.params.secondary_structure.
protein.restrain_hbond_angles,
log=log)
if (proxies.size() == 0):
print >> log, " No H-bonds generated for '%s'" % helix.selection
continue
else:
generated_proxies.extend(proxies)
hb_angle_proxies += angle_proxies
for k, sheet in enumerate(
self.params.secondary_structure.protein.sheet):
print >> log, " Processing sheet with id=%s, first strand: %s" % (
sheet.sheet_id, sheet.first_strand)
if sheet.first_strand is not None:
proxies, angle_proxies = proteins.create_sheet_hydrogen_bond_proxies(
sheet_params=sheet,
pdb_hierarchy=self.pdb_hierarchy,
selection_cache=self.selection_cache,
weight=1.0,
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
restrain_hbond_angles=self.params.secondary_structure.
protein.restrain_hbond_angles,
log=log)
if (proxies.size() == 0):
print >> log, \
" No H-bonds generated for sheet with id=%s" % sheet.sheet_id
continue
else:
generated_proxies.extend(proxies)
hb_angle_proxies += angle_proxies
n_proxies = generated_proxies.size()
print >> log, ""
if (n_proxies == 0):
print >> log, " No hydrogen bonds defined for protein."
else:
print >> log, " %d hydrogen bonds defined for protein." % n_proxies
print >> log, " %d hydrogen bond angles defined for protein." % len(
hb_angle_proxies)
return generated_proxies, geometry_restraints.shared_angle_proxy(
hb_angle_proxies)
def create_protein_hbond_proxies (self,
annotation=None,
log=sys.stdout):
# assert as_regular_bond_proxies=True
if annotation is None:
annotation = self.actual_sec_str
remove_outliers = self.params.secondary_structure.protein.remove_outliers
from scitbx.array_family import flex
atoms = self.pdb_hierarchy.atoms()
hbond_counts = flex.int(atoms.size(), 0)
selection_cache = self.pdb_hierarchy.atom_selection_cache()
distance_ideal = self.params.secondary_structure.protein.distance_ideal_n_o
distance_cut = self.params.secondary_structure.protein.distance_cut_n_o
if (distance_cut is None) :
distance_cut = -1
generated_proxies = geometry_restraints.shared_bond_simple_proxy()
if self.params.secondary_structure.protein.enabled:
for helix in self.params.secondary_structure.protein.helix :
if helix.selection is not None:
print >> log, " Processing helix ", helix.selection
proxies = proteins.create_helix_hydrogen_bond_proxies(
params=helix,
pdb_hierarchy=self.pdb_hierarchy,
selection_cache=selection_cache,
weight=1.0,
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
log=log)
if (proxies.size() == 0) :
print >> log, " No H-bonds generated for '%s'" % helix.selection
continue
else:
generated_proxies.extend(proxies)
for k, sheet in enumerate(self.params.secondary_structure.protein.sheet) :
print >> log, " Processing sheet with id=%s, first strand: %s" % (
sheet.sheet_id, sheet.first_strand)
if sheet.first_strand is not None:
proxies = proteins.create_sheet_hydrogen_bond_proxies(
sheet_params=sheet,
pdb_hierarchy=self.pdb_hierarchy,
weight=1.0,
hbond_counts=hbond_counts,
distance_ideal=distance_ideal,
distance_cut=distance_cut,
remove_outliers=remove_outliers,
log=log)
if (proxies.size() == 0) :
print >> log, \
" No H-bonds generated for sheet with id=%s" % sheet.sheet_id
continue
else:
generated_proxies.extend(proxies)
n_proxies = generated_proxies.size()
print >> log, ""
if (n_proxies == 0) :
print >> log, " No hydrogen bonds defined for protein."
else :
print >> log, " %d hydrogen bonds defined for protein." % n_proxies
# reg_proxies = []
# for hb_p in build_proxies.proxies:
# reg_proxy = geometry_restraints.bond_simple_proxy(
# i_seqs=hb_p.i_seqs,
# distance_ideal=hb_p.distance_ideal,
# weight=hb_p.weight,
# slack=hb_p.slack,
# top_out=hb_p.top_out,
# limit=hb_p.limit,
# origin_id=1)
# reg_proxies.append(reg_proxy)
# return geometry_restraints.shared_bond_simple_proxy(reg_proxies)
return generated_proxies
