def create_all_new_restraints(self, pdb_hierarchy, grm, log=sys.stdout):
# initialize cache and monomer library server for underlying procedures
if self.mon_lib_srv is None:
from mmtbx.monomer_library import server
self.mon_lib_srv = server.server()
plane_cache = {}
t0 = time.time()
proteins_hbonds, prot_angle_proxies = self.create_protein_hbond_proxies(
log=log, annotation=self.actual_sec_str)
t1 = time.time()
# print >> log, " Time for creating protein proxies:%f" % (t1-t0)
stacking_proxies = nucleic_acids.get_stacking_proxies(
pdb_hierarchy=pdb_hierarchy,
stacking_phil_params=self.params.secondary_structure.\
nucleic_acid.stacking_pair,
grm=grm,
mon_lib_srv=self.mon_lib_srv,
plane_cache=plane_cache)
t2 = time.time()
# print >> log, " Time for creating stacking proxies:%f" % (t2-t1)
(hb_bond_proxies, hb_angle_proxies, planarity_bp_proxies,
parallelity_bp_proxies) = nucleic_acids.get_basepair_proxies(
pdb_hierarchy=pdb_hierarchy,
bp_phil_params=self.params.secondary_structure.nucleic_acid.base_pair,
grm=grm,
mon_lib_srv=self.mon_lib_srv,
plane_cache=plane_cache,
hbond_distance_cutoff=self.params.secondary_structure.\
nucleic_acid.hbond_distance_cutoff,
scale_bonds_sigma=self.params.secondary_structure.\
nucleic_acid.scale_bonds_sigma)
t4 = time.time()
# print >> log, " Time for creating basepair proxies (hbond, angle, planarity):%f" % (t4-t2)
self.stats = {
'n_protein_hbonds': 0,
'n_na_hbonds': 0,
'n_na_hbond_angles': 0,
'n_na_basepairs': 0,
'n_na_stacking_pairs': 0
}
print(" Restraints generated for nucleic acids:", file=log)
print(" %d hydrogen bonds" % len(hb_bond_proxies), file=log)
print(" %d hydrogen bond angles" % len(hb_angle_proxies),
file=log)
print(" %d basepair planarities" % len(planarity_bp_proxies),
file=log)
print(" %d basepair parallelities" % len(parallelity_bp_proxies),
file=log)
print(" %d stacking parallelities" % len(stacking_proxies),
file=log)
all_hbonds = proteins_hbonds.deep_copy()
all_hbonds.extend(hb_bond_proxies)
all_angle = prot_angle_proxies.deep_copy()
all_angle.extend(hb_angle_proxies)
return (all_hbonds, all_angle, planarity_bp_proxies,
parallelity_bp_proxies + stacking_proxies)
def create_all_new_restraints(self,
pdb_hierarchy,
grm,
log=sys.stdout):
# initialize cache and monomer library server for underlying procedures
if self.mon_lib_srv is None:
from mmtbx.monomer_library import server
self.mon_lib_srv = server.server()
plane_cache = {}
t0 = time.time()
proteins_hbonds = self.create_protein_hbond_proxies(
log=log,
annotation=self.actual_sec_str)
t1 = time.time()
# print >> log, " Time for creating protein proxies:%f" % (t1-t0)
stacking_proxies = nucleic_acids.get_stacking_proxies(
pdb_hierarchy=pdb_hierarchy,
stacking_phil_params=self.params.secondary_structure.\
nucleic_acid.stacking_pair,
grm=grm,
mon_lib_srv=self.mon_lib_srv,
plane_cache=plane_cache)
t2 = time.time()
# print >> log, " Time for creating stacking proxies:%f" % (t2-t1)
planarity_bp_proxies, parallelity_bp_proxies = nucleic_acids.\
get_basepair_plane_proxies(
pdb_hierarchy=pdb_hierarchy,
bp_phil_params=self.params.secondary_structure.nucleic_acid.base_pair,
grm=grm,
mon_lib_srv=self.mon_lib_srv,
plane_cache=plane_cache)
t3 = time.time()
# print >> log, " Time for creating planar/parall proxies:%f" % (t3-t2)
hb_bond_proxies, hb_angle_proxies = nucleic_acids.\
get_basepair_hbond_proxies(
pdb_hierarchy=pdb_hierarchy,
bp_phil_params=self.params.secondary_structure.nucleic_acid.base_pair,
hbond_distance_cutoff=self.params.secondary_structure.\
nucleic_acid.hbond_distance_cutoff)
t4 = time.time()
# print >> log, " Time for creating hbond-angle proxies:%f" % (t4-t3)
self.stats = {'n_protein_hbonds':0, 'n_na_hbonds':0, 'n_na_hbond_angles':0,
'n_na_basepairs':0, 'n_na_stacking_pairs':0}
print >> log, " Restraints generated for nucleic acids:"
print >> log, " %d hydrogen bonds" % len(hb_bond_proxies)
print >> log, " %d hydrogen bond angles" % len(hb_angle_proxies)
print >> log, " %d basepair planarities" % len(planarity_bp_proxies)
print >> log, " %d basepair parallelities" % len(parallelity_bp_proxies)
print >> log, " %d stacking parallelities" % len(stacking_proxies)
all_hbonds = proteins_hbonds.deep_copy()
all_hbonds.extend(hb_bond_proxies)
return (all_hbonds, hb_angle_proxies,
planarity_bp_proxies, parallelity_bp_proxies+stacking_proxies)
